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Comparisons of Wheat Genetic Diversity Point to Selection Targets

NEW YORK (GenomeWeb News) – An international team of researchers looking into genomic patterns in wheat has developed a map of genetic variability and unearthed alleles that were subject to selection, according to a study published in the Proceedings of the National Academy of Sciences yesterday.

Researchers led by Eduard Akhunov at Kansas State University and Matthew Hayden from Victorian AgriBiosciences Center in Australia developed an array containing 9,000 SNPs that they applied to the study of nearly 3,000 hexaploid wheat accessions representing both cultivars and landraces from a broad swath of geographical regions.

Drawing on Roche 454 sequence reads from nine wheat accessions originating from Australia, Mexico, and the US, Akhunov, Hayden, and their colleagues identified more than 25,500 SNPs, which they then whittled down to 9,000 SNPs to include on their Illumina iSelect SNP assay. Of those SNPs, 7,770 were genotyped across 2,994 wheat accessions that included cultivars and landraces, and both spring and winter wheat, from Asia, Australia, Europe, and North America. The researchers then built a consensus SNP map on which they positioned 7,504 polymorphic loci.

Both landraces and cultivars, the researchers found, have similar levels of genetic diversity. The 134 landraces analyzed contained nearly all the alleles found in the 2,860 cultivars — only 1.3 percent of the variants were limited to the cultivars. This suggested to the researchers that "most of the diversity present in the modern cultivars was also present in landraces."

Through principal component analyses, the researchers examined the population structure of wheat, and found that the populations clustered first by whether they were winter wheat or spring wheat and then by geographical origin.

They also noted a higher level of admixture in spring wheat, pointing out that spring wheat from the Pacific Northwest and from Australia clustered with wheat from Mexico and that spring and winter wheat from China grouped with winter wheat from the Pacific Northwest. This, the researchers said, suggested "extensive use of lines sharing common ancestry in the development of these varieties."

While most cultivars and landraces belonged to separate clusters, the researchers found that some landraces grouped with populations from different geographic origins, possibly reflecting the use of landraces in breeding programs.

"The genetic composition of local populations can be shaped by alleles contributed by founding landraces, as well as by the divergence of these populations from the ancestral population of landraces," the researchers added.

Further, different genomic regions appeared to be under selection in winter wheat and spring wheat populations. Based on a combination of comparing genetic differentiation and pair-wise haplotype sharing, they found 21 regions in spring wheat and 39 regions in winter wheat that seemed to be under selection. Fifteen regions could be used to differentiate spring from winter wheat. Those regions include ones like Vrn-A1 and Vrn-B1, which had already been linked to flowering time.

Then, by comparing cultivars and landraces, the researchers found 32 regions that differed between the groups — especially strong evidence of differentiation was near Rht-B1, a dwarfism gene that was involved in the so-called "green revolution" that increased agricultural production.

By examining haplotype sharing between spring wheat population, winter wheat population, and a mixed population, the researchers uncovered 308 SNPs that exhibited evidence of selection. Twenty percent of those SNPs were also linked to genetic differentiation between the populations.

Those 61 SNPs mapped to 23 regions on 10 wheat chromosomes. Some alleles, the researchers added, had a limited geographic range. For example, an allele of the SNP wsnp_BE499016B_Ta_2_1 located on chromosome 6B was common in spring wheat cultivars in Mexico while an allele of SNP wsnp_Ku_c28756_38667953 near Rht-B1 was common in North American winter wheat populations.

"These distinct patterns of geographic distribution of alleles subjected to selection can potentially be linked with adaptation to local environmental conditions," the study authors said.

They added that a number of regions that appeared to be under selection included genes linked to agronomically important traits, like Rht-B1 as well as Ppd-B1 and Vrn1 — both of which are associated with day-length insensitivity and flowering time — and Sr36, which is linked to fungal pathogen resistance.

"We have identified a number of candidate selection targets associated with wheat improvement including regions containing genes involved in the regulation of flowering, development, and stress response," the researchers noted. "Although the biological function of many selection targets is unknown, the genomic resources developed in our study provide an opportunity for the identification of genes underlying wheat adaptation to diverse climatic conditions."