SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Ching, Ada; Caldwell, Katherine S.; Jung, Mark; Dolan, M Eileen; Smith, O. S.; Tingey, Scott V.; Morgante, Michèle; Rafalski, Antoni

doi:10.1186/1471-2156-3-19

Cited by 391 publications

(116 citation statements)

References 44 publications

(53 reference statements)

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“…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%

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: Haplotype Structuresupporting

confidence: 75%

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 selective sweep covering Ͼ0.5 Mb is much broader than the domestication-related selective sweep observed at tb1 (7). The extent of LD in the region may be the largest reported to date in maize (27)(28)(29)(30). This is presumably the result of the qualitative nature of the trait, the short time since the selection was imposed, and partial genetic isolation of the yellow germplasm after selection (8).…”

Section: Discussionmentioning

confidence: 94%

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Palaisa

Morgante

Tingey

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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205

153

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Both yellow and white corn occurs among ancestral open pollinated varieties. More recently, breeders have selected yellow endosperm variants of maize over ancestral white phenotypes for their increased nutritional value resulting from the up-regulation of the Y1 phytoene synthase gene product in endosperm tissue. As a result, diversity within yellow maize lines at the Y1 gene is dramatically decreased as compared to white corn. We analyzed patterns of sequence diversity and linkage disequilibrium in nine low copy regions located at varying distances from the Y1 gene, including a homolog of the barley Mlo gene. Patterns consistent with a selective sweep, such as significant associations of informative single-nucleotide polymorphisms with endosperm color phenotype, linkage disequilibrium, and significantly reduced diversity within the yellow endosperm haplotypes, were observed up to 600 kb downstream of Y1, whereas the upstream region showed a more rapid recovery. The starch branching enzyme 1 (sbe1) gene is the first region downstream of Y1 that does not have a highly conserved haplotype in the yellow endosperm germplasm.S elective forces acting on allelic variants of genes have a profound effect on local levels of genetic diversity and linkage disequilibria (LD). Positive directional selection leads to reduced variability and increased LD in the respective region (1-6), and the so-called selective sweep regions provide clues to genes that have been subjects of evolutionary forces as well as selection by humans. Recently, Clark et al. (7) characterized a selective sweep in the promoter region of teosinte branched1 (tb1). The sweep extends 60-90 kb upstream of the gene and is indicative of the gene's role in the domestication of maize from teosinte between 6,000 and 10,000 years ago.The maize Y1 gene on chromosome 6 has undergone recent selection for endosperm color phenotype. A recent study (8) uncovered a dramatic reduction in diversity at this gene for the yellow endosperm maize inbred lines only, over the entire 6-kb gene region. This footprint of selection was characterized by a conserved yellow endosperm haplotype at the 5Ј end of the gene with evidence of recombination toward the 3Ј end. Strong haplotype conservation at the 5Ј end is suggestive of the location of the causal variant associated with the gain-of-function mutation to yellow endosperm and may be indicative of further extension of the selective sweep in the 5Ј direction. The presence of recombinants in the 3Ј UTR region, however, suggested that the extent of the selective sweep may be limited downstream of the coding region.The white endosperm lines did not show characteristics of a selective sweep (8), despite the fact that the white endosperm phenotype is also a target of selection due to human taste preference (9). This is because white is the predicted ancestral state of the gene (John Doebley, personal communication), and thus multiple haplotypes are associated with the white endosperm phenotype.Understanding the boundaries of the selective ...

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“…If the causative mutation is not genotyped, it is still possible to identify association via markers that are in LD with the causative mutation. However, the extent of LD can vary dramatically among plant species (53,54), among genomic regions within plants (55), and among population samples (56)(57)(58). The distribution of LD is also affected by homologous gene conversion, which predominantly disrupts short-range LD patterns (43,59,60).…”

Section: From the Top Down: Qtl And Ld Mappingmentioning

confidence: 99%

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

Ross‐Ibarra

Morrell

Gaut

2007

Proc. Natl. Acad. Sci. U.S.A.

396

318

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Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype-genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.selection ͉ agronomic traits ͉ quantitative trait locus ͉ phenotype ͉ association mapping

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SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Cited by 391 publications

References 44 publications

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

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

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Plant domestication, a unique opportunity to identify the genetic basis of adaptation

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