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

Ain QU, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia X, He Z, Quraishi UM - Front Plant Sci (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, 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.

No MeSH data available.


Related in: MedlinePlus

Distribution of 2203 MTA on wheat chromosomes bin based on their—log P-value. Orthologous chromosome are presented in different color codes.
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Figure 2: Distribution of 2203 MTA on wheat chromosomes bin based on their—log P-value. Orthologous chromosome are presented in different color codes.

Mentions: A total, 2094 MTA were detected at -log P >3 using MLM; however, only 44 MTAs with -log P >4 were considered to avoid false positive impact of alleles (Table 3). The highest numbers of MTAs were detected for PH (10) and TGW (10), followed by GY (5), BY (5), DH (5), DM (3), SN (3) and HI (3). The highest numbers of MTAs were identified on chromosomes 2B (6) and 5B (6), followed by 1A (5) and 2A (5), whereas no MTA was found on chromosomes 1D, 2D, 3D, and 5D. The D genome had the lowest number of MTAs (4), whereas the B genome had the highest number (23), followed by the A genome (17). Multi-trait loci were detected on chromosome 1A (BY and GY), 1B (DH and DM), 2B (DH, DM, and PH), 4B (BY and GY), and 6B (HI, BY, and GY). MTAs on chromosomes 5B and 6B were frequently detected for different traits across years. Haplotypes generated for all yield components are compared based on—log P-values on bin based synteny maps of wheat, rice, and sorghum (Figure 2).


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

Ain QU, Rasheed A, Anwar A, Mahmood T, Imtiaz M, Mahmood T, Xia X, He Z, Quraishi UM - Front Plant Sci (2015)

Distribution of 2203 MTA on wheat chromosomes bin based on their—log P-value. Orthologous chromosome are presented in different color codes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585131&req=5

Figure 2: Distribution of 2203 MTA on wheat chromosomes bin based on their—log P-value. Orthologous chromosome are presented in different color codes.
Mentions: A total, 2094 MTA were detected at -log P >3 using MLM; however, only 44 MTAs with -log P >4 were considered to avoid false positive impact of alleles (Table 3). The highest numbers of MTAs were detected for PH (10) and TGW (10), followed by GY (5), BY (5), DH (5), DM (3), SN (3) and HI (3). The highest numbers of MTAs were identified on chromosomes 2B (6) and 5B (6), followed by 1A (5) and 2A (5), whereas no MTA was found on chromosomes 1D, 2D, 3D, and 5D. The D genome had the lowest number of MTAs (4), whereas the B genome had the highest number (23), followed by the A genome (17). Multi-trait loci were detected on chromosome 1A (BY and GY), 1B (DH and DM), 2B (DH, DM, and PH), 4B (BY and GY), and 6B (HI, BY, and GY). MTAs on chromosomes 5B and 6B were frequently detected for different traits across years. Haplotypes generated for all yield components are compared based on—log P-values on bin based synteny maps of wheat, rice, and sorghum (Figure 2).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Plant Breeding, Department of Plant Sciences, Quaid-i-Azam University Islamabad, 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.

No MeSH data available.


Related in: MedlinePlus