Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Aflitos, S.A. ; Schijlen, E.G.W.M. ; Jong, J.H.S.G.M. de; Ridder, D. de; Smit, S. ; Finkers, H.J. ; Bakker, F.T. ; Geest, H.C. van de; Lintel Hekkert, B. te; Haarst, J.C. van; Smits, L.W.M. ; Koops, A.J. ; Sanchez-Perez, M.J. ; Heusden, A.W. van; Visser, R.G.F. ; Schranz, M.E. ; Peters, S.A. - \ 2014
The Plant Journal 80 (2014)1. - ISSN 0960-7412 - p. 136 - 148.
single-nucleotide polymorphisms - burrows-wheeler transform - wild tomatoes - genus lycopersicon - read alignment - fruit size - evolution - domestication - solanaceae - plant
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment reveals group-, species-, and accession-specific polymorphisms, which explains characteristic fruit traits and growth habits in the different cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, pointing to positive selection and to differences in selection pressure between crop accessions and wild species. In wild species SNPs are found in excess of 10 million, i.e. 20 fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, highest levels of heterozygosity were found for allogamous SI wild species, while facultative and autogamous SC species display a lower heterozygosity level. Using whole genome SNP information for Maximum Likelihood analysis we achieved complete tree resolution, whereas ML trees based on SNPs from 10 fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat pointing at the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
Design and Characterization of a 52K SNP Chip for Goats
Tosser-klopp, G. ; Bardou, P. ; Bouchez, O. ; Cabau, C. ; Crooijmans, R.P.M.A. ; Dong, Y. ; Donnadieu-Tonon, C. ; Eggen, A. ; Heuven, H.C.M. ; Jamli, S. ; Jiken, A.J. ; Klopp, C. ; Lawley, C.T. ; McEwen, J. ; Martin, P. ; Moreno, C.R. ; Mulsant, P. ; Nabihoudine, I. ; Pailhoux, E. ; Palhiere, I. ; Rupp, R. ; Sarry, J. ; Sayre, B.L. ; Tircazes, A. ; Wang, J. ; Wang, W. ; Zhang, W.G. - \ 2014
PLoS ONE 9 (2014)1. - ISSN 1932-6203
single-nucleotide polymorphisms - classical scrapie - genotyping assay - capra-hircus - prp gene - genome - association - polledness - generation - discovery
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding
Calingacion, M.N. ; Laborte, A.G. ; Nelson, A. ; Resurreccion, A. ; Chrystal Concepcion, J. ; Dara Daygon, V. ; Mumm, R. ; Reinke, R. ; Dipti, S. ; Zaczuk Bassinello, P. ; Manful, J. ; Sophany, S. ; Cordero Lara, K. ; Bao, J. ; Xie, L. ; Loaiza, K. ; El-hissewy, A. ; Gayin, J. ; Sharma, N. ; Rajeswari, S. ; Manonmani, S. ; Shobha Rani, N. ; Kota, S. ; Dewi Indrasari, S. ; Habibi, F. ; Hosseini, M. ; Tavasoli, F. ; Suzuki, K. ; Umemoto, T. ; Boualaphanh, C. ; Hong Lee, H. ; Pang Hung, Y. ; Ramli, A. ; Pa Aung, P. ; Ahmad, R. ; Iqbal Wattoo, J. ; Bandonill, E. ; Romero, M. ; Moita Brites, C. ; Hafeel, R. ; Sheng Lur, H. ; Cheaupun, K. ; Jongdee, S. ; Blanco, P. ; Bryant, R. ; Thi Lang, N. ; Hall, R.D. - \ 2014
PLoS ONE 9 (2014)1. - ISSN 1932-6203 - 12 p.
single-nucleotide polymorphisms - oryza-sativa l. - starch-synthase-iia - grain length - gelatinization temperature - gel consistency - eating quality - gene - gs3 - association
With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a ‘one size fits all’ crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.
A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
Uitdewilligen, J.G.A.M.L. ; Wolters, A.M.A. ; hoop, B.B. D'; Borm, T.J.A. ; Visser, R.G.F. ; Eck, H.J. van - \ 2013
PLoS ONE 8 (2013)5. - ISSN 1932-6203 - 14 p.
single-nucleotide polymorphisms - genome-wide association - chloroplast dna - solanum-tuberosum - agronomic traits - hybrid selection - discovery - enrichment - resistance - diversity
Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (p = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ~60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle
Hulsegge, B. ; Calus, M.P.L. ; Windig, J.J. ; Hoving, A.H. ; Maurice - Van Eijndhoven, M.H.T. ; Hiemstra, S.J. - \ 2013
Journal of Animal Science 91 (2013)11. - ISSN 0021-8812 - p. 5128 - 5134.
single-nucleotide polymorphisms - population divergence - informative markers - assignment - ancestry - individuals - inference - holstein - jersey - phase
Reliable breed assignment can be performed with SNP. Currently, high density SNP chips are available with large numbers of SNP from which the most informative SNP can be selected for breed assignment. Several methods have been published to select the most informative SNP to distinguish among breeds. In this study, we evaluated Delta, Wright's FST, and Weir and Cockerham's FST, and extended these methods by adding a rule to avoid selection of sets of SNP in high linkage disequilibrium (LD) providing the same information. The SNP that had a r2 value>0.3 with any of the SNP already selected were discarded. The different selection methods were evaluated for both the 50K SNP and 777K Bovine BeadChip. Animals from 4 cattle breeds (989 Holstein Friesian, 97 Groningen White headed, 137 Meuse-Rhine-Yssel, and 64 Dutch Friesian) were genotyped. After editing 30,447 and 452,525 SNP were available for the 50K and 777K SNP chip, respectively. All selection methods showed that only a small set of SNP is needed to differentiate among the 4 Dutch cattle breeds, whereas comparison of the selection methods showed only small differences. In general, the 777K performed marginally better than the 50K BeadChip, especially at higher confidence thresholds. The rule to avoid selection of SNP in high LD reduced the required number of SNP to achieve correct breed assignment. The Global Weir and Cockerham's FST performed marginally better than other selection methods. There was little overlap in the SNP selected from the 2 BeadChips, whereas the number of SNP selected was about the same.
In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences
Agren, J. ; Hamidjaja, R.A. ; Hansen, T. ; Ruuls, R.C. ; Thierry, S. ; Vigre, H. ; Janse, I. ; Sundström, A. ; Segerman, B. ; Koene, M.G.J. ; Löfström, Ch. ; Rotterdam, B. van; Derzelle, S. - \ 2013
Virulence 4 (2013)8. - ISSN 2150-5594 - p. 671 - 685.
real-time pcr - single-nucleotide polymorphisms - closely-related bacteria - rapid-detection methods - cereus group - environmental-samples - multiplex pcr - toxin genes - nasal swabs - identification
Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European laboratories was then performed to evaluate six assays, including the WHO recommended procedures, using a collection of 90 Bacillus strains. Three assays performed adequately, yielding no false positive or negative results. All three assays target chromosomal markers located within the lambdaBa03 prophage region (PL3, BA5345, and BA5357). Detection limit was further assessed for one of these highly specific assays.
Signatures of selection in the genomes of commercial and non-commercial chicken breeds
Elferink, M.G. ; Megens, H.J.W.C. ; Vereijken, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2012
PLoS ONE 7 (2012). - ISSN 1932-6203
quantitative trait loci - single-nucleotide polymorphisms - pulmonary-hypertension syndrome - genetic diversity - ascites syndrome - body-composition - growth-factor - layer cross - dna pools - domestication
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
SNP marker detection and genotyping in tilapia
Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Dibbits, B.W. ; Komen, J. - \ 2012
Molecular Ecology Resources 12 (2012)5. - ISSN 1755-098X - p. 932 - 941.
single-nucleotide polymorphisms - salmon oncorhynchus-nerka - oreochromis-niloticus l. - genetic-linkage map - nile tilapia - sockeye-salmon - population-structure - growth-performance - farmed tilapias - lake victoria
We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288–305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei’s genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.
Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)
Aslam, M.L. ; Bastiaansen, J.W.M. ; Elferink, M.G. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Blomberg, L.A. ; Fleischer, R.C. ; Tassell, C.P. van; Sonstegard, T.S. ; Schroeder, S.G. ; Groenen, M. ; Long, J.A. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164
single-nucleotide polymorphisms - breast meat yield - linkage disequilibrium - evolutionary genomics - sequencing technology - body-composition - holstein cattle - farm-animals - dna analysis - chicken
Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey
Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
Chagné, D. ; Crowhurst, R.N. ; Troggio, M. ; Davey, M.W. ; Gilmore, B. ; Lawley, C. ; Vanderzande, S. ; Hellens, R.P. ; Kumar, S. ; Cestaro, A. ; Velasco, R. ; Main, D. ; Rees, J.D. ; Iezzoni, A.F. ; Mockler, T. ; Wilhelm, L. ; Weg, W.E. van de; Gardiner, S.E. ; Bassil, N. ; Peace, C. - \ 2012
PLoS ONE 7 (2012)2. - ISSN 1932-6203
x-domestica borkh. - single-nucleotide polymorphisms - transcription factor - malus-domestica - genus vitis - shelf-life - fruit - markers - diversity - discovery
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple
A pipeline for high throughput detection and mapping of SNPs from EST databases
Anithakumari, A.M. ; Tang, Jifeng ; Eck, H.J. van; Visser, R.G.F. ; Leunissen, J.A.M. ; Vosman, B. ; Linden, C.G. van der - \ 2010
Molecular Breeding 26 (2010)1. - ISSN 1380-3743 - p. 65 - 75.
single-nucleotide polymorphisms - map-based cloning - linkage maps - genome - markers - potato - discovery - construction - varieties - haplotype
Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. Electronic supplementary material The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
Amaral, A.J. ; Kerstens, H.H.D. ; Megens, H.J.W.C. ; Heuven, H.C.M. ; Dibbits, B.W. ; Dungen, J. den; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164
single-nucleotide polymorphisms - reduced representation - linkage disequilibrium - pig genome - technologies - populations - diversity - selection - sites - swine
Background - Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the International Porcine SNP Chip Consortium, this pilot study aimed to evaluate the impact of the quality level of the sequenced bases on mapping quality and identification of true SNPs on a large scale. Results - DNA pooled from five animals from a commercial boar line was digested with DraI; 150–250-bp fragments were isolated and end-sequenced using the Illumina 1 G Genome Analyzer, yielding 70,348,064 sequences 36-bp long. Rules were developed to select sequences, which were then aligned to unique positions in a reference genome. Sequences were selected based on quality, and three thresholds of sequence quality (SQ) were compared. The highest threshold of SQ allowed identification of a larger number of SNPs (17,489), distributed widely across the pig genome. In total, 3,142 SNPs were validated with a success rate of 96%. The correlation between estimated minor allele frequency (MAF) and genotyped MAF was moderate, and SNPs were highly polymorphic in other pig breeds. Lowering the SQ threshold and maintaining the same criteria for SNP identification resulted in the discovery of fewer SNPs (16,768), of which 259 were not identified using higher SQ levels. Validation of SNPs found exclusively in the lower SQ threshold had a success rate of 94% and a low correlation between estimated MAF and genotyped MAF. Base change analysis suggested that the rate of transitions in the pig genome is likely to be similar to that observed in humans. Chromosome X showed reduced nucleotide diversity relative to autosomes, as observed for other species. Conclusion - Large numbers of SNPs can be identified reliably by creating strict rules for sequence selection, which simultaneously decreases sequence ambiguity. Selection of sequences using a higher SQ threshold leads to more reliable identification of SNPs. Lower SQ thresholds can be used to guarantee sufficient sequence coverage, resulting in high success rate but less reliable MAF estimation. Nucleotide diversity varies between porcine chromosomes, with the X chromosome showing less variation as observed in other species
Bioactive compounds: Safety and efficacy (Consensus Meeting - Part II)
Biesalski, H.K. ; Dragsted, L.O. ; Elmadfa, I. ; Grossklaus, R. ; Müller, M.R. ; Schrenk, D. ; Walter, P. ; Weber, P. - \ 2009
Nutrition 25 (2009)11-12. - ISSN 0899-9007 - p. 1206 - 1211.
single-nucleotide polymorphisms - human genome - receptors - sequence - disease - diet
The efficacy and safety of bioactive compounds depend on a few known and unknown parameters. What is a physiologic dose and how can that dose be defined in cases of bioactive compounds with a poor knowledge of supply and distribution? What safety sets are needed? How can individual aspects such as polymorphisms or differences in absorption be considered? A group of experts tried to answer these and related questions during the 23rd Hohenheim Consensus Meeting at the University of Hohenheim in Stuttgart. (C) 2009 Elsevier Inc. All rights reserved.
Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean
Li, Y.H. ; Zhang, C. ; Gao, Z.S. ; Smulders, M.J.M. ; Ma, Z. ; Liu, Z.X. ; Nan, H.Y. ; Chang, R.Z. ; Qiu, L. - \ 2009
Molecular Breeding 24 (2009)1. - ISSN 1380-3743 - p. 63 - 76.
single-nucleotide polymorphisms - rice blast resistance - loci underlying resistance - quantitative trait loci - heterodera-glycines - dna polymorphism - metaanalysis - diversity - qtls
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26¿27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima¿s D and Fu and Li¿s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.
Tetraploid and hexaploid wheat varieties reveal large differences in expression of alpha-gliadins from homoelogous Gli-loci
Salentijn, E.M.J. ; Goryunova, S.V. ; Bas, N. ; Meer, I.M. van der; Broeck, H.C. van den; Bastien, T.A. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164 - p. 48 - 48.
single-nucleotide polymorphisms - celiac-disease patients - t-cell epitope - gene family - dna pools - protein - gluten - pyrosequencing(tm) - diversity - genomes
Background - A-gliadins form a multigene protein family encoded by multiple ¿-gliadin (Gli-2) genes at three genomic loci, Gli-A2, Gli-B2 and Gli-D2, respectively located on the homoeologous wheat chromosomes 6AS, 6BS, and 6DS. These proteins contain a number of important celiac disease (CD)-immunogenic domains. The ¿-gliadins expressed from the Gli-B2 locus harbour fewer conserved CD-epitopes than those from Gli-A2, whereas the Gli-D2 gliadins have the highest CD-immunogenic potential. In order to detect differences in the highly CD-immunogenic ¿-gliadin fraction we determined the relative expression level from the homoeologous Gli-2 loci in various tetraploid and hexaploid wheat genotypes by using a quantitative pyrosequencing method and by analyzing expressed sequence tag (EST) sequences. Results - We detected large differences in relative expression levels of ¿-gliadin genes from the three homoeologous loci among wheat genotypes, both as relative numbers of expressed sequence tag (EST) sequences from specific varieties and when using a quantitative pyrosequencing assay specific for Gli-A2 genes. The relative Gli-A2 expression level in a tetraploid durum wheat cultivar ('Probstdorfer Pandur') was 41%. In genotypes derived from landraces, the Gli-A2 frequency varied between 12% and 58%. In some advanced hexaploid bread wheat cultivars the genes from locus Gli-B2 were hardly expressed (e.g., less than 5% in 'Lavett') but in others they made up more than 40% (e.g., in 'Baldus'). Conclusion - Here, we have shown that large differences exist in relative expression levels of ¿-gliadins from the homoeologous Gli-2 loci among wheat genotypes. Since the homoelogous genes differ in the amount of conserved CD-epitopes, screening for differential expression from the homoeologous Gli-2 loci can be employed for the pre-selection of wheat varieties in the search for varieties with very low CD-immunogenic potential. Pyrosequencing is a method that can be employed for such a 'gene family-specific quantitative transcriptome profiling'
Beyond induced mutants: using worms to study natural variation in genetic pathways
Kammenga, J.E. ; Philips, P.C. ; Bono, M. de; Doroszuk, A. - \ 2008
Trends in Genetics 24 (2008)4. - ISSN 0168-9525 - p. 178 - 185.
quantitative trait loci - life-history traits - genotype-environment interactions - single-nucleotide polymorphisms - nematode caenorhabditis-elegans - c-elegans - linkage disequilibrium - genus caenorhabditis - wild populations - expression
Induced mutants in the nematode Caenorhabditis elegans are used to study genetic pathways of processes ranging from aging to behavior. The effects of such mutations are usually analyzed in a single wildtype background: N2. However, studies in other species demonstrate that the phenotype(s) of induced mutations can vary widely depending on the genetic background. Moreover, induced mutations in one genetic background do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation. Because other wildtype Caenorhabditis spp., including C. elegans, are now available, we review how current mapping resources and methodologies within and between species support the use of Caenorhabditis spp. for studying genetic variation, with a focus on pathways associated with human disease.
Second report on chicken genes and chromosomes 2005
Schmid, M. ; Nanda, I. ; Hoehn, H. ; Schartl, M. ; Haaf, T. ; Buerstedde, J.M. ; Arakawa, H. ; Caldwell, R.B. ; Weigend, S. ; Burt, D.W. ; Smith, J. ; Griffin, D.K. ; Masabanda, J.S. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Vignal, A. ; Fillon, V. ; Morisson, M. ; Pitel, F. ; Vignoles, M. ; Garrigues, A. ; Gellin, J. ; Rodionov, A.V. ; Galkina, S.A. ; Lukina, N.A. ; Ben-Ari, G. ; Blum, S. ; Hillel, J. ; Twito, T. ; Lavi, U. ; David, L. ; Feldman, M.W. ; Delany, M.E. ; Conley, C.C. ; Fowler, V.M. ; Hedges, S.B. ; Godbout, R. ; Katyal, S. ; Smith, C. ; Hudson, Q. ; Sinclair, A. ; Mizuno, S. - \ 2005
Cytogenetic and Genome Research 109 (2005)4. - ISSN 1424-8581 - p. 415 - 479.
single-nucleotide polymorphisms - expressed sequence tags - dt40 cell-line - in-situ hybridization - telomerase rna gene - 5s ribosomal-rna - mhc class-i - major histocompatibility complex - translation initiation factor-4a - nucleolar-size polymorphisms
Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana
Wittenberg, A.H.J. ; Lee, T.A.J. van der; Cayla, C. ; Kilian, A. ; Visser, R.G.F. ; Schouten, H.J. - \ 2005
Molecular Genetics and Genomics 274 (2005)1. - ISSN 1617-4615 - p. 30 - 39.
single-nucleotide polymorphisms - large-scale identification - map-based cloning - primer extension - genome sequence - dna - methylation - arrays - information - inheritance
Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F2 population obtained from a Col × Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms
Data mining of public SNP databases for the selection of intragenic SNPs
Aerts, J. ; Wetzels, Y. ; Cohen, N. ; Aerssens, J. - \ 2002
Human Mutation 20 (2002)3. - ISSN 1059-7794 - p. 162 - 173.
single-nucleotide polymorphisms - human genes - identification
Different strategies to search public single nucleotide polymorphism (SNP) databases for intragenic SNPs were evaluated. First, we assembled a strategy to annotate SNPs onto candidate genes based on a BLAST search of public SNP databases (Intragenic SNP Annotation by BLAST, ISAB). Only BLAST hits that complied with stringent criteria according to 1) percentage identity (minimum 98%), 2) BLAST hit length (the hit covers at least 98% of the length of the SNP entry in the database, or the hit is longer than 250 base pairs), and 3) location in non-repetitive DNA, were considered as valid SNPs. We assessed the intragenic context and redundancy of these SNPs, and demonstrated that the SNP content of the dbSNP and HGBASE/HGVbase databases are highly complementary but also overlap significantly. Second, we assessed the validity of intragenic SNP annotation available on the dbSNP and HGVbase websites by comparison with the results of the ISAB strategy. Only a minority of all annotated SNPs was found in common between the respective public SNP database websites and the ISAB annotation strategy. A detailed analysis was performed aiming to explain this discrepancy. As a conclusion, we recommend the application of an independent strategy (such as ISAB) to annotate intragenic SNPs, complementary to the annotation provided at the dbSNP and HGVbase websites. Such an approach might be useful in the selection process of intragenic SNPs for genotyping in genetic studies
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