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Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan

Author: Mahmood, T.
Author: Qurat-ul Ain
Author: Rasheed, A.
Author: Anwar, A.
Author: Imtiaz, M.
Author: Xianchun Xia
Author: He, Zhonghu
Author: Quraishi, U.M.
Year: 2015
URI: http://hdl.handle.net/10883/4488
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.
Format: PDF
Language: English
Publisher: Frontiers
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Type: Article
Country focus: Pakistan
Place of Publication: Switzerland
Pages: 1-15
Issue: 743
Volume: 6
DOI: 10.3389/fpls.2015.00743
Keywords: Spring Bread Wheat
Keywords: Genome-Wide Association Study
Keywords: GWAS
Keywords: Marker Trait Association
Keywords: 90 K SNP Assay
Keywords: Gene Annotation
Keywords: Grain Yield
Country of Focus: PAKISTAN
Agrovoc: SOFT WHEAT
Agrovoc: GENOMICS
Agrovoc: GENETIC MARKERS
Agrovoc: SINGLE NUCLEOTIDE POLYMORPHISM
Agrovoc: GRAIN
Agrovoc: YIELDS
Related Datasets: https://www.frontiersin.org/articles/10.3389/fpls.2015.00743/full#h9
Journal: Frontiers in Plant Science


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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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