ARS | Publication request: Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 21, 2010
Publication Date: December 31, 2010
Citation: Chao, S., Dubcovsky, J., Dvoral, J., Luo, M., Baenziger, S.P., Matnyazov, R., Clark, D.R., Talbert, L., Anderson, J.A., Dreisigacker, S., Glover, K., Chen, J., Campbell, K., Bruckner, P.L., Rudd, J.C., Haley, S., Carver, B.F., Sims, R., Sorrells, M.E., Akhunov, E.D. 2010. Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat. Biomed Central (BMC) Genomics. 11:727.

Interpretive Summary: We conducted high throughput genotyping using a set of 1,536 single nucleotide polymorphism (SNP) markers to genotype 478 spring and winter wheat lines originated from eight spring and nine winter breeding programs in the U.S. and CIMMYT in Mexico. The objective was to evaluate the extent of genetic diversity among US spring and winter wheat breeding lines. Wheat breeders can benefit from the knowledge of genetic diversity among the lines that are used to initiate the breeding process. Our results demonstrated that the spring wheat lines were generally grouped separately from the winter lines. This low genetic similarity shared between the two growth habits was mostly due to low level of cross-breeding between them in the breeding history, even though significant amount of genetic variants detected by SNP markers were shared in both spring and winter lines. Within each spring and winter wheat groups, the spring wheat lines from the Northern Plains region were genetically more similar than those from the Pacific Northwest region, whereas low levels of genetic differentiation were found among the winter lines derived from the breeding programs located in the Central Plains region, including CO, NE and SD. These results indicated that breeders from the same geographic region tend to use the locally adapted lines as parents in their breeding programs. We further showed that the extent of genetic variations differed greatly among three wheat genomes and among different breeding populations. It was suggested that these differences are the consequences of breeding history and selection pressure applied to genes in the different genomes specific to each breeding program. This study provides critical information for using breeding germplasm as a means to identify genetic markers associated with agronomic traits that can be applied readily to crop improvement.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in the panel of 478 spring and winter wheat cultivars from 17 populations. Higher level of genetic differentiation was observed among wheat lines within populations than among wheat populations. A total of nine genetically distinct clusters were identified suggesting that the 17 pre-defined populations shared significant proportion of genetic ancestry. Locus-specific estimates of population structure (FST) showed a high level of heterogeneity across the genome. Seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL suggesting that they may harbor candidate genes involved in the regulation of growth habit. The higher extent of LD in the wheat D genome than in the A and B genomes is likely linked with the recent introgressions and population bottleneck accompanying the origin of hexaploid wheat. Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. The variation of population-specific LD suggests that breeding and selection had a different impact on the wheat genomes in different populations highlighting the significance of allopolyploidy for the development of locally adapted cultivars. The assessment of LD and population structure in the assembled panel of diverse lines provides information critical for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.