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United States Department of Agriculture

Agricultural Research Service

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

Author
item Chao, Shiaoman
item Zhang, Wenjun
item Akhunov, Eduard
item Sherman, Jamie
item Ma, Yaqin
item Luo, Mingcheng
item Dvorak, Jan
item Dubcovsky, Jorge

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract only
Publication Acceptance Date: 11/5/2007
Publication Date: 1/12/2008
Citation: Chao, S., Zhang, W., Akhunov, E., Sherman, J., Ma, Y., Luo, M., Dvorak, J., Dubcovsky, J. Analysis of gene-derived SNP marker polymorphism in wheat (Triticum aestivum L.). Plant and Animal Genome Conference. p. 157

Interpretive Summary:

Technical Abstract: In this study, we analyzed 359 single nucleotide polymorphisms (SNPs) previously discovered in intron sequences of wheat genes to evaluate SNP marker polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.181 among 20 US wheat cultivars representing seven market classes. PIC values increased to 0.227 when SNPs were pre-selected for polymorphisms among 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 13 more diverse wheat accessions. We further analyzed the distribution of gene frequencies and confirmed that D genome SNPs have a higher proportion of alleles with minor allele frequencies (<0.125) than the other two genomes. These data suggest that the higher reduction of PIC values in the D genome was caused by the bottleneck that accompanied the development of US adapted germplasm, resulting in preferential loss of low frequency alleles. Additional targeted SNP discovery efforts for the D genome of elite wheat germplasm will likely be required to offset its lower diversity. In spite of this limitation, the observed level of diversity together with the development of high-throughput SNP assay technologies suggest that SNP markers will play an important role in wheat genetics and breeding applications.

Last Modified: 8/24/2016
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