CIMMYT

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Browsing CIMMYT by Subject "90 K SNP Assay"

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    Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan
    (Frontiers, 2015) Qurat-ul Ain; Rasheed, A.; Anwar, A.; Mahmood, T.; Imtiaz, M.; Xianchun Xia; He Zhonghu; Quraishi, U.M.
    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.
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    Genome-wide association mapping of vitamins B1 and B2 in common wheat
    (Elsevier, 2018) Jieyun Li; Jindong Liu; Weie Wen; Pingzhi Zhang; Yingxiu Wan; Xianchun Xia; Zhang, Y.; He Zhonghu
    Vitamin B is essential for maintaining normal life activities in humans and animals who have to intake the microelement from the outside, especially from cereal products. In the present study 166 Chinese and foreign wheat cultivars planted in two environments were characterized for variation in vitamin B1 and B2 contents. A genome-wide association study (GWAS) using the wheat 90 K SNP assay identified 17 loci for vitamin B1 and 7 for vitamin B2 contents. Linear regression analysis showed a significantly positive correlation of the number of favorable alleles with vitamin B1 and B2 contents. Marker-trait associations (MTAs) at IWB43809 (6AS, 0 cM) and IWB69903 (6AS, 13 cM) were new and stable, and significantly associated with vitamin B1 content across two environments. The loci identified in this study and associated SNP markers could be used for improvement of vitamin B1 and B2 contents to obtain superior quality along with grain yield in wheat.
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