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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 #396337
Research Project: Genetic Improvement of Biotic and Abiotic Stress Tolerance and Nutritional Quality in Hard Winter Wheat

Location: Hard Winter Wheat Genetics Research

Title: Genotyping-by-sequencing based molecular genetic diversity of Pakistani bread wheat (Triticum aestivum L.) accessions

Author
item HUSSAIN, SHABBIR - University Of Agriculture, Faisalabad
item HABIB, MADIHA - University Of Agriculture, Faisalabad
item AHMED, ZAHEER - University Of Agriculture, Faisalabad
item SADIA, BUSHRA - University Of Agriculture, Faisalabad
item Bernardo, Amy
item St Amand, Paul
item Bai, Guihua
item GHORI, NIDA - Kansas State University
item KHAN, AZEEM - University Of Agriculture, Faisalabad
item AWAN, FAISAL - University Of Agriculture, Faisalabad
item MAQBOOL, RIZWANA - University Of Agriculture, Faisalabad

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2022
Publication Date: 4/22/2022
Citation: Hussain, S., Habib, M., Ahmed, Z., Sadia, B., Bernardo, A.E., St Amand, P.C., Bai, G., Ghori, N., Khan, A., Awan, F., Maqbool, R. 2022. Genotyping-by-sequencing based molecular genetic diversity of Pakistani bread wheat (Triticum aestivum L.) accessions. Frontiers in Genetics. 13. Article 772517. https://doi.org/10.3389/fgene.2022.772517.
DOI: https://doi.org/10.3389/fgene.2022.772517

Interpretive Summary: Genetic diversity is the key to breeding better wheat varieties. To study genetic diversity of spring wheat in Pakistan, a diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 single-nucleotide polymorphism (SNP) markers. The population was structured as three subgroups with 31, 33, and 120 accessions in subgroup 1, subgroup 2, and subgroup 3, respectively. Knowledge about genetic diversity in Pakistani spring wheat will be a useful tool for selection of breeding parents.

Technical Abstract: Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ~40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.