title: Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan.
abstract: Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011-2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.
authors.affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, Pakistan.
authors.forename: Qurat-Ul
authors.initials: QU
authors.lastname: Ain
authors.affiliation: National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences Beijing, China ; International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Awais
authors.initials: A
authors.lastname: Rasheed
authors.affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, Pakistan.
authors.forename: Alia
authors.initials: A
authors.lastname: Anwar
authors.affiliation: Higher Education Commission, Research and Development Islamabad, Pakistan.
authors.forename: Tariq
authors.initials: T
authors.lastname: Mahmood
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), C/O National Agriculture Research Center Islamabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Imtiaz
authors.affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, Pakistan.
authors.forename: Tariq
authors.initials: T
authors.lastname: Mahmood
authors.affiliation: National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Xianchun
authors.initials: X
authors.lastname: Xia
authors.affiliation: National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences Beijing, China ; International Maize and Wheat Improvement Center (CIMMYT), C/O Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Zhonghu
authors.initials: Z
authors.lastname: He
authors.affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, Pakistan.
authors.forename: Umar M
authors.initials: UM
authors.lastname: Quraishi
keywords: 90K SNP assay; gene annotation; genome-wide association studies (GWAS); grain yield; marker trait association; single nucleotide polymorphism (SNP); spring bread wheat