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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #366315

Research Project: Genetic Improvement of Biotic and Abiotic Stress Tolerance and Nutritional Quality in Hard Winter Wheat

Location: Hard Winter Wheat Genetics Research

Title: Genotype imputation in winter wheat using first-generation haplotype map SNPs improves genome-wide association mapping and genomic prediction of traits

Author
item NYINE, MOSES - KANSAS STATE UNIVERSITY
item WANG, SHICHEN - KANSAS STATE UNIVERSITY
item KIANI, KIAN - KANSAS STATE UNIVERSITY
item JORDAN, KATHERINE - KANSAS STATE UNIVERSITY
item LIU, SHUYU - TEXAS A&M AGRILIFE
item BYRNE, PATRICK - COLORADO STATE UNIVERSITY
item HALEY, SCOTT - COLORADO STATE UNIVERSITY
item BAENZIGER, STEPHEN - UNIVERSITY OF NEBRASKA
item CHAO, SHIAOMAN
item Bowden, Robert - Bob
item AKHUNOV, EDUARD - KANSAS STATE UNIVERSITY

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2018
Publication Date: 1/1/2019
Citation: Nyine, M., Wang, S., Kiani, K., Jordan, K., Liu, S., Byrne, B., Haley, S., Baenziger, S., Chao, S., Bowden, R.L., Akhunov, E. 2019. Genotype imputation in winter wheat using first-generation haplotype map SNPs improves genome-wide association mapping and genomic prediction of traits. G3, Genes/Genomes/Genetics. 9:125-133. https://doi.org/10.1534/g3.118.200664.
DOI: https://doi.org/10.1534/g3.118.200664

Interpretive Summary: Geneticists need a high-density set of DNA markers to help map the locations of important genes along the twenty-one chromosomes of wheat. However, cost constraints often dictate that low-density markers must be used instead. One way to improve the utility of a low-density marker set is to use high-density marker information from a reference panel of wheat varieties and then infer the missing data in the original data set. This process is called imputation. This method exploits the fact that small DNA segments are often identical between varieties because they are derived from the same source. These small regions of identity are called haplotypes. In this case study, imputation using haplotypes substantially increased the power and precision of trait mapping and prediction for stripe rust of wheat. This method can easily be expanded to include more reference varieties to further increase power and precision for mapping and prediction for any traits in wheat breeding programs.

Technical Abstract: Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.