QTL mapping of pomological traits in peach and related species breeding germplasm
Fresnedo-Ramírez, J. ; Bink, M.C.A.M. ; Weg, W.E. van de; Famula, T.R. ; Crisosto, C.H. ; Frett, T. ; Gasic, K. ; Peace, C.P. ; Gradziel, T.M. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 19 p.
persica l. batsch - prunus-persica - linkage disequilibrium - fruit size - population-structure - candidate genes - genome database - sweet cherry - almond - cultivars
Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in marker-assisted breeding.
The epigenetic footprint of poleward range-expanding plants in apomictic dandelions
Preite, V. ; Snoek, L.B. ; Oplaat, C. ; Biere, A. ; Putten, W.H. van der; Verhoeven, K.J.F. - \ 2015
Molecular Ecology 24 (2015)17. - ISSN 0962-1083 - p. 4406 - 4418.
dna methylation polymorphism - arabidopsis-thaliana - geographic parthenogenesis - ecological epigenetics - phenotypic plasticity - cytosine methylation - population-structure - japanese knotweed - common dandelion - taraxacum
Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant populations is poorly documented and little understood. Here, we test if northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA-methylation variation in greenhouse-reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS-AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the Southern, Central and Northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage-specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment-specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher-resolution methods to understand the functional significance of such natural occurring epigenetic differentiation.
Biogeography of Fusarium graminearum species complex and chemotypes: a review
Lee, T.A.J. van der; Zhang, H. ; Diepeningen, A. ; Waalwijk, C. - \ 2015
Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 32 (2015)4. - ISSN 1944-0049 - p. 453 - 460.
head blight pathogen - nivalenol-producing chemotypes - small-grain cereals - trichothecene genotypes - new-zealand - genealogical concordance - mycotoxin chemotypes - population-structure - southern brazil - sensu-stricto
Differences in the geographic distribution of distinct trichothecene mycotoxins in wheat and barley were first recorded two decades ago. The different toxicological properties of deoxynivalenol (DON), nivalenol (NIV) and their acetylated derivatives require careful monitoring of the dynamics of these mycotoxins and their producers. The phylogenetic species concept has become a valuable tool to study the global occurrence of mycotoxin-producing Fusarium species. This has revolutionised our views on the terrestrial distribution of trichothecene-producing Fusaria in the context of agronomics, climatic conditions, and human interference by the global trade and exchange of agricultural commodities. This paper presents an overview of the dynamics of the different trichothecene-producing Fusarium species as well as their chemotypes and genotypes across different continents. Clearly not one global population exists, but separate ones can be distinguished, sometimes even sympatric in combination with different hosts. A population with more pathogenic strains and chemotypes can replace another. Several displacement events appear to find their origin in the inadvertent introduction of new genotypes into new regions: 3-acetyl-DON-producing F. graminearum in Canada; 3-acetyl-DON-producing F. asiaticum in Eastern China; 15-acetyl-DON F. graminearum in Uruguay; and NIV-producing F asiaticum in the southern United States
Prolonged isolation and persistence of a common endemic on granite outcrops in both mesic and semi-arid environments
Tapper, S.L. ; Byrne, M. ; Yates, C.J. ; Keppel, G. ; Hopper, S.D. ; Niel, K.P. Van; Schut, A.G.T. ; Mucina, L. ; Wardell-Johnson, G.W. - \ 2014
Journal of Biogeography 41 (2014)11. - ISSN 0305-0270 - p. 2032 - 2044.
population-structure - climate-change - genetic diversity - dna polymorphism - plant diversity - cpdna variation - phylogeography - chloroplast - myrtaceae - patterns
Granite outcrops may be able to act as refugia for species during adverse climate change, owing to their topographic complexity. We assessed this hypothesis by examining phylogeographical patterns in a common, geographically widespread granite endemic, Stypandra glauca (Hemerocallidaceae).
A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry
Peace, C.P. ; Luby, J. ; Weg, W.E. van de; Bink, M.C.A.M. ; Iezzoni, A.F. - \ 2014
Tree Genetics and Genomes 10 (2014)6. - ISSN 1614-2942 - p. 1679 - 1694.
x domestica borkh. - marker-assisted selection - fire blight resistance - breeding program - population-structure - pyrus-communis - fruit firmness - map position - md-acs1 - gene
Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.
Isolated with persistence or dynamically connected? Genetic patterns in a common granite outcrop endemic
Tapper, S.L. ; Byrne, M. ; Yates, C.J. ; Keppel, G. ; Hopper, S.D. ; Niel, K.P. Van; Schut, A.G.T. ; Mucina, L. ; Wardell-Johnson, G.W. - \ 2014
Diversity and Distributions 20 (2014)9. - ISSN 1366-9516 - p. 987 - 1001.
population-structure - western-australia - climate-change - microsatellite markers - pleistocene refugia - molecular phylogeny - dna polymorphism - cpdna variation - phylogeography - myrtaceae
Aim Granite outcrops are prominent throughout the world and harbour many endemic species. Their topographic complexity and range of environments have led to the hypothesis that they act as refugia facilitating the persistence of species through climate change. We evaluate this hypothesis by investigating the phylogeographic patterns in a common granite endemic shrub. Location Granite outcrops of the Southwest Australian Floristic Region. Methods Chloroplast haplotypes of 89 Kunzea pulchella individuals from 16 granite outcrops were determined from sequences of three chloroplast intergenic spacer regions. Phylogenetic reconstruction and divergence dating was inferred using Bayesian and Parsimony analyses and phylogenetic relationships between haplotypes were examined in relation to geographic distributions. Nuclear diversity and differentiation of populations were assessed through analysis of 11 nuclear microsatellite loci across 384 individuals from the 16 granite outcrops. Results Kunzea pulchella exhibited low haplotype and allelic diversity within outcrops and high levels of divergence among outcrops, indicating an ancient restriction to specific outcrops with genetic drift as the main driver of evolution. Two divergent lineages were revealed in the chloroplast phylogeny dating to the Pliocene and potentially reflecting the initial impact of increased aridity prior to isolation on individual outcrops. Main conclusions Rather than uncovering the typical pattern for Pleistocene refugia with contraction to, and expansion from particular granite outcrops, we observed persistence, prolonged isolation and divergence of populations. We suggest the persistence of K. pulchella on multiple outcrops through a period of considerable climatic change may be a result of broad climatic tolerances or contraction and expansion dynamics operating at microrefugial scales within outcrops. Our observations of low haplotype and allelic diversity within populations of K. pulchella provide some support for the latter. The enduring nature of K. pulchella and evolutionary potential of populations on individual outcrops accentuates the value of these environments for biodiversity conservation planning in a changing climate.
Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis
hoop, B.B. D'; Keizer, L.C.P. ; Paulo, M.J. ; Visser, R.G.F. ; Eeuwijk, F.A. van; Eck, H.J. van - \ 2014
Theoretical and Applied Genetics 127 (2014)3. - ISSN 0040-5752 - p. 731 - 748.
tuberosum subsp tuberosum - late blight resistance - foliage maturity type - beta-vulgaris l. - linkage disequilibrium - solanum-tuberosum - diploid potato - population-structure - quality traits - candidate genes
Two association mapping panels were analysed for marker–trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
Genetic diversity and linkage disequilibrium analysis in elite sugar beet breeding lines and wild beet accessions
Adetunji, I. ; Willems, G. ; Tschoep, H. ; Bürkholz, A. ; Barnes, S. ; Boer, M.P. ; Malosetti, M. ; Horemans, S. ; Eeuwijk, F. van - \ 2014
Theoretical and Applied Genetics 127 (2014)3. - ISSN 0040-5752 - p. 559 - 571.
beta-vulgaris l. - genome-wide association - yellow-vein-virus - population-structure - ssp maritima - rhizomania resistance - restorer gene - markers - map - dna
Linkage disequilibrium decay in sugar beet is strongly affected by the breeding history, and varies extensively between and along chromosomes, allowing identification of known and unknown signatures of selection. Genetic diversity and linkage disequilibrium (LD) patterns were investigated in 233 elite sugar beet breeding lines and 91 wild beet accessions, using 454 single nucleotide polymorphisms (SNPs) and 418 SNPs, respectively. Principal coordinate analysis suggested the existence of three groups of germplasm, corresponding to the wild beets, the seed parent and the pollen parent breeding pool. LD was investigated in each of these groups, with and without correction for genetic relatedness. Without correction for genetic relatedness, in the pollen as well as the seed parent pool, LD persisted beyond 50 centiMorgan (cM) on four (2, 3, 4 and 5) and three chromosomes (2, 4 and 6), respectively; after correction for genetic relatedness, LD decayed after
The domestication and evolutionary ecology of apples
Cornille, A. ; Giraud, T. ; Smulders, M.J.M. ; Roldán-Ruiz, I. ; Gladieux, P. - \ 2014
Trends in Genetics 30 (2014)2. - ISSN 0168-9525 - p. 57 - 65.
wild malus-orientalis - genetic-structure - population-structure - venturia-inaequalis - crop domestication - cultivated apple - fruit - sylvestris - markers - mill.
The cultivated apple is a major fruit crop in temperate zones. Its wild relatives, distributed across temperate Eurasia and growing in diverse habitats, represent potentially useful sources of diversity for apple breeding. We review here the most recent findings on the genetics and ecology of apple domestication and its impact on wild apples. Genetic analyses have revealed a Central Asian origin for cultivated apple, together with an unexpectedly large secondary contribution from the European crabapple. Wild apple species display strong population structures and high levels of introgression from domesticated apple, and this may threaten their genetic integrity. Recent research has revealed a major role of hybridization in the domestication of the cultivated apple and has highlighted the value of apple as an ideal model for unraveling adaptive diversification processes in perennial fruit crops. We discuss the implications of this knowledge for apple breeding and for the conservation of wild apples.
Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon
Banaticla-Hilario, M.C.N. ; Berg, R.G. van den; Hamilton, N.R.S. ; McNally, K.L. - \ 2013
Ecology and Evolution 3 (2013)9. - ISSN 2045-7758 - p. 3047 - 3062.
asian wild-rice - multilocus genotype data - cultivated rice - population-structure - genetic-structure - phylogenetic analysis - evolutionary relationships - insertion-polymorphism - island populations - species cohesion
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F-ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H-E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H-E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers
Tang, N. ; Shahin, A. ; Bijman, P.J.J. ; Liu, J. ; Tuyl, J.M. van; Arens, P. - \ 2013
Scientia Horticulturae 161 (2013). - ISSN 0304-4238 - p. 286 - 292.
single nucleotide polymorphisms - population-structure - genome - identification - conservation - liliaceae - program - power
Although tulip is one of the most important bulbous crops worldwide, the genetic background of most cultivars is unclear at present. The purposes of this study are to investigate genetic diversity and to identify the genetic structure and relationships among tulip cultivars. A total of 236 polymorphic single nucleotide polymorphisms (SNPs) were obtained from 'Kees Nelis' and 'Cantata', from which 121 SNPs with a minor allele frequency above 0.1 were selected for genetic analysis. The total observed heterozygosity (Ho) among the 72 accessions was 0.35, Ho of cultivar groups ranged from 0.22 (Tulipa fosteriana) to 0.43 (Tulipa gesneriana x T. fosteriana hybrids). Rather small genetic distances were found among T. gesneriana cultivar groups which are defined according to flowering time and morphology. In both PCoA (principle coordinate analysis) and STRUCTURE analysis, the 72 accessions were separated into three clusters (F-ST =0.208, P
The use of statistical tools in field testing of putative effects of genetically modified plants on nontarget organisms
Semenov, A.V. ; Elsas, J.D. van; Glandorf, D.C.M. ; Schilthuizen, M. ; Boer, W.F. de - \ 2013
Ecology and Evolution 3 (2013)8. - ISSN 2045-7758 - p. 2739 - 2750.
herbicide-tolerant crops - farm-scale evaluations - gene flow - population-structure - habitat preference - land snail - dispersal - design - power - invertebrates
To fulfill existing guidelines, applicants that aim to place their genetically modified (GM) insect-resistant crop plants on the market are required to provide data from field experiments that address the potential impacts of the GM plants on nontarget organisms (NTO's). Such data may be based on varied experimental designs. The recent EFSA guidance document for environmental risk assessment (2010) does not provide clear and structured suggestions that address the statistics of field trials on effects on NTO's. This review examines existing practices in GM plant field testing such as the way of randomization, replication, and pseudoreplication. Emphasis is placed on the importance of design features used for the field trials in which effects on NTO's are assessed. The importance of statistical power and the positive and negative aspects of various statistical models are discussed. Equivalence and difference testing are compared, and the importance of checking the distribution of experimental data is stressed to decide on the selection of the proper statistical model. While for continuous data (e.g., pH and temperature) classical statistical approaches - for example, analysis of variance (ANOVA) - are appropriate, for discontinuous data (counts) only generalized linear models (GLM) are shown to be efficient. There is no golden rule as to which statistical test is the most appropriate for any experimental situation. In particular, in experiments in which block designs are used and covariates play a role GLMs should be used. Generic advice is offered that will help in both the setting up of field testing and the interpretation and data analysis of the data obtained in this testing. The combination of decision trees and a checklist for field trials, which are provided, will help in the interpretation of the statistical analyses of field trials and to assess whether such analyses were correctly applied.
Climate change and the spread of vector-borne diseases: using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy
Mardulyn, P. ; Goffredo, M. ; Conte, A. ; Hendrickx, G. ; Meiswinkel, R. ; Balenghien, T. ; Sghaier, S. ; Lohr, Y. ; Gilbert, M. - \ 2013
Molecular Ecology 22 (2013)9. - ISSN 0962-1083 - p. 2456 - 2466.
multilocus genotype data - chain monte-carlo - population-structure - mediterranean basin - entomological surveillance - statistical evaluation - expanding populations - genetic diversity - range expansion - history
Bluetongue (BT) is a commonly cited example of a disease with a distribution believed to have recently expanded in response to global warming. The BT virus is transmitted to ruminants by biting midges of the genus Culicoides, and it has been hypothesized that the emergence of BT in Mediterranean Europe during the last two decades is a consequence of the recent colonization of the region by Culicoides imicola and linked to climate change. To better understand the mechanism responsible for the northward spread of BT, we tested the hypothesis of a recent colonization of Italy by C. imicola, by obtaining samples from more than 60 localities across Italy, Corsica, Southern France, and Northern Africa (the hypothesized source point for the recent invasion of C. imicola), and by genotyping them with 10 newly identified microsatellite loci. The patterns of genetic variation within and among the sampled populations were characterized and used in a rigorous approximate Bayesian computation framework to compare three competing historical hypotheses related to the arrival and establishment of C. imicola in Italy. The hypothesis of an ancient presence of the insect vector was strongly favoured by this analysis, with an associated P = 99%, suggesting that causes other than the northward range expansion of C. imicola may have supported the emergence of BT in southern Europe. Overall, this study illustrates the potential of molecular genetic markers for exploring the assumed link between climate change and the spread of diseases.
Genetic diversity and differentiation in roses: A gardenrose perspective
Vukosavljev, M. ; Zhang, J. ; Esselink, G. ; Westende, W.P.C. van 't; Cox, P. ; Visser, R.G.F. ; Arens, P. ; Smulders, M.J.M. - \ 2013
Scientia Horticulturae 162 (2013). - ISSN 0304-4238 - p. 320 - 332.
population-structure - markers - identification - varieties - assignment
tFor the first time genetic diversity among modern garden rose cultivars has been evaluated using a setof 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtainedin the set of 138 rose cultivars and this led to the conclusion that in terms of genetic diversity cut rosescan be considered as a subgroup of the garden roses.Genetic differentiation among types of garden roses (Fst= 0.022) was four times that among cut roses,and similar in magnitude to the differentiation among breeders, due to the fact that horticultural groupsand breeders overlap largely in classification. Winter hardy Svejda’s cultivars (Canadian Explorer roses)showed the least similarities to European roses, and introgression from wild species for winter hardinesswas clearly visible. Roses of Harkness and Olesen shared a similar genepool. Comparison of the differen-tiation among linkage groups indicated that linkage group 5 is potentially a region containing importantQTLs for winter hardiness. Linkage group 6 contains the largest amount of genetic diversity, while linkagegroup 2 is the most differentiated among types of garden roses.
Association mapping of salt tolerance in barley (Hordeum vulgare L.)
Nguyen Viet Long, L. ; Dolstra, O. ; Malosetti, M. ; Kilian, B. ; Graner, A. ; Visser, R.G.F. ; Linden, C.G. van der - \ 2013
Theoretical and Applied Genetics 126 (2013)9. - ISSN 0040-5752 - p. 2335 - 2351.
genome-wide association - abiotic stress tolerance - quantitative trait loci - linkage disequilibrium - population-structure - salinity stress - expression analysis - ion homeostasis - wild barley - molecular markers
A spring barley collection of 192 genotypes from a wide geographical range was used to identify quantitative trait loci (QTLs) for salt tolerance traits by means of an association mapping approach using a thousand SNP marker set. Linkage disequilibrium (LD) decay was found with marker distances spanning 2–8 cM depending on the methods used to account for population structure and genetic relatedness between genotypes. The association panel showed large variation for traits that were highly heritable under salt stress, including biomass production, chlorophyll content, plant height, tiller number, leaf senescence and shoot Na+, shoot Cl- and shoot, root Na+/K+ contents. The significant correlations between these traits and salt tolerance (defined as the biomass produced under salt stress relative to the biomass produced under control conditions) indicate that these traits contribute to (components of) salt tolerance. Association mapping was performed using several methods to account for population structure and minimize false-positive associations. This resulted in the identification of a number of genomic regions that strongly influenced salt tolerance and ion homeostasis, with a major QTL controlling salt tolerance on chromosome 6H, and a strong QTL for ion contents on chromosome 4H.
Association mapping and meta-analysis: two complementary approaches for the detection of reliable Septoria tritici blotch quantitative resistance in bread wheat (Triticum aestivum L.)
Goudemand, E. ; Laurent, V. ; Duchalais, L. ; Tabib Ghaffary, M.S. ; Kema, G.H.J. ; Lonnet, P. ; Margalé, E. ; Robert, O. - \ 2013
Molecular Breeding 32 (2013)3. - ISSN 1380-3743 - p. 563 - 584.
genome-wide association - mycosphaerella-graminicola - winter-wheat - trait loci - dwarfing genes - plant height - population-structure - azole fungicides - qtl metaanalysis - hexaploid wheat
Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most ubiquitous and important diseases of bread wheat worldwide. The aim of this study was to identify markers linked to loci conferring resistance to STB from seven biparental populations. Linkage analysis, meta-analysis and association mapping were combined to identify robust quantitative trait loci (QTLs) for resistance. Linkage analysis led to the detection of 115 QTLs for resistance to STB and 66 QTLs linked to plant height and/or earliness. Meta-analysis clustered these 115 QTLs into 27 Meta-QTLs (MQTLs) of pathogen resistance, of which 14 were found to be linked to plant height and/or earliness. Both the relationship between dwarfing and susceptibility to STB and the significant negative correlation between earliness and STB symptoms were confirmed. Eleven loci were linked to STB resistance by association mapping using a general linear model and/or a mixed linear model, of which eight co-located with STB MQTLs and two co-located with individual QTLs. Associated markers located in MQTL regions enhanced the relevance of the results and validated the potential of an association mapping approach. With several biparental populations, meta-analysis is the most relevant form of genetic analysis study, but association mapping can be used as a validation method. Regions linked to resistance in both methods should be relevant for use in breeding programs for improving resistance to STB in wheat varieties. The main interest in comparing both approaches is to detect robust loci that will be functional in many genetic backgrounds rather than just in one or a few specific backgrounds
Friend or foe: genetic and functional characterization of plant endophytic Pseudomonas aeruginosa
Kumar, A. ; Munder, A. ; Aravind, R. ; Eapen, S.J. ; Tümmler, B. ; Raaijmakers, J.M. - \ 2013
Environmental Microbiology 15 (2013)3. - ISSN 1462-2912 - p. 764 - 779.
iii secretion system - fluorescent pseudomonas - population-structure - opportunistic pathogen - biological-control - swarming motility - botrytis-cinerea - salicylic-acid - lung infection - diversity
Endophytic Pseudomonas aeruginosa strain BP35 was originally isolated from black pepper grown in the rain forest in Kerala, India. Strain PaBP35 was shown to provide significant protection to black pepper against infections by Phytophthora capsici and Radopholus similis. For registration and implementation in disease management programmes, several traits of PaBP35 were investigated including its endophytic behaviour, biocontrol activity, phylogeny and toxicity to mammals. The results showed that PaBP35 efficiently colonized black pepper shoots and displayed a typical spatiotemporal pattern in its endophytic movement with concomitant suppression of Phytophthora rot. Confocal laser scanning microscopy revealed high populations of PaBP35::gfp2 inside tomato plantlets, supporting its endophytic behaviour in other plant species. Polyphasic approaches to genotype PaBP35, including BOX-PCR, recN sequence analysis, multilocus sequence typing and comparative genome hybridization analysis, revealed its uniqueness among P.¿aeruginosa strains representing clinical habitats. However, like other P.¿aeruginosa strains, PaBP35 exhibited resistance to antibiotics, grew at 25–41°C and produced rhamnolipids and phenazines. PaBP35 displayed strong type II secretion effectors-mediated cytotoxicity on mammalian A549 cells. Coupled with pathogenicity in a murine airway infection model, we conclude that this plant endophytic strain is as virulent as clinical P.¿aeruginosa strains. Safety issues related to the selection of plant endophytic bacteria for crop protection are discussed.
Potential barriers to gene flow in the endangered European wildcat (Felis silvestris)
Hartmann, S.A. ; Steyer, K. ; Kraus, R.H.S. ; Segelbacher, G. ; Nowak, C. - \ 2013
Conservation Genetics 14 (2013)2. - ISSN 1566-0621 - p. 413 - 426.
maximum-likelihood-estimation - population-structure - computer-program - domestic cats - southern california - coalescent approach - landscape genetics - differentiation - hybridization - conservation
The European wildcat (Felis silvestris silvestris) is a focal species for conservation in many European countries. After a severe population decline during the 19th century, many populations became extinct or isolated. Within Germany, suitable wildcat habitat is assumed to be highly fragmented. We thus investigated fine-scale genetic structure of wildcat populations in Central Germany across two major potential barriers, the Rhine River with its valley and a major highway. We analyzed 260 hair and tissue samples collected between 2006 and 2011 in the Taunus and Hunsrück mountain ranges (3,500 km2 study area). We identified 188 individuals by genotyping 14 microsatellite loci, and found significant genetic substructure in the study area. Both the Rhine River and the highway were identified as significant barrier to gene flow. While the long-term effect of the river has led to stronger genetic differentiation in the river compared to the highway, estimates of current gene flow and relatedness across barriers indicated a similar or even stronger barrier effect to ongoing wildcat dispersal of the highway. Despite these barrier effects, we found evidence for the presence of recent migration across both the river and the highway. Our study thus suggests that although wildcats have the capability of dispersal across major anthropogenic and natural landscape barriers, these structures still lead to an effective isolation of populations as reflected by genetic analysis. The results strengthen the need for currently ongoing national strategies of wildcat conservation aiming for large scale habitat connectivity.
Pan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence
Smitz, N. ; Berthouly, C. ; Cornelis, D. ; Heller, R. ; Hooft, W.F. van; Chardonnet, P. ; Caron, A. ; Prins, H.H.T. ; Jansen van Vuuren, B. ; Iongh, H.H. de; Michaux, J. - \ 2013
PLoS ONE 8 (2013)2. - ISSN 1932-6203
mitochondrial control region - impala aepyceros-melampus - giant sable antelope - dog lycaon-pictus - microsatellite loci - forest buffalo - population-structure - national-park - cape buffalo - evolutionary history
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple
Cornille, A. ; Giraud, T. ; Bellard, C. ; Tellier, A. ; Cam, B. le; Smulders, M.J.M. ; Kleinschmit, J. ; Roldan-Ruiz, I. ; Gladieux, P. - \ 2013
Molecular Ecology 22 (2013)8. - ISSN 0962-1083 - p. 2249 - 2263.
spatial genetic-structure - chloroplast dna variation - population-structure - glacial refugia - climate-change - ice-ages - comparative phylogeography - microsatellite markers - species distributions - contrasting patterns
Understanding the way in which the climatic oscillations of the Quaternary Period have shaped the distribution and genetic structure of extant tree species provides insight into the processes driving species diversification, distribution and survival. Deciphering the genetic consequences of past climatic change is also critical for the conservation and sustainable management of forest and tree genetic resources, a timely endeavour as the Earth heads into a period of fast climate change. We used a combination of genetic data and ecological niche models to investigate the historical patterns of biogeographic range expansion of a wild fruit tree, the European crabapple (Malus sylvestris), a wild contributor to the domesticated apple. Both climatic predictions for the last glacial maximum and analyses of microsatellite variation indicated that M. sylvestris experienced range contraction and fragmentation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one genetic cluster spanning a large area in Western Europe and two other genetic clusters with a more limited distribution range in Eastern Europe, one around the Carpathian Mountains and the other restricted to the Balkan Peninsula. Approximate Bayesian computation appeared to be a powerful technique for inferring the history of these clusters, supporting a scenario of simultaneous differentiation of three separate glacial refugia. Admixture between these three populations was found in their suture zones. A weak isolation by distance pattern was detected within each population, indicating a high extent of historical gene flow for the European crabapple.