Extreme Population-Dependent Linkage Disequilibrium Detected in an Inbreeding Plant Species, <i>Hordeum vulgare</i>

Caldwell, Katherine S.; Russell, Joanne; Langridge, Peter; Powell, W.

doi:10.1534/genetics.104.038489

Cited by 227 publications

(188 citation statements)

References 42 publications

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“…We found limited evidence of breakdown of intrachromosomal LD (Supplementary Figure 2), contrasting with previous findings in both wild barley (Morrell et al, 2005;Caldwell et al, 2006) and barley cultivars (Caldwell et al, 2006) but showing striking similarities to the landrace dataset from Syria and Jordan studied by Caldwell et al (2006). Average intrachromosomal LD was also similar to that reported for landrace barley from Syria and Jordan by Russell et al (2011) but higher than in wild barley from the same area and lower than in a worldwide set of both two-and six-row barley cultivars (Malysheva-Otto et al, 2006).…”

Section: Discussioncontrasting

confidence: 99%

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

et al. 2014

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The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. F ST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.

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Section: Discussioncontrasting

confidence: 99%

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

et al. 2014

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“…Taking into account that T. dicoccoides is a selfer, LD decay in Lr10 was very rapid, within 1-2 kb. This LD extent was also found in wild barley, Hordeum spontaneum, a relative of wheat and a selfer as well (Morrell et al 2006;Caldwell et al 2006). Whole genome LD studies in the selfer A. thaliana have shown a longer extent of LD, up to 250 kb (Nordborg et al 2002).…”

Section: Lr10 Diversity Within and Between Populationsmentioning

confidence: 57%

“…LD was rapidly decaying over the first kb in the wild forms while extending over more than 200 kb in elite cultivars (Caldwell et al 2006). 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.…”

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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“…In addition, Caldwell et al 7 described the three hin genes in DNA and amino sequences for over 70 commercial varieties in detail, but failed to identify any of the hin b haplotypes (unpublished http://www.ncbi.nih.gov). However, a number of SNPs on both hin a and hin b alleles have been described in wild accessions (Caldwell et al unpublished).…”

Section: Discussionmentioning

confidence: 99%

Relationship Between Hardness Genes and Quality in Barley (Hordeum vulgare)

Fox

Nguyen

Bowman

et al. 2007

Journal of the Institute of Brewing

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Barley (Hordeum vulgare) genotypes were sequenced for polymorphism in the hardness genes, these being the three hordoindoline (hin a, hin b1 and hin b2) genes. The variation in haplotype was determined by sequencing for single nucleotide polymorphisms (SNPs). Polymorphism between each gene was then compared to grain hardness (three methods), malt quality characteristics (hot water extract and friability) and cattle feed quality. Two haplotypes were found in a set of forty barley genotypes. For hin a, two alleles were present, namely hin a1 and hin a2. However, there was no specific hin a allele that was associated with grain hardness, malt and feed quality. Barley has two hin b genes, namely hin b1 and hin b2, and the genotypes tested here had one of two alleles for each gene. However, there were no obvious effects on hardness or quality from either of these hin b alleles. Unlike wheat, where a clear relationship has been demonstrated between a number of SNPs in the wheat hardness genes and quality (soft or hard wheat), there was no such relationship for barley. Despite the wide range in hardness, malt and feed quality, there were only two haplotypes for each of the hin a, hin b1 and hin b2 genes and there was no clear relationship between grain hardness, malt or feed quality. The genotypes used in this study demonstrated that there was a low level of polymorphism in hardness genes in current commercial varieties as well as breeding lines and these polymorphisms had no impact on quality.

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Extreme Population-Dependent Linkage Disequilibrium Detected in an Inbreeding Plant Species, Hordeum vulgare

Cited by 227 publications

References 42 publications

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

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

Relationship Between Hardness Genes and Quality in Barley (Hordeum vulgare)

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