Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan
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 semi-arid field conditions. The population was genotyped in a high-density Illumina iSele...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00743/full |
| _version_ | 1819149443057844224 |
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| author | Qurat-ul eAin Awais eRasheed Awais eRasheed Alia eAnwar Tariq eMahmood Tariq eMahmood Muhammad eImtiaz Zhonghu eHe Zhonghu eHe Xianchun eXia Umar Masood Quraishi |
| author_facet | Qurat-ul eAin Awais eRasheed Awais eRasheed Alia eAnwar Tariq eMahmood Tariq eMahmood Muhammad eImtiaz Zhonghu eHe Zhonghu eHe Xianchun eXia Umar Masood Quraishi |
| author_sort | Qurat-ul eAin |
| collection | DOAJ |
| description | 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 semi-arid field conditions. The population was genotyped in a 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 tonnes in 1947 to 25.7 million tonnes in 2015. Future breeding strategy can be devised to initiate marker-based 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. |
| first_indexed | 2024-12-22T14:01:41Z |
| format | Article |
| id | doaj.art-f75e1e4e784d4d71bb132f95e217417a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T14:01:41Z |
| publishDate | 2015-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f75e1e4e784d4d71bb132f95e217417a2022-12-21T18:23:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-09-01610.3389/fpls.2015.00743147583Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from PakistanQurat-ul eAin0Awais eRasheed1Awais eRasheed2Alia eAnwar3Tariq eMahmood4Tariq eMahmood5Muhammad eImtiaz6Zhonghu eHe7Zhonghu eHe8Xianchun eXia9Umar Masood Quraishi10Quaid-i-Azam UniversityChinese Academy of Agriculture Sciences (CAAS)International Maize and wheat improvement center (CIMMYT)Quaid-i-Azam UniversityHigher Education ComissionQuaid-i-Azam UniversityCIMMYTChinese Academy of Agriculture Sciences (CAAS)International Maize and wheat improvement center (CIMMYT)International Maize and wheat improvement center (CIMMYT)Quaid-i-Azam UniversityGenome-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 semi-arid field conditions. The population was genotyped in a 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 tonnes in 1947 to 25.7 million tonnes in 2015. Future breeding strategy can be devised to initiate marker-based 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00743/fullSyntenyGWASgene annotationwheatgrain yield90K SNP chip |
| spellingShingle | Qurat-ul eAin Awais eRasheed Awais eRasheed Alia eAnwar Tariq eMahmood Tariq eMahmood Muhammad eImtiaz Zhonghu eHe Zhonghu eHe Xianchun eXia Umar Masood Quraishi Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan Frontiers in Plant Science Synteny GWAS gene annotation wheat grain yield 90K SNP chip |
| title | Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan |
| title_full | Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan |
| title_fullStr | Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan |
| title_full_unstemmed | Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan |
| title_short | Genome-wide association for grain yield under semi-arid conditions in historical wheat cultivars from Pakistan |
| title_sort | genome wide association for grain yield under semi arid conditions in historical wheat cultivars from pakistan |
| topic | Synteny GWAS gene annotation wheat grain yield 90K SNP chip |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00743/full |
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