Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis
Pang, W. ; Li, X. ; Choi, S.R. ; Dhandapani, V. ; Im, S. ; Park, M.Y. ; Jang, C.S. ; Yang, M.S. ; Ham, I.K. ; Lee, E.M. ; Kim, W. ; Lee, S.S. ; Bonnema, A.B. ; Park, S. ; Piao, Z. ; Lim, Y.P. - \ 2015
Molecular Breeding 35 (2015)1. - ISSN 1380-3743
genome sequencing project - microspore culture - linkage map - napus l. - microsatellite markers - repeat markers - construction - crop - association - centers
Brassica rapa is an economically important crop with a wide range of morphologies. Developing a set of fixed lines and understanding their diversity has been challenging, but facilitates resource conservation. We investigated the genetic diversity and population structure of 238 fixed lines of leafy B. rapa with 45 new simple sequence repeat markers and 109 new NGS (next-generation sequencing)-generated single nucleotide polymorphism markers evenly distributed throughout the B. rapa genome. Phylogenetic analysis classified the vegetable fixed lines into four subgroups, with the three oil types forming a separate and relatively distant cluster. A model-based population structure analysis identified four subpopulations corresponding to geographical origins and morphological traits, and revealed extensive allelic admixture. In particular, the Chinese cabbage cluster was subdivided into three groups and showed considerable correlation with leaf- and heading-related traits (leaf and heading shape). The vegetable B. rapa fixed lines successfully developed in our study could be valuable materials for establishing a multinational Brassica rapa diversity resource. Understanding the genetic diversity and population structure could be useful for utilization of the representative genetic variation and further genomic analysis.
QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population
Tondelli, A. ; Francia, E. ; Visioni, A. ; Comadran, J. ; Mastrangelo, A.M. ; Akar, T. ; Al-Yassina, A. ; Ceccarelli, S. ; Grando, S. ; Eeuwijk, F.A. van; Thomas, W.T.B. ; Stanca, A.M. ; Romagosa, I. ; Pecchioni, N. - \ 2014
Euphytica 197 (2014)1. - ISSN 0014-2336 - p. 73 - 86.
quantitative trait loci - hordeum-vulgare - drought tolerance - agronomic traits - flowering time - abiotic stress - grain-yield - major genes - linkage map - wheat
Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’
Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
Oers, K. van; Santure, A.W. ; Cauwer, I. de; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Sheldon, B.C. ; Visser, M.E. ; Slate, J. ; Groenen, M.A.M. - \ 2014
Heredity 112 (2014)3. - ISSN 0018-067X - p. 307 - 316.
wild bird population - linkage map - zebra finch - parus-major - synteny conservation - ficedula-albicollis - personality-traits - turkey genome - evolution - chicken
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010¿cM and 1917¿cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.
Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
Bianco, L. ; Cestaro, A. ; Sargent, D.J. ; Guardo, M. Di; Jansen, J. ; Weg, W.E. van de - \ 2014
PLoS ONE 9 (2014)10. - ISSN 1932-6203 - 9 p.
linkage map - construction - cultivars - alignment - accurate - barley
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
‘Schmidt's Antonovka’ is identical to ‘Common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses
Pikunova, A. ; Madduri, M. ; Sedov, E. ; Noordijk, Y. ; Peil, A. ; Troggio, M. ; Bus, V.G.M. ; Visser, R.G.F. ; Weg, W.E. van de - \ 2014
Tree Genetics and Genomes 10 (2014)2. - ISSN 1614-2942 - p. 261 - 271.
x-domestica borkh. - resistance gene - linkage map - scab - genome
Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breeding programs as a source of scab resistance. The identity of SA has remained obscure, especially due to the existence of a series of ‘Antonovka’ cultivars with different origins. In this paper we show Schmidt's Antonovka to be identical to ¿¿¿¿´¿¿¿¿¿ ¿¿¿¿¿¿¿¿¿¿¿¿ or ‘Common Antonovka’ (CA), an old Russian cultivar of unknown origin, by comparing simple sequence repeat (SSR) and SNP genotyping data from several first-generation descendants of SA from two European collections and a CA accession from the germplasm collection held at VNIISPK (The All-Russian Research Institute of Horticultural Breeding, Orel, Russia). The use of CA in Russian breeding programs is also briefly reviewed.
High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV
Lüpken, T. ; Stein, N. ; Perovic, D. ; Habekuss, A. ; Serfling, A. ; Krämer, I. ; Hähnel, U. ; Steuernagel, B. ; Scholz, U. ; Ariyadasa, R. ; Martis, M. ; Mayer, K. ; Niks, R.E. ; Collins, N.C. ; Friedt, W. ; Ordon, F. - \ 2014
Molecular Breeding 33 (2014)2. - ISSN 1380-3743 - p. 477 - 488.
yellow-dwarf-virus - hordeum-vulgare l. - recessive bymovirus resistance - leaf rust resistance - comparative genomics - consensus map - winter barley - linkage map - yd2 gene - sequence
Barley yellow dwarf disease (BYD) is transmitted by aphids and is caused by different strains of Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV). Economically it is one of the most important diseases of cereals worldwide. Besides chemical control of the vector, growing of tolerant/resistant cultivars is an effective way of protecting crops against BYD. The Ryd3 gene in barley (Hordeum vulgare L.) confers tolerance to BYDV-PAV and BYDV-MAV and the locus was previously mapped on the short arm of barley chromosome 6H near the centromere. We applied a strategy for high-resolution mapping and marker saturation at the Ryd3 locus by exploiting recent genomic tools available in barley. In a population of 3,210 F2 plants, 14 tightly linked markers were identified, including 10 that co-segregated with Ryd3. The centromeric region where Ryd3 is located suffers suppressed recombination or reduced recombination rate, suggesting potential problems in achieving (1) map-based cloning of Ryd3 and (2) marker selection of the resistance in breeding programmes without the introduction of undesirable traits via linkage drag.
Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms
The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.
Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
Oers, K. van; Santure, A.W. ; Cauwer, I. de; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Sheldon, B.C. ; Visser, M.E. ; Slate, J. ; Groenen, M. - \ 2013
linkage map - heterochiasmy - chromosomal rearrangements - population comparison
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between- species karyotype evolution. Here we used genotype data, generated from a 10k SNP-chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird, which serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.
Chromosome evolution in Solanum traced by cross-species BAC-FISH
Szinay, D. ; Wijnker, E. ; Berg, R.G. van den; Visser, R.G.F. ; Jong, J.H.S.G.M. de; Bai, Y. - \ 2012
New Phytologist 195 (2012)3. - ISSN 0028-646X - p. 688 - 698.
l. section lycopersicon - resistance gene - mill. wettst. - linkage map - tomato - solanaceae - potato - reveals - rearrangements - recombination
Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence / absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees. Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and / or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding.
A century of poultry genetics
Tixier-Boichard, M. ; Leenstra, F.R. ; Flock, D. ; Hocking, A.D. ; Weigend, S. - \ 2012
Worlds Poultry Science Journal 68 (2012)2. - ISSN 0043-9339 - p. 307 - 321.
major histocompatibility complex - chicken genome - nucleolar organizer - molecular-cloning - linked factors - linkage map - egg-white - rfp-y - diversity - selection
The 20th Century saw an astonishing advance in our understanding of genetics and the scientific basis of the genetic improvement of farm animals. The application of genetic principles to chickens in the 1950s and 1960s led to a rapid change in the productivity and efficiency of laying hens and broiler chickens, turkeys and ducks. Subsequently, the application of increasingly powerful computers and sophisticated mathematical algorithms has increased the range of traits that could be successfully incorporated into breeding programs. Random sample tests of the performance of laying hens enjoyed a period of popularity and more recently the few remaining tests included husbandry systems in addition to strain evaluation. Characterisation of avian blood groups has led to the identification of the B21 haplotype that confers resistance to Marek's disease and to selection for this locus in commercial lines. The decade following the millennium saw the publication of the genome sequence of the chicken and the identification of millions of single nucleotide polymorphisms that, coupled with technological advances, made the application of whole genome selection practical in poultry. In parallel, the molecular basis for some Mendelian traits described a century ago is now being deciphered. Similar technologies have been applied to study genetic diversity in chickens and have provided insights into the evolution and domestication of chicken breeds. Finally, in this review, the recent development of the European Poultry Genetics Symposia coordinated by Working Group 3 ‘Genetics and Breeding’ that was based on combining the British Poultry Breeders Round Table and AVIAGEN from West and Eastern Europe, is discussed
Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids
Dijk, T. van; Noordijk, Y. ; Dubos, T. ; Bink, M.C.A.M. ; Visser, R.G.F. ; Weg, W.E. van de - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
polysomic inheritance - octoploid strawberry - diploid fragaria - dosage analysis - linkage map - dna - evolution - potato - genome - plants
BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.
A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome
Boer, J.M. de; Borm, T.J.A. ; Jesse, T. ; Brugmans, B.W. ; Tang, X. ; Bryan, G.J. ; Bakker, J. ; Eck, H.J. van; Visser, R.G.F. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 60 p.
quantitative trait loci - candidate genes - disease resistance - linkage map - tomato - aflp - solanum - markers - dna - construction
Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental traits and disease resistances
Shahin, A. ; Arens, P.F.P. ; Heusden, S. van; Linden, C.G. van der; Kaauwen, M.P.W. van; Nadeem Khan, M. ; Schouten, H.J. ; Weg, W.E. van de; Visser, R.G.F. ; Tuyl, J.M. van - \ 2011
Plant Breeding 130 (2011)3. - ISSN 0179-9541 - p. 372 - 382.
diversity arrays technology - linkage map - zea-mays - segregation distortion - wild relatives - durum-wheat - markers - dart - construction - pollination
Construction of genetic linkage maps for lily was achieved using two populations, LA and AA that share one parent ‘Connecticut King’. Three different molecular marker systems (AFLP™, DArT and NBS profiling) were used in generating linkage maps for ‘Connecticut King’. The LA and the AA populations consist of 20 and 21 linkage groups (LGs), respectively. Average density between markers was 3.9 cM for the LA and 5 cM for the AA population. Several horticultural traits were mapped for the first time in Lilium and showed to be single gene based. We propose to name these genes as LFCc for flower colour, lfs for flower spots, LSC for stem colour, lal for antherless phenotype and lfd for flower direction whereby upper and lower case names refer to dominant and recessive genes, respectively. Additionally, resistance to Lily mottle virus (LMoV) was mapped as a locus on LG AA10. For Fusarium resistance, the Kruskal–Wallis test identified six putative quantitative trait loci (QTL) in the AA population of which one QTL (explaining 25% of the variation in resistance) could be confirmed by interval mapping
A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
Ciobanu, D.C. ; Bastiaansen, J.W.M. ; Magrin, J. ; Rocha, J.L. ; Jiang, D.H. ; Yu, N. ; Geiger, B. ; Deeb, N. ; Rocha, D. ; Gong, H. ; Kinghorn, B.P. ; Plastow, G.S. ; Steen, H.A.M. van der; Mileham, A.J. - \ 2010
Animal Genetics 41 (2010)1. - ISSN 0268-9146 - p. 39 - 47.
taura-syndrome virus - pig skeletal-muscle - linkage map - glycogen-content - penaeus - markers - mutation - resistance - discovery - growth
Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r2-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei
Genome-wide SNP detection in the great tit Parus major using high throughput sequencing
Bers, N.E.M. van; Oers, K. van; Dibbits, B.W. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. - \ 2010
Molecular Ecology 19 (2010)Suppl. s1. - ISSN 0962-1083 - p. 89 - 99.
wild bird population - natural-populations - climate-change - linkage map - phenotypic plasticity - future-directions - genotyping assay - passerine bird - dna-sequences - evolution
Identifying genes that underlie ecological traits will open exiting possibilities to study gene–environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines.
The development of Arabidopsis as a plant model
Koornneef, M. ; Meinke, D.W. - \ 2010
The Plant Journal 61 (2010). - ISSN 0960-7412 - p. 909 - 921.
thaliana l heynh - agrobacterium-mediated transformation - dna insertion mutagenesis - recombinant inbred lines - embryo-lethal mutants - linkage map - natural variation - crucifer arabidopsis - reverse genetics - high-frequency
Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom
Regional differences in recombination hotspots between two chicken populations
Elferink, M.G. ; As, P. van; Veenendaal, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2010
BMC Genetics 11 (2010). - ISSN 1471-2156
ascites-related traits - whole genome scan - linkage map - physical map - broilers - markers
Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management
Wiel, C.C.M. van de; Sretenovic Rajicic, T. ; Treuren, R. van; Dehmer, K.J. ; Linden, C.G. van der; Hintum, T.J.L. van - \ 2010
Plant genetic resources: characterization and utilization 8 (2010)2. - ISSN 1479-2621 - p. 171 - 181.
molecular markers - linkage map - asteraceae - evolution - netherlands - acquisition - cluster - spp. - aflp - l.
Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.
Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers
Smulders, M.J.M. ; Esselink, G. ; Everaert, I. ; Riek, J. de; Vosman, B. - \ 2010
BMC Genetics 11 (2010). - ISSN 1471-2156 - 11 p.
genetic diversity - linkage map - wild relatives - flow - crop - identification - populations - database - complex - tomato
Background - Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research. Results - We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient Fis was 0.282 +/- 0.124, but it varied widely among marker loci, from Fis = +0.876 (heterozygote deficiency) to Fis = -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (Fst = 0.232 +/- 0.027). Among triploid varieties the genetic differentiation was much lower (Fst = 0.100 +/- 0.010). The overall genetic differentiation between diploid and triploid varieties was Fst = 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was Fst = 0.063. Conclusions - Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.
Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA
Zanten, M. van; Snoek, L.B. ; Eck-Stouten, E. van; Proveniers, M.C.G. ; Torii, K.U. ; Voesenek, L.A.C.J. ; Peeters, A.J.M. ; Millenaar, F.F. - \ 2010
The Plant Journal 61 (2010)1. - ISSN 0960-7412 - p. 83 - 95.
natural allelic variation - receptor-like kinase - quantitative trait loci - inbred line population - shade-avoidance - genetic-variation - secretory peptide - circadian clock - abscisic-acid - linkage map
Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of the phytohormone ethylene in the plant. Currently, only limited information is available on how this response is molecularly controlled. In this study, we utilized quantitative trait loci (QTL) analysis of natural genetic variation among Arabidopsis accessions to isolate novel factors controlling constitutive petiole angles and ethylene-induced hyponastic growth. Analysis of mutants in various backgrounds and complementation analysis of naturally occurring mutant accessions provided evidence that the leucin-rich repeat receptor-like Ser/Thr kinase gene, ERECTA, controls ethylene-induced hyponastic growth. Moreover, ERECTA controls leaf positioning in the absence of ethylene treatment. Our data demonstrate that this is not due to altered ethylene production or sensitivity
Mapping markers linked to porcine salmonellosis susceptibility
Galina-Pantoja, L. ; Siggens, K. ; Schriek, M.G.M. van; Heuven, H.C.M. - \ 2009
Animal Genetics 40 (2009)6. - ISSN 0268-9146 - p. 795 - 803.
quantitative trait loci - differential gene-expression - population-structure - natural-resistance - linkage map - aflp - choleraesuis - infection - pig - polymorphisms
The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7 post-infection (dpi; Van Diemen et al. 2002) was used. These samples belonged to the offspring of a sire thought to be heterozygous for genes involved in susceptibility to salmonellosis. Amplified fragment length polymorphism (AFLP) markers were created and used to determine associations with spleen or bacterial counts at 7 dpi. To position linked markers, two mapping populations, the Roslin and Uppsala PiGMaP pedigrees were used to create an integrated map which included the AFLP markers associated with salmonellosis. Twenty-six AFLP markers located in 14 different chromosomal regions in the porcine genome were found to be significantly associated with susceptibility (Chi-square P <0.05). More than one linked marker was found on chromosomes 1, 7, 13, 14 and 18. It is likely that these regions contain genes involved in Salmonella susceptibility. Regions on chromosomes 1, 7 and 14 were significantly associated with Salmonella counts in the liver and regions on chromosomes 11, 13 and 18 with counts in spleen. The identification of these chromosomal regions highlights specific areas to search for candidate genes that may be involved in innate or adaptive immunity. Further investigation into these chromosomal regions would be useful to improve our understanding of host responses to infection with this widespread pathogen.
PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana
Tessadori, F. ; Zanten, M. van; Pavlova, P. ; Clifton, R. ; Pontvianne, F. ; Snoek, L.B. ; Millenaar, F.F. ; Schulkes, R.K. ; Driel, R. van; Voesenek, L.A.C.J. ; Spillane, C. ; Pikaard, C.S. ; Fransz, P.F. ; Peeters, A.J.M. - \ 2009
Plos Genetics 5 (2009)9. - ISSN 1553-7404 - 13 p.
natural allelic variation - inbred line population - dna methylation - flowering time - genome regulation - genetic-variation - circadian clock - linkage map - h3 lysine-9 - heterochromatin
Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process
Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke
Acquadro, A. ; Lanteri, S. ; Scaglione, D. ; Arens, P.F.P. ; Vosman, B. ; Portis, E. - \ 2009
Theoretical and Applied Genetics 118 (2009)8. - ISSN 0040-5752 - p. 1573 - 1587.
cynara-cardunculus l. - fragment length polymorphisms - transcription factor-binding - cultured rat hepatocytes - linkage map - scolymus l. - mediterranean environment - medicago-truncatula - potential source - dna-sequences
Cynara cardunculus includes three taxa, the globe artichoke (subsp. scolymus L. Hegi), the cultivated cardoon (var. altilis) and their progenitor, the wild cardoon (var. sylvestris). Globe artichoke is an important component of the Mediterranean rural economy, but its improvement through breeding has been rather limited and its genome organization remains largely unexplored. Here, we report the isolation of 61 new microsatellite loci which amplified a total of 208 alleles in a panel of 22 C. cardunculus genotypes. Of these, 51 were informative for linkage analysis and 39 were used to increase marker density in the available globe artichoke genetic maps. Sequence analysis of the 22 loci associated with genes showed that 9 are located within coding sequence, with the repetitive domain probably being involved in DNA binding or in protein¿protein interactions. The expression of the genes associated with 9 of the 22 microsatellite loci was demonstrated by RT-PCR.
Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
Botton, A. ; Galla, G. ; Conesa, A. ; Bachem, C.W.B. ; Ramina, A. ; Barcaccia, G. - \ 2008
BMC Genomics 9 (2008). - ISSN 1471-2164 - 19 p.
genome-wide expression - pseudo-testcross strategy - poa-pratensis l - cdna-aflp - candidate genes - seed-germination - cell-division - linkage map - identification - markers
Background: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results: Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion: Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome- anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.
Marle-Koster, E. van; Hefer, C.A. ; Nel, L.H. ; Groenen, M.A.M. - \ 2008
South African Journal of Animal Science = Suid-Afrikaanse Tydskrif Vir Veekun 38 (2008)4. - ISSN 0375-1589 - p. 271 - 281.
kippen - inheems vee - rassen (dieren) - differentiatie - genetische variatie - genetische diversiteit - microsatellieten - merkers - bevolkingsstructuur - conservering - zuid-afrika - fowls - native livestock - breeds - differentiation - genetic variation - genetic diversity - microsatellites - markers - population structure - conservation - south africa - domestic-animal diversity - microsatellite markers - linkage map - naked neck - polymorphisms - biodiversity - genome
In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program.
Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA
Zannou, A. ; Kossou, D.K. ; Ahanchédé, A. ; Zoundjihékpon, J. ; Agbicodo, E. ; Struik, P.C. ; Sanni, A. - \ 2008
African journal of biotechnology 7 (2008)24. - ISSN 1684-5315 - p. 4407 - 4414.
linkage map - diversity - aflp - markers - populations - model - wild
Characterization of genetic diversity among cultivated cowpea [Vigna unguiculata (L.) Walp.] varieties is important to optimize the use of available genetic resources by farmers, local communities, researchers and breeders. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic diversity in 70 cowpea accessions collected throughout Benin. Nine random primers were screened on 24 accessions to assess their ability to reveal polymorphisms in cowpea and four of them were selected for use in characterizing the total sample. A total of 32 amplified bands were generated by the four primers. The number of loci detected varied from 5 to 11. RAPD profiles were analysed and amplified polymorphic DNA fragments were used to construct a dendrogram, clustering the accessions into nine groups at a similarity index of 71% based on the Unweighted Pair-Group Method using Arithmetic Averages. The genetic diversity among the cowpea cultivars investigated was large and the RAPD proved to be a useful technique to characterise it. Based on the molecular variance, the fixation index suggests a large differentiation of cowpea cultivars in Benin.
Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa
Jianjun Zhao, Jianjun ; Jamar, D.C.L. ; Lou, P. ; Wang, Y. ; Wu, J. ; Wang, X. ; Bonnema, A.B. ; Koornneef, M. ; Vreugdenhil, D. - \ 2008
Plant, Cell & Environment 31 (2008)7. - ISSN 0140-7791 - p. 887 - 900.
phytic-acid - arabidopsis-thaliana - natural variation - comparative genomics - flowering time - linkage map - phosphorus - sequence - accumulation - resistance
Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway
Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines
Loywyck, V. ; Bed'hom, B. ; Pinard-van der Laan, M.H. ; Pitel, F. ; Verrier, E. ; Bijma, P. - \ 2008
Genetics, Selection, Evolution 40 (2008). - ISSN 0999-193X - p. 639 - 661.
effective population-size - quantitative trait loci - laying hens - antibody-responses - immune-response - allele frequency - genetic drift - linkage map - signatures - chromosome
We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14 were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone
Comparison of information content for microsatellites and SNPs in poultry and cattle
Schopen, G.C.B. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Arendonk, J.A.M. van - \ 2008
Animal Genetics 39 (2008)4. - ISSN 0268-9146 - p. 451 - 453.
quantitative trait loci - linkage map - genetic-map - markers - genome - population - chicken
Data were available for 12 poultry microsatellites and 29 poultry single nucleotide polymorphisms (SNPs), and for 34 cattle microsatellites and 36 cattle SNPs. Stochastic permutation was used to determine the number of SNPs needed to obtain the same average information content as a given number of microsatellites. For poultry, the information content averaged 0.71 for the 12 microsatellites compared to 0.72 for the 29 SNPs. For cattle, the information content averaged 0.92 for the 34 microsatellites compared with 0.79 for the 36 SNPs. This study shows that, for each microsatellite, three SNPs are needed to obtain the same average information content.
Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini
Greyling, B.J. ; Kryger, P. ; Plessis, S. du; Hooft, W.F. van; Helden, P. van; Getz, W.M. ; Bastos, A.D.S. - \ 2008
African journal of biotechnology 7 (2008)5. - ISSN 1684-5315 - p. 655 - 660.
syncerus caffer - polymorphic bovine - southern africa - linkage map - buffalo - markers - identification - cattle
Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was established for this purpose. Mean allelic richness per locus was 8.24 and 6.47, for buffalo and Bonsmara cattle, respectively, whilst an unbiased match probability of 6.5x×10-17 and 1.03 × 10-16 was obtained for each. These results confirm the usefulness of this rapid, cost-effective typing approach for forensic, paternity and fine-scale genetic analyses of wild and domestic African Bovini tribe members
Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.).
Studer, B. ; Asp, T. ; Frei, U. ; Hentrup, S. ; Meally, H. ; Guillard, A. ; Barth, S. ; Muylle, H. ; Roldan-Ruiz, I. ; Barre, P. ; Boucoiran, C.F.S. ; Stunnenberg, G. ; Dolstra, O. ; Skot, L. ; Skot, K.P. ; Turner, B. ; Humphreys, M. ; Kolliker, R. ; Roulund, N. ; Nielsen, K.K. ; Lubberstedt, T. - \ 2008
Molecular Breeding 21 (2008)4. - ISSN 1380-3743 - p. 533 - 548.
repeat ssr markers - multiflorum lam. - linkage map - plants - transferability - construction - reveals - qtl
An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was tested in eight genotypes of L. perenne and L. multiflorum representing (grand-) parents of four mapping populations and resulted in 464 successfully amplified EST-SSRs. Three hundred and six primer pairs successfully amplified products in the mapping population VrnA derived from two of the eight genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage and turf grasses. Electronic supplementary material The online version of this article (doi:10.1007/s11032-007-9148-0) contains supplementary material, which is available to authorized users.
High diversity of genes for nonhost resistance of barley to heterologous rust fungi
Jafary, H. ; Albertazzi, G. ; Marcel, T.C. ; Niks, R.E. - \ 2008
Genetics 178 (2008)4. - ISSN 0016-6731 - p. 2327 - 2339.
puccinia-hordei - leaf rust - linkage map - iii effector - defense - plants - pathogens - qtls - identification - accumulation
Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley¿Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes
Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola
Goodwin, S.B. ; Lee, T.A.J. van der; Cavaletto, J.R. ; Lintel Hekkert, B. te; Crane, C.F. ; Kema, G.H.J. - \ 2007
Fungal Genetics and Biology 44 (2007)5. - ISSN 1087-1845 - p. 398 - 414.
simple sequence repeats - magnaporthe-grisea - lobaria-pulmonaria - ascochyta-rabiei - fungal genomes - ribosomal dna - linkage map - markers - wheat - population
A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species
In silico identification and mapping of microsatellite markers on Sus scrofa chromosome 4
Wijk, H.J. van; Liefers, S.C. ; Buschbell, H. ; Dibbits, B.W. ; Harlizius, B. ; Groenen, M.A.M. - \ 2007
Animal Biotechnology 18 (2007)4. - ISSN 1049-5398 - p. 251 - 261.
carcass composition - porcine genome - linkage map
Apolipoprotein B (APOB) serves an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport. This study was designed to clone the full-length cDNA of the chicken APOB gene, to characterize the expression profile, and investigate the differential expression between layer and broiler of the chicken APOB gene. The full-length cDNA sequence (14,150-bp) that contained a 13,896-bp ORF encoding 4,631 amino acids was obtained by RT-PCR, RACE, and bioinformatics analysis. qReal-Time PCR analysis showed that the chicken APOB gene was highly expressed in kidney, liver, and intestine. The results of differential expression showed that the APOB gene was more highly expressed in intestine and kidney in Bai'er layer than in broiler, but there was no significant difference in liver between the two breeds. The results of this study provided basic molecular information for studying the role of APOB in the energy transportation in avian species.
Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet
Riek, J. de; Everaert, I. ; Esselink, D. ; Calsyn, E. ; Smulders, M.J.M. ; Vosman, B. - \ 2007
Crop Science 47 (2007)5. - ISSN 0011-183X - p. 1964 - 1974.
beta-vulgaris l - linkage map - aflp - construction - regression - database - rapd - l.
High genetic variation within sugar beet (Beta vulgaris L.) varieties hampers reliable classification procedures independent of the type of marker technique applied. Datasets on amplified fragment length polymorphisms, sequence tagged microsatellite sites, and cleaved amplified polymorphic sites markers in eight sugar beet varieties were subjected to supervised classifiers, methods in which individual assignments are made to predefined classes, and unsupervised classifiers, defined afterward on the similarity in marker composition from sampled individuals. Major issues addressed are (i) which classification method gives the most consistent results when three marker techniques are compared, and (ii) given different classification techniques available, for which marker technique is the output generated least constrained by the way data analysis is performed. Assignment tests showed a higher consistency across classifications independent from the marker technique. A good allocation to the proper variety was obtained, together with a reliable allocation pattern among the other varieties. Both aspects deal with the variation within a variety and the distance to other varieties. Assignment data were transformed into an average similarity measure, similarity by assignment (Sax,y), which is a new genetic distance measure with interesting properties
A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues
Marcel, T.C. ; Varshney, R.K. ; Barbieri, M. ; Jafary, H. ; Kock, M.J.D. de; Graner, A. ; Niks, R.E. - \ 2007
Theoretical and Applied Genetics 114 (2007)3. - ISSN 0040-5752 - p. 487 - 500.
powdery mildew resistance - quantitative trait loci - aflp markers - microsatellite markers - disease-resistance - ssr-markers - linkage map - genome - rice - cloning
A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin
Further isolation of AFLP and LMS markers for the mapping of the Ol-2 locus related to powdery mildew (Oidium neolycopersici) resistance in tomato (Solanum lycopersicum L.)
Ricciardi, L. ; Lotti, C. ; Pavan, S.N.C. ; Bai, Y. ; Lindhout, P. ; Giovanni, C. de - \ 2007
Plant Science 172 (2007)4. - ISSN 0168-9452 - p. 746 - 755.
bulked segregant analysis - mediated suppression-pcr - conferring resistance - disease-resistance - molecular markers - linkage map - gene ol-1 - identification - dna - chromosome-6
Tomato powdery mildew (Oidium neolycopersici) is a new plant disease that in recent years has frequently occurred in open field and protected environments to cause serious damage to tomato crops. Currently, the development of resistant cultivars appear to be the best eco-compatible solution to control the fungus. Several studies are in progress to increase knowledge on a recessive gene named ol-2 that confers complete resistance to powdery mildew. In this paper, we report results of research aimed at further isolation of new PCR-based markers linked to ol-2. This goal was pursued by means of bulk segregant analysis (BSA) applied to an F2 population segregating for the ol-2 gene and derived from the pair cross between a resistant line of Solanum lycopersicum L. var. cerasiforme and the susceptible cultivar Super Marmande. Eight new amplified fragment length polymorphism (AFLP) markers tightly linked to ol-2 were isolated, adding useful mapping information to the chromosome four region where Ol-2 locus is located. Results from the application of the ligation-mediated suppression PCR (LMS-PCR) technique are also reported for the first time in plant material. These results, combined with those obtained applying low ionic strength single strand conformation polymorphism (LIS-SSCP) analysis, were of value to detect polymorphism between parents characterised by high genetic similarities and also useful in avoiding "linkage drag" during marker assisted selection (MAS) programs
Innate nonhost immunity in barley to different heterologous rust fungi is controlled by sets of resistance genes with different and overlapping specificities
Jafary, H. ; Szabo, L.J. ; Niks, R.E. - \ 2006
Molecular Plant-Microbe Interactions 19 (2006)11. - ISSN 0894-0282 - p. 1270 - 1279.
puccinia-hordei - linkage map - leaf rust - plant defense - arabidopsis - identification - prehaustorial - perception - morphology - pathogens
We developed an evolutionary relevant model system, barley-Puccini rust fungi, to study the inheritance and specificity of plant factors that determine to what extent innate nonhost immunity can be suppressed. A mapping population was developed from a cross between an experimental barley line (Suspired) with exceptional susceptibility to several heterogonous (nonhost) rust fungi and regular, immune, cv. Veda. Seedlings were inoculated with five heterogonous and two homologous (host) species of rust fungi. Resistance segregated quantitatively for each of the rust fungi. In total, 18 chromosomal regions were implicated. For each rust species, a different set of genes was effective. Of the 18 chromosomal regions, 11 were significantly effective to only one rust species and 7 were effective to more than one rust species, implying genetic linkage or pleiotropy. One resistance (R) gene for hypersensitive resistance to Puccinia hordei-secalini was mapped, suggesting occasional contribution of R genes to nonhost resistance in barley. Quantitative trait loci (QTLs) with effects to multiple rust fungi did not tend to be particularly effective to rust species that were phylogenetically related, as determined from their internal transcribed spacer sequence. We suggest that the QTLs described here play a role as specific and quantitative recognition factors that are specifically negated by the rust to successfully suppress innate immunity.
Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map
Os, H. van; Andrzejewski, S. ; Bakker, E.H. ; Barrena, I. ; Bryan, G.J. ; Caromel, B. ; Ghareeb, B. ; Isidore, E. ; Jong, W. de; Koert, P. van; Lefebvre, V. ; Milbourne, D. ; Ritter, E. ; Rouppe van der Voort, J.N.A.M. ; Rousselle-Bourgeois, F. ; Vliet, J.M. van; Waugh, R. ; Visser, R.G.F. ; Bakker, J. ; Eck, H.J. van - \ 2006
Genetics 173 (2006)2. - ISSN 0016-6731 - p. 1075 - 1087.
quantitative trait loci - sequence-tagged sites - solanum-tuberosum - linkage map - resistance-gene - aflp markers - mapping strategy - density - tomato - populations
An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
Vigour evaluation for genetics and breeding in rose
Yan, Z. ; Dolstra, O. ; Hendriks, T. ; Prins, T.W. ; Stam, P. ; Visser, P.B. - \ 2005
Euphytica 145 (2005)3. - ISSN 0014-2336 - p. 339 - 347.
seedling-vigor - linkage map - traits - growth - potato - rflp - aflp - construction - resistance - markers
Breeding of cut and pot rose cultivars for efficient production under low-energy conditions in greenhouses will be facilitated by understanding the inheritance of vigour. To get insight into the genetic variation of vigour-related traits, a diploid rose population was employed for an evaluation study in greenhouses in The Netherlands and Denmark. For all the traits investigated the population showed a continuous quantitative variation as well as a considerable transgression. For most of the traits, the genetic variation found among the tested entries was highly significant and tended to be large in comparison to the effects of genotype by environment interaction. The heritability based on means of the traits was high and ranged from 68 to 92%. Strong simple correlations (r = 0.65 to 0.95) were found among the traits shoot length, leaf area, leaf dry weight, stem dry weight, total dry weight and growth rate. The total dry weight and leaf area are suggested to be good parameters for early selection of rose genotypes with vigorous growth under suboptimal growth conditions.
Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop the Pulmonary Hypertension Syndrome (PHS)
Rabie, T.S.K.M. ; Crooijmans, R.P.M.A. ; Bovenhuis, H. ; Vereijken, A.L.J. ; Veenendaal, A. ; Poel, J.J. van der; Arendonk, J.A.M. van; Pakdel, A. ; Groenen, M.A.M. - \ 2005
Animal Genetics 36 (2005)6. - ISSN 0268-9146 - p. 468 - 476.
whole genome scan - right ventricular hypertrophy - broiler-chickens - ascites syndrome - high-altitude - linkage map - growth - heart - failure - poultry
Pulmonary hypertension syndrome (PHS), also referred to as ascites syndrome, is a growth-related disorder of chickens frequently observed in fast-growing broilers with insufficient pulmonary vascular capacity at low temperature and/or at high altitude. A cross between two genetically different broiler dam lines that originated from the White Plymouth Rock breed was used to produce a three-generation population. This population was used for the detection and localization of quantitative trait loci (QTL) affecting PHS-related traits. Ten full-sib families consisting of 456 G2 birds were typed with 420 microsatellite markers covering 24 autosomal chromosomes. Phenotypic observations were collected on 4202 G3 birds and a full-sib across family regression interval mapping approach was used to identify QTL. There was statistical evidence for QTL on chicken chromosome 2 (GGA2), GGA4 and GGA6. Suggestive QTL were found on chromosomes 5, 8, 10, 27 and 28. The most significant QTL were located on GGA2 for right and total ventricular weight as percentage of body weight (%RV and %TV respectively). A related trait, the ratio of right ventricular weight as percentage to total ventricular weight (RATIO), reached the suggestive threshold on this chromosome. All three QTL effects identified on GGA2 had their maximum test statistic in the region flanked by markers MCW0185 and MCW0245 (335-421 cM)
Genetic and physiological architecture of early vigor in Aegilops tauschii, the D-genome of hexaploid wheat. A quantitative trait loci analysis
Steege, M.W. ter; Ouden, F.M. den; Lambers, H. ; Stam, P. ; Peeters, A.J.M. - \ 2005
Plant Physiology 139 (2005)2. - ISSN 0032-0889 - p. 1078 - 1094.
relative growth-rate - applied gibberellic-acid - leaf elongation rates - water-use efficiency - biomass allocation - qtl analysis - hordeum-spontaneum - temperate cereals - seedling-vigor - linkage map
Plant growth can be studied at different organizational levels, varying from cell, leaf, and shoot to the whole plant. The early growth of seedlings is important for the plant's establishment and its eventual success. Wheat (Triticum aestivum, genome AABBDD) seedlings exhibit a low early growth rate or early vigor. The germplasm of wheat is limited. Wild relatives constitute a source of genetic variation. We explored the physiological and genetic relationships among a range of early vigor traits in Aegilops tauschii, the D-genome donor. A genetic map was constructed with amplified fragment-length polymorphism and simple sequence repeat markers, and quantitative trait loci (QTL) analysis was performed on the F4 population of recombinant inbred lines derived from a cross between contrasting accessions. The genetic map consisted of 10 linkage groups, which were assigned to the seven chromosomes and covered 68% of the D genome. QTL analysis revealed 87 mapped QTLs (log of the odds >2.65) in clusters, 3.1 QTLs per trait, explaining 32% of the phenotypic variance. Chromosomes 1D, 4D, and 7D harbored QTLs for relative growth rate, biomass allocation, specific leaf area, leaf area ratio, and unit leaf rate. Chromosome 2D covered QTLs for rate and duration of leaf elongation, cell production rate, and cell length. Chromosome 5D harbored QTLs for the total leaf mass and area and growth rate of the number of leaves and tillers. The results show that several physiological correlations between growth traits have a genetic basis. Genetic links between traits are not absolute, opening perspectives for identification of favorable alleles in A. tauschii to improve early vigor in wheat
Construction of an integrated map of rose with AFLP, SSR, PK, RGA, SCAR and morphological markers
Yan Zifu, Z. ; Denneboom, C. ; Hattendorf, A. ; Dolstra, O. ; Debener, T. ; Stam, P. ; Visser, P.B. - \ 2005
Theoretical and Applied Genetics 110 (2005)4. - ISSN 0040-5752 - p. 766 - 777.
disease resistance genes - linkage map - pto-like - identification - sequence - tomato - maize - arabidopsis - populations - blackspot
A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Seven linkage groups, putatively corresponding to the seven haploid rose chromosomes, were identified for each parent, spanning 487 cM and 490 cM, respectively. The average length of 70 cM may cover more than 90% of the rose genome. An integrated map was constructed by incorporating the homologous parental linkage groups, resulting in seven linkage groups with a total length of 545 cM. The present linkage map is currently the most advanced map in rose with regard to marker density, genome coverage and with robust markers, giving good perspectives for QTL mapping and marker-assisted breeding in rose. The SSR markers, together with RFLP markers, provide good anchor points for future map alignment studies in rose and related species. Codominantly scored AFLP markers were helpful in the integration of the parental maps.
Genomics for food safety and sustainable animal production
Harlizius, B. ; Wijk, H.J. van; Merks, J.W.M. - \ 2004
Journal of Biotechnology 113 (2004)1-3. - ISSN 0168-1656 - p. 33 - 42.
quantitative trait loci - leukocyte adhesion deficiency - meat quality traits - linkage map - dairy-cattle - muscle mass - photoperiod sensitivity - antibody-response - holstein cattle - flowering time
There is a growing concern in society about the safety of animal-derived food, the health and welfare of farm animals and the sustainability of current animal production systems. Along farm animal, breeding genomics may contribute to a solution for these concerns. The use of genomic analysis tools, to achieve genetic progress in typical out-bred populations of farm animals, seems to be more difficult compared to `model` organisms or plants. However, identification of positional candidate genes may be accelerated by linkage disequilibrium (LD) mapping. Recording of sustainable traits requires a large financial and logistic input and the economic advantages for the market are not as clear as for traditional selection traits. Examples show that the major genes causing variability for similar traits in different species are rarely the same. Therefore, for breeding purposes genomic analysis of the species of interest is needed. The fundamental knowledge obtained on the genetic architecture of complex traits will open new perspectives for the use of DNA tests in selection schemes. For food safety and traceability, DNA-based techniques evolve for monitoring and early warning systems
QTL mapping of anthracnose (Colletotrichum spp.) resistance in a cross between Capsicum annuum and C-chinense
Voorrips, R.E. ; Finkers, H.J. ; Sanjaya, L. ; Groenwold, R. - \ 2004
Theoretical and Applied Genetics 109 (2004)6. - ISSN 0040-5752 - p. 1275 - 1282.
linkage map - genes - aflp
Anthracnose fruit rot is an economically important disease that affects pepper production in Indonesia. Strong resistance to two causal pathogens, Colletotrichum gloeosporioides and C. capsici, was found in an accession of Capsicum chinense. The inheritance of this resistance was studied in an F2 population derived from a cross of this accession with an Indonesian hot pepper variety (Capsicum annuum) using a quantitative trait locus (QTL) mapping approach. In laboratory tests where ripe fruits were artificially inoculated with either C. gloeosporioides or C. capsici, three resistance-related traits were scored: the infection frequency, the true lesion diameter (averaged over all lesions that actually developed), and the overall lesion diameter (averaged over all inoculation points, including those that did not develop lesions). One main QTL was identified with highly significant and large effects on all three traits after inoculation with C. gloeosporioides and on true lesion diameter after inoculation with C. capsici. Three other QTL with smaller effects were found for overall lesion diameter and true lesion diameter after inoculation with C. gloeosporioides, two of which also had an effect on infection frequency. Interestingly, the resistant parent carried a susceptible allele for a QTL for all three traits that was closely linked to the main QTL. The results with C. capsici were based on less observations and therefore less informative. Although the main QTL was shown to have an effect on true lesion diameter after inoculation with C. capsici, no significant QTL were identified for overall lesion diameter or infection frequency
A radiation hybrid map of chicken Chromosome 4
Rabie, T. ; Crooijmans, R.P.M.A. ; Morisson, M. ; Andryszkiewicz, J. ; Poel, J.J. van der; Vignal, A. ; Groenen, M.A.M. - \ 2004
Mammalian Genome 15 (2004)7. - ISSN 0938-8990 - p. 560 - 569.
whole-genome - functional genes - linkage map - mammals - panel - conservation - sequence - database - synteny - loci
The mapping resolution of the physical map for chicken Chromosome 4 (GGA4) was improved by a combination of radiation hybrid (RH) mapping and bacterial artificial chromosome (BAC) mapping. The ChickRH6 hybrid panel was used to construct an RH map of GGA4. Eleven microsatellites known to be located on GGA4 were included as anchors to the genetic linkage map for this chromosome. Based on the known conserved synteny between GGA4 and human Chromosomes 4 and X, sequences were identified for the orthologous chicken genes from these human chromosomes by BLAST analysis. These sequences were subsequently used for the development of STS markers to be typed on the RH panel. Using a logarithm of the odds (LOD) threshold of 5.0, nine linkage groups could be constructed which were aligned with the genetic linkage map of this chromosome. The resulting RH map consisted of the 11 microsatellite markers and 50 genes. To further increase the number of genes on the map and to provide additional anchor points for the physical BAC map of this chromosome, BAC clones were identified for 22 microsatellites and 99 genes. The combined RH and BAC mapping approach resulted in the mapping of 61 genes on GGA4 increasing the resolution of the chicken-human comparative map for this chromosome. This enhanced comparative mapping resolution enabled the identification of multiple rearrangements between GGA4 and human Chromosomes 4q and Xp.
A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa
Choi, H.K. ; Kim, D. ; Uhm, T. ; Limpens, E.H.M. ; Lim, H. ; Mun, J.H. ; Kalo, P. ; Penmetsa, R.V. ; Seres, A. ; Kulikova, O. ; Roe, B.A. ; Bisseling, T. ; Kiss, G.B. ; Cook, D.R. - \ 2004
Genetics 166 (2004)3. - ISSN 0016-6731 - p. 1463 - 1502.
nod factor transduction - pcr-based markers - arabidopsis-thaliana - linkage map - expression - construction - leguminosae - mutants - model - identification
A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map) transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes: thus 60 of the EST-based printer pairs were designed to amplify orthologons sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map.
Quantitative trait loci affecting growth-related traits in wild barley (Hordeum spontaneum) grown under different levels of nutrient supply
Elberse, I.A.M. ; Vanhala, T. ; Turin, J.H.B. ; Stam, P. ; Damme, J.M.M. van; Tienderen, P.H. van - \ 2004
Heredity 93 (2004)1. - ISSN 0018-067X - p. 22 - 33.
fragment length polymorphisms - mendelian factors - agronomic traits - qtl analysis - linkage map - leaf-area - populations - plasticity - plants - rice
The genetic basis of phenotypic plasticity of relative growth rate (RGR), its components and associated morphological traits was studied in relation to nutrient limitation. In all, 140 F-3 lines from a cross, made between two Hordeum spontaneum ( wild barley) accessions sampled in Israel, were subjected to growth analysis under two nutrient levels. Quantitative trait loci (QTLs) were detected for RGR and three of its components, leaf area ratio (LAR), specific leaf area and leaf mass fraction (LMF). Indications for close linkage ( potential pleiotropy) were found, for example, for LAR and LMF. An interesting case is on chromosome 6, at which QTLs for RGR and seed mass were detected in the same region. These QTLs had opposite additive effects, supporting earlier results that plants growing from lighter seeds had a higher RGR. Only two QTLs were significant under both nutrient conditions, suggesting large QTL x environment interactions for most traits. For 21 out of 26 QTLs, however, the additive genetic effect was of identical sign in both nutrient environments, but reached the significance threshold in only one of them. Nevertheless, some QTLs detected in one of the two environments had virtually no effect in the other, and QTLs for plasticity were detected for RGR, LAR and LMF, as well as for some morphological traits. QTLs with opposite effects under high and low nutrients were not found. Thus, at the genetic level, there was no evidence for a trade-off between faster growth at high versus low nutrient levels.
Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana
Alonso-Blanco, C. ; Bentsink, L. ; Hanhart, C.J. ; Vries, M.H.C. de; Koornneef, M. - \ 2003
Genetics 164 (2003)2. - ISSN 0016-6731 - p. 711 - 729.
quantitative trait loci - flowering time - abscisic-acid - l heynh - linkage map - germination - mutants - gibberellin - gene - light
Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a quantitative trait loci (QTL) mapping approach to identify loci affecting the after-ripening requirement measured as the number of days of seed dry storage required to reach 50% germination. Thus, seven QTL were identified and named delay of germination (DOG) 1-7. To confirm and characterize these loci, we developed 12 near-isogenic lines carrying single and double Cvi introgression fragments in a Ler genetic background. The analysis of these lines for germination in water confirmed four QTL (DOG1, DOG2, DOG3, and DOG6) as showing large additive effects in Ler background. In addition, it was found that DOG1 and DOG3 genetically interact, the strong dormancy determined by DOG1-Cvi alleles depending on DOG-3-Ler alleles. These genotypes were further characterized for seed dormancy/germination behavior in five other test conditions, including seed coat removal, gibberellins, and an abscisic acid biosynthesis inhibitor. The role of the Ler/Cvi allelic variation in affecting dormancy is discussed in the context of current knowledge of Arabidopsis germination.
The genetics of phytate and phosphate accumulation in seeds and leaves of Arabidopsis thaliana, using natural variation
Bentsink, L. ; Yuan, K. ; Koornneef, M. ; Vreugdenhil, D. - \ 2003
Theoretical and Applied Genetics 106 (2003)7. - ISSN 0040-5752 - p. 1234 - 1243.
phytic acid - inositol hexakisphosphate - soybean seeds - linkage map - metabolism - loci - expression - phosphorus - phenotype - mutations
Phytate (myo-inositol-1,2,3,4,5,6-hexakisphosphate, InsP6) is the most abundant P-containing compound in plants, and an important anti-nutritional factor, due to its ability to complex essential micro-nutrients, e.g. iron and zinc. Analysis of natural variation for InsP6 and Pi accumulation in seeds and leaves for a large number of accessions of Arabidopsis thaliana, using a novel method for InsP6 detection, revealed a wide range of variation in InsP6 and Pi levels, varying from 7.0 mg to 23.1 mg of InsP6 per gram of seed. Quantitative trait locus (QTL) analysis of InsP6 and Pi levels in seeds and leaves, using an existing recombinant inbred line population, was performed in order to identify a gene(s) that is (are) involved in the regulation of InsP6 accumulation. Five genomic regions affecting the quantity of the InsP6 and Pi in seeds and leaves were identified. One of them, located on top of chromosome 3, affects all four traits. This QTL appears as the major locus responsible for the observed variation in InsP6 and Pi contents in the L er/Cvi RIL population; the L er allele decreases the content of both InsP6 and Pi in seeds and in leaves. The InsP6/Pi locus was further fine-mapped to a 99-kb region, containing 13 open reading frames. The maternal inheritance of the QTL and the positive correlation between InsP6 and total Pi levels both in seeds and in leaves indicate that the difference in InsP6 level between L er and Cvi is likely to be caused by a difference in transport rather than by an alteration in the biosynthesis. Therefore, we consider the vacuolar membrane ATPase subunit G, located in the region of interest, as the most likely candidate gene for InsP6/Pi.
Comparative map between chicken chromosome 15 and human chromosomal region 12q24 and 22q11-q12
Jennen, D.G.J. ; Crooijmans, R.P.M.A. ; Kamps, B. ; Acar, R. ; Poel, J.J. van der; Groenen, M.A.M. - \ 2003
Mammalian Genome 14 (2003)9. - ISSN 0938-8990 - p. 629 - 639.
genome rearrangements - mouse chromosome-5 - linkage map - genes - human-chromosome-22 - evolution
The physical and comparative map of GGA15 was improved by the construction of 9 BAC contigs around loci previously mapped on GGA15 by linkage analysis. In total, 240 BAC clones were isolated, covering 30-35% of GGA15, and 120 STS were developed (104 STS derived from BAC end sequences and 18 STS derived within genes). Seventeen chicken orthologues of human genes located on human Chr 22q11-q12 were directly mapped within BAC contigs of GGA15. Furthermore, the partial sequences of the chicken BAC clones were compared with sequences present in the EMBL/GenBank databases and revealed matches to 26 genes, ESTs, and genomic clones located on HSA22q11-q12 and HSA12q24. These results provide a better alignment of GGA15 with the corresponding regions in human and mouse, and improve our knowledge of the evolution and dynamics of the vertebrate genome.
Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools
Hillel, J. ; Groenen, M.A.M. ; Tixier-Boichard, M. ; Korol, A.B. ; David, L. ; Kirzhner, V.M. ; Burke, T. ; Barre-Dirie, A. ; Crooijmans, R.P.M.A. ; Elo, K. ; Fieldman, M.W. ; Freidlin, P.J. ; Maki-Tanila, A. ; Oortwijn, M.E.P. - \ 2003
Genetics, Selection, Evolution 35 (2003)5. - ISSN 0999-193X - p. 533 - 557.
genetic-distance - linkage map - markers - origin - breeds - lines - heterozygosity - fingerprints - diversity - samples
In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population ( inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.
Mapping of quantitative trait loci affecting quality and production traits in egg layers
Tuiskula-Haavisto, M. ; Honkatukia, M. ; Vilkki, J. ; Koning, D.J. de; Schulman, N.F. ; Maki-Tanila, A. - \ 2002
Poultry Science 81 (2002)7. - ISSN 0032-5791 - p. 919 - 927.
hormone receptor gene - chicken genome - growth-hormone - mareks-disease - linkage map - affecting susceptibility - body-weight - lines - association - resistance
A mapping population segregating for egg quality traits was created by a line cross between two egg layer lines and screened by a genome scan. The F2 generation consisted of 307 hens, which were scored for egg quality and production traits. The mapping population was genotyped for 99 microsatellite loci, spanning nine macrochromosomes and five small linkage groups. The linkage maps were used in mapping QTL affecting 14 traits, by using multiple markers and a least-squares approach. We detected 14 genomewide significant and six suggestive QTL that were located on chromosomes 2, 3, 4, 5, and, 8 and sex chromosome Z. A significant QTL affecting egg white thinning was found on chromosome 2. For eggshell strength, a significant QTL was found on chromosome Z. For production traits, the most interesting area was on chromosome 4, where highly significant QTL effects were detected for BW, egg weight, and feed intake in the same area. The most significant QTL explains 25.8% of the phenotypic variance in F2 of body weight. An area affecting the age at first egg, egg weight, and the number of eggs was located on chromosome Z
Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.)
Liebhard, R. ; Gianfranceschi, L. ; Koller, B. ; Ryder, C.D. ; Tarchini, R. ; Weg, W.E. van de; Gessler, C. - \ 2002
Molecular Breeding 10 (2002)4. - ISSN 1380-3743 - p. 217 - 241.
scab resistance - linkage map - genetic diversity - aflp markers - ssr markers - rapd - vf - identification - polymorphism - construction
The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross Fiesta × Discovery. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed
Comparative mapping of human Chromosome 19 with the chicken show conserved synteny and vies an insight into chromosomal evolution
Smith, J. ; Paton, I.R. ; Murray, F. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Burt, D.W. - \ 2002
Mammalian Genome 13 (2002)6. - ISSN 0938-8990 - p. 310 - 315.
linkage map - mouse - genes - human-chromosome-19 - genome - construction - library - regions - density
Human Chromosome 19 (HSA19) is virtually completely sequenced. A complete physical contig map made up of BACs and cosmids is also available for this chromosome. It is, therefore, a rich source of information that we have used as the basis for a comparative mapping study with the chicken. Various orthologs of genes known to map to HSA19 have been mapped in the chicken. Five chicken microchromosomes (two of which were previously undefined) are seen to show conserved synteny with this chromosome, along with individual gene homologs on Chr 1 and another tiny microchromosome. Compared with the mouse, which has 12 chromosomal regions homologous to HSA19, the chicken genotype displays fewer evolutionary rearrangements. The ancestral nature of the chicken karyotype is demonstrated and may prove to be an excellent tool for studying genome evolution
Improvement of the comparative map of chicken chromosome 13
Buitenhuis, A.J. ; Crooijmans, R.P.M.A. ; Bruijnestein van Coppenraet, E.S. ; Veenendaal, A. ; Groenen, M.A.M. ; Poel, J.J. van der - \ 2002
Animal Genetics 33 (2002)4. - ISSN 0268-9146 - p. 249 - 254.
human genomes - linkage map
A comparative map was made of chicken chromosome 13 (GGA13) with a part of human chromosome 5 (HSA5). Microsatellite markers specific for GGA13 were used to screen the Wageningen chicken bacterial artificial chromosome (BAC) library. Selected BAC clones were end sequenced and 57 sequence tag site (STS) markers were designed for contig building. In total, 204 BAC clones were identified which resulted in a coverage of about 20% of GGA13. Identification of genes was performed by a bi-directional approach. The first approach starting with sequencing mapped chicken BAC subclones, where sequences were used to identify orthologous genes in human and mouse by a basic local alignment search tool (BLAST) database search. The second approach started with the identification of chicken orthologues of human genes in the HSA5q23-35 region. The chicken orthologous genes were subsequently mapped by fluorescent in situ hybridisation (FISH) and/or single neucleotide polymorphism typing. The total number of genes mapped on GGA13 is increased from 14 to a total of 20 genes. Genes mapped on GGA13 have their orthologues on HSA5q23-5q35 in human and on Mmu11, Mmu13 and Mmu18 in mouse.