Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat

Somers, Daryl J.; Banks, Travis BanksT.; DePauw, Ron DePauwR.; Fox, S. L.; Clarke, John ClarkeJ.; Pozniak, Curtis; McCartney, Curt

doi:10.1139/g07-031

Cited by 97 publications

(76 citation statements)

References 17 publications

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“…; Raboin et al, 2008), sunflower (H. annuus;Fusari et al, 2008), tomato (Mazzucato et al, 2008;van Berloo et al, 2008) and wheat (Triticum spp. ; Somers et al, 2007). In S. peruvianum and S. chilense intragenic LD decayed within 150 and 750 bp, respectively, suggestive of high recombination rates and large effective population sizes in these species (Arunyawat et al, 2007).…”

Section: Neutrality Testsmentioning

confidence: 98%

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Labate¹,

Robertson²,

Baldo³

2009

Heredity

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Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (23.2 kb) per plant in a 31 plant diversity panel. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by y and p was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and withinlocus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Rare, highly diverged alleles were observed, involving at least seven tomato lines and five loci. Some of these may represent introgressions that originated both from natural hybridization with Solanum pimpinellifolium L. and from crosses with S. pimpinellifolium and additional wild relatives for crop improvement. The former was reported from classical field studies carried out by CM Rick; the latter has been extensively documented in the crop, particularly for transfer of disease resistance alleles. Extensive introgression and frequent bottlenecks within S. lycopersicum will pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.

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Section: Neutrality Testsmentioning

confidence: 98%

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Labate¹,

Robertson²,

Baldo³

2009

Heredity

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“…Whole genome LD studies in the selfer A. thaliana have shown a longer extent of LD, up to 250 kb (Nordborg et al 2002). LD in bread wheat collections extended 1-5 cM (Chao et al 2007;Horvath et al 2009;Somers et al 2007). Longer LD extent may be due to longer stretches between the sampled loci that overlooks local gene conversion events and only displays crossing over events (Plagnol et al 2006).…”

Section: Lr10 Diversity Within and Between Populationsmentioning

confidence: 99%

“…In durum wheat (Triticum durum), LD stretches for a long distance (Maccaferri et al 2005), with high LD values found between loci located 50 cM apart. In bread wheat collections (T. aestivum), LD extent ranged from 1 cM to 5 cM (Chao et al 2007;Horvath et al 2009;Somers et al 2007). In Aegilops tauschii, the wild donor of the D genome to T. aesitvum, a 1400 bp LD block was observed in the grain softness locus (Massa and…”

Section: Introductionmentioning

confidence: 99%

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

et al. 2010

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INTRODUCTION: Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). RESULTS: Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (d (S) = 0.029, d (N) = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (d (S) = 0.069 vs. 0.029, d (N) = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r (2) = 0.5 to r (2) = 0.1 within a 2-kb span. CONCLUSION: These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat. AbstractRecombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbours rich genetic resources for disease resistance. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains ( d S = 0.069 vs. 0.029, d N =0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r 2 =0.5 to r 2 =0.1 within a 2 kb span. These results suggest that recombination is a diversifying force of the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short range LD decay in wild emmer wheat.

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“…However, intrachromosomal LD was much higher with r 2 = 0.551 (chromosome 2D) or r 2 = 0.909 (chromosome 5A) and decayed within a distance of < 1 cM (2D) and < 5 cM (5A) (Breseghello and Sorrells, 2006). In the study of the bread and durum wheat cultivars Somers et al (2007) observed that only a small fraction of the locus pairs approximately 2-3 cM apart showed r 2 values > 0.2, but few loci at longer distances showed high levels of LD with r 2 = 0.7 and 1.0 at 25.5 and 41.2 cM, respectively. In subpopulations LD extended for longer distances and even higher r 2 values were detected (Somers et al, 2007).…”

Section: Linkage Disequilibrium Measurement Visualization and Scope mentioning

confidence: 86%

“…In the study of the bread and durum wheat cultivars Somers et al (2007) observed that only a small fraction of the locus pairs approximately 2-3 cM apart showed r 2 values > 0.2, but few loci at longer distances showed high levels of LD with r 2 = 0.7 and 1.0 at 25.5 and 41.2 cM, respectively. In subpopulations LD extended for longer distances and even higher r 2 values were detected (Somers et al, 2007). Studies of LD across specific genomic regions were carried out for the region surrounding the yellow rust resistance gene Yr17 (Rhone et al, 2007) and for the region of QSng.sfr-3BS, a major QTL for resistance to Stagonospora nodorum glume blotch on chromosome 3B (Tommasini et al, 2007).…”

Section: Linkage Disequilibrium Measurement Visualization and Scope mentioning

confidence: 99%

Linkage disequilibrium, genetic association mapping and gene localization in crop plants

Sorkheh¹,

Malysheva-Otto²,

Wirthensohn³

et al. 2008

Genet. Mol. Biol.

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DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant populations. Therefore, alternative approach has been suggested, linkage disequilibrium-based association analysis which detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. Although association analysis has already been used for studies on genetics of complex traits in humans, its use in plants has newly started. In the present review, we describe what is known about variation in linkage disequilibrium (LD) and summarize published results on association studies in crop plant species. We give a list of different factors affecting LD, and discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in crop plants research and summarize the present status of LD researches in different plant genomes. Finally, future key issues about the application of these studies on the localization of genes in these crop plants have been also discussed.

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Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat

Cited by 97 publications

References 17 publications

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

Linkage disequilibrium, genetic association mapping and gene localization in crop plants

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