Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

被引:0
作者
Shiaoman Chao
Wenjun Zhang
Eduard Akhunov
Jamie Sherman
Yaqin Ma
Ming-Cheng Luo
Jorge Dubcovsky
机构
[1] USDA-ARS Biosciences Research Lab,Department of Plant Sciences
[2] University of California,Department of Plant Pathology
[3] Davis,Department of Plant and Soil Sciences
[4] Kansas State University,undefined
[5] Montana State University,undefined
来源
Molecular Breeding | 2009年 / 23卷
关键词
EST; SSR; SNP; Wheat;
D O I
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中图分类号
学科分类号
摘要
In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.
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页码:23 / 33
页数:10
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