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.
Highlights
Breeding has contributed to radical increases in cereal production, by the use of dwarf genes and exploitation of heterosis
Phenotypic Evaluation The planting sites were located in the rainfed agroclimatic zone with reliability on rainfall, with 400, 406, and 560 mm in 2011– 12, 2012–2013, and 2013–2014 seasons, respectively
plant height (PH) was significantly higher in 2013–14 (93.3 cm), while thousand grain weight (TGW) was higher in year 2012–13 (Table 1)
Summary
Breeding has contributed to radical increases in cereal production, by the use of dwarf genes and exploitation of heterosis. Grain production must increase by 70% from present levels to meet projected world food requirements by 2050 (Ray et al, 2013). Wheat varieties with high yield and an appropriate end-use quality is the primary objective of all breeding programs around the world. Grain yield (GY) is governed by numerous genes that interact with each other and with the environment (Quarrie et al, 2006). Total Grain yield is a complex trait contributed by multiple yield components, and each component is a quantitative trait controlled or affected by several genes (Zhang et al, 2010b). There must be detailed genetic dissection of the yield trait in order to manipulate each gene to greatest advantage
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