Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley

Bundock, Peter C; Henry, Robert J

doi:10.1007/s00122-004-1675-z

Cited by 40 publications

(35 citation statements)

References 27 publications

(19 reference statements)

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“…However, the sequences of PCR products obtained using 10 primers (see above) gave a lower density (1 SNP/520 bp), which is also understandable in view of the fact that only 7 out of 30 SNPs could be validated. The density of SNPs reported during the present study, however, falls within the range (1SNP/21bp to 1SNP/8500bp) of densities of SNPs reported in earlier studies on different tree and plant species (Bryan et al 1999;Schmid et al 2003;Blake et al 2004;Bundock & Henry 2004;Feltus et al 2004;Gupta & Rustgi 2004;Le Dantec et al 2004;Morales et al 2004;Russell et al 2004;Shen et al 2004;Yang et al 2004;Rostoks et al 2005), but is little above the density reported for bread wheat in an earlier study (1 SNP/540 bp; Somers et al 2003). We also noticed that in bread wheat the density of SNPs scored in EST databases (1SNP/144.9 bp; 1 SNP/540 bp) was higher than that reported in sequences of genes of economic importance (1SNP/1000bp to 1SNP/1700bp; Bryan et al 1999;Mochida et al 2003;Somers et al 2003;Zhang et al 2003;Blake et al 2004).…”

Section: Density Of Snpssupporting

confidence: 84%

“…It was shown that allelic variants at this locus consisted of haplotypes rather than single base replacements. Similar studies on haplotyping were conducted earlier in bread wheat (Caldwell et al 2004;Beales et al 2005), barley (Bundock & Henry 2004;Russell et al 2004) and maize (Ching et al 2002;Palaisa et al 2003). Taken together, these studies suggest that on average there are fewer SNPs/haplotype in inbreeders like wheat and barley than in outbreeders like maize (Clark et al 2004;Jung et al 2004;Palaisa et al 2004;Buntjer et al 2005).…”

Section: Haplotype Structuresupporting

confidence: 75%

“…Taken together, these studies suggest that on average there are fewer SNPs/haplotype in inbreeders like wheat and barley than in outbreeders like maize (Clark et al 2004;Jung et al 2004;Palaisa et al 2004;Buntjer et al 2005). This has been attributed to selective constraints, absence of recombination and narrow genetic base of the inbreeders (Kanazin et al 2002;Zhu et al 2003;Bundock & Henry 2004;Caldwell et al 2004;Russell et al 2004). During the present study, out of the seven haplotypes, haplotype 1 (GTGC) was the most abundant.…”

Section: Haplotype Structuresupporting

confidence: 55%

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EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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Abstract:The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1-18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

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Section: Density Of Snpssupporting

confidence: 84%

Section: Haplotype Structuresupporting

confidence: 75%

Section: Haplotype Structuresupporting

confidence: 55%

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EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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“…The typical outcome of such introgressions has been analyzed elsewhere (Ivandic et al 1998;Pillen et al 2004). While it initially generates a spike in genetic diversity, strong selection for the exotic allele will gradually erode the frequencies of the ''old'' alleles, even leading to their complete loss (Russell et al 2000;Collins et al 2001;Bundock and Henry 2004). Such a scenario is likely to have occurred during breeding for resistance to BYMV.…”

Section: Discussionmentioning

confidence: 99%

Effects of Introgression and Recombination on Haplotype Structure and Linkage Disequilibrium Surrounding a Locus EncodingBymovirusResistance in Barley

Stracke

Presterl²,

Stein

et al. 2007

Genetics

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We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eightythree SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.T HE ever-increasing availability of nucleotide sequence, and the concomitant improvement that this brings to our understanding of the organization of complex crop plant genomes, has created the opportunity to identify trait-related genes and to analyze their allelic diversity. The association between phenotype and genotype in diverse populations represents a powerful approach, but the applicability and design of such analyses depend critically on the extent and pattern of linkage disequilibrium (LD) present in the study population. Cultivated barley (Hordeum vulgare ssp. vulgare) has many of the hallmarks known to be associated with a high level of LD. Its effective recombination rate is dramatically reduced by its predominantly inbreeding habit, with an estimated outcrossing rate of 5% in winter barley and ,0.5% in spring barley (Giles et al. 1974;Doll 1987;Abdel-Ghani et al. 2005). Domestication and intensive selection have introduced major bottlenecks in genetic variation, and these are thought to be largely responsible for the perceived narrowness of the modern gene pool (Badr et al. 2000;Russell et al. 2000;Matus and Hayes 2002). LD in modern spring barley, as estimated from a whole-genome survey, extends over distances of at least 10 cM, indicative of an extensive conservation of the genetic identity of barley chromosomes (Kraakman et al. 2004). However, estimates of genomewide LD conceal localized variation, which, as has been shown for a number of species, can be substantial and independent of the mating system (Gupta et al. 2005). In the self-pollinating species Arabidopsis thaliana LD varies from ,10 kb in global (Tian et al. 2002) to 50-250 kb in local populations (Nordborg et al. , 2005Aranzana et al. 2005). Within a given set of maize (an outbreeding species) accessions, the extent of LD has been documented to vary widely around different genes and chr...

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“…However, whether this bottleneck was incurred during the initial domestication process, or during subsequent barley breeding, cannot currently be determined. Reduction of diversity in the cultivated gene pool of barley has been previously reported by Bundock and Henry (2004) Evidence for selection?…”

Section: Loss Of Nucleotide Diversity In Domesticated Barleymentioning

confidence: 99%

Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication

et al. 2006

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Archaeological remains indicate that the origin of western agriculture occurred in a brief period about 10,500 years ago in a region of the Middle East known as the Fertile Crescent, where the wild progenitors of several key agricultural cereal species are endemic. Domestication entailed the appearance of agronomic traits such as seed size and threshability. For a representative sample of 20 domesticated barley (Hordeum vulgare) lines, including 13 two-rowed and 7 six-rowed varieties, we determined the haplotypes at seven loci-Adh2, Adh3, Amy1, Dhn9, GAPDH, PEPC and WAXY encompassing 5,616 bases per line-and compared them to the haplotypes at the same loci for 25 wild forms (Hordeum spontaneum) collected within and outside the Fertile Crescent. In comparisons of wild versus domesticated barley, the number of haplotypes (70 vs. 17), average nucleotide diversity, , (0.0077 vs. 0.0028), and Watterson's theta at silent sites (0.0104 vs. 0.0028) was reduced in domesticated lines. Two loci, Amy1 and PEPC, were monomorphic in domesticated lines; Amy1 and GAPDH produced signiWcant values of Tajima's D. At GAPDH, was slightly higher in domesticated than wild forms, due to divergent high-frequency haplotypes; for the remaining six loci, 87% of nucleotide diversity has been lost in the domesticated forms. Bottlenecks acting on neutrally evolving loci either during the domestication process, during subsequent breeding, or both, are suYcient to account for reduced diversity and the results of Tajima's test, without the need to evoke selection at these loci. Phylogenetic networks data uncover distinct wild and domesticated barley genotypes and suggest that barley may have been domesticated in the Jordan valley. Because, based on AFLP data, the domesticated Turkish cultivars had a genetic basis as large as that present in large germplasm collections, all comparisons provided in this paper are of general value more than being restricted to the Turkish barley germplasm.

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Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley

Cited by 40 publications

References 27 publications

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Effects of Introgression and Recombination on Haplotype Structure and Linkage Disequilibrium Surrounding a Locus EncodingBymovirusResistance in Barley

Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication

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