Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/9/2008
Publication Date: 7/29/2008
Citation: Chao, S., Zhang, W., Akhunov, E., Sherman, J., Ma, Y., Luo, M., Dubcovsky, J. 2008. Analysis of gene-derived SNP marker polymorphism in wheat (Triticum aestivum L.). Molecular Breeding. 23:23-33 Interpretive Summary: Single nucleotide polymorphism (SNP) is a marker system that can differentiate individuals based on variations detected at the level of a single nucleotide base in the genome. Such variations are present in high abundance in the genomes of higher organisms including plants. Thus, it is possible to tag the entire genome with SNP markers. To date, approximately 5500 SNP markers have been developed from 1680 gene regions in wheat. In this study, we selected a small set of 359 SNPs distributed across all 21 wheat chromosomes to evaluate the level of SNP marker polymorphism and to determine their utility for genetic mapping and genetic diversity applications in commercial wheat varieties. Included in this study were twenty elite U.S. wheat cultivars representing seven U.S. wheat market classes. The level of SNP marker polymorphism was found to be at least three fold less than that found with a commonly used DNA marker system known as simple sequence repeat (SSR) among the 20 cultivars analyzed. This is mostly due to the higher mutation rate found in the SSR markers than in the SNP markers. Wheat, being a hexaploid, contains three sets of genomes termed A, B and D that originated from three different ancestors sharing some level of sequence similarity among them. When the individual genomes were investigated separately, the results showed that the level of SNP marker polymorphism in the D genome was approximately half of that in the A and B genomes. The low level of genetic diversity found in the D genome is expected if one considers the evolutionary history of hexaploid wheat. It is thought that a small number of the D genome progenitor was involved at the time hexaploid wheat originated less than 10,000 years ago, thus creating a diversity bottleneck. Development of cultivars through man-made selection during the breeding process has further reduced diversity, more so in the D genome than in the A and B genomes. Our results suggested that 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, suggests that SNP markers will play an important role in wheat genetics and breeding applications.
Technical Abstract: In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered in intron sequences of wheat genes, and used them to evaluate SNP marker polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 U.S. wheat cultivars representing seven market classes. PIC values increased to 0.23 when SNPs were pre-selected for polymorphisms among a 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 U.S. cultivars were compared with the set of 13 diverse wheat accessions. Within these 13 accessions, 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 preferential loss of low frequency alleles during the 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 new high-throughput SNP assay technologies, it is anticipated that SNP markers will play an important role in wheat genetics and breeding applications.