Limits...
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

Linear regression between number of favored alleles and (A) days to heading (DH), (B) Plant Height (PH), (C) Thousand Grain Weight (TGW), and (D) Grain Yield (GY).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585131&req=5

Figure 3: Linear regression between number of favored alleles and (A) days to heading (DH), (B) Plant Height (PH), (C) Thousand Grain Weight (TGW), and (D) Grain Yield (GY).

Mentions: The favorable alleles of significantly associated SNPs had minor additive effects on DH, PH, TGW, and GY (Figure 3). DH and PH were decreased by increasing the number of favorable alleles and linear regressions (R2) between numbers of favorable alleles and phenotype were 0.15 and 0.06, respectively. Similarly, the higher frequency of favorable alleles of associated SNPs additively enhanced TGW and GY with R2 of 0.22 and 0.32, respectively (Figure 3). There had been no selection pressure on any of these favorable alleles, which were evenly distributed across old and modern cultivars. However, the frequency of favorable alleles for DH, PH, TGW, and GY were slightly higher in cultivars released post-2000, compared to those released before 2000 (Table 3). DH and PH fell from 108.7 to 106.7 days and 94.0 to 91.8 cm, and TGW and GY increased from 32.2 to 36.4 (g) and 422.4 to 521.5 (g m−2) in pre-2000 compared to post-2000 cultivars, respectively (Table 4).


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)

Linear regression between number of favored alleles and (A) days to heading (DH), (B) Plant Height (PH), (C) Thousand Grain Weight (TGW), and (D) Grain Yield (GY).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Linear regression between number of favored alleles and (A) days to heading (DH), (B) Plant Height (PH), (C) Thousand Grain Weight (TGW), and (D) Grain Yield (GY).
Mentions: The favorable alleles of significantly associated SNPs had minor additive effects on DH, PH, TGW, and GY (Figure 3). DH and PH were decreased by increasing the number of favorable alleles and linear regressions (R2) between numbers of favorable alleles and phenotype were 0.15 and 0.06, respectively. Similarly, the higher frequency of favorable alleles of associated SNPs additively enhanced TGW and GY with R2 of 0.22 and 0.32, respectively (Figure 3). There had been no selection pressure on any of these favorable alleles, which were evenly distributed across old and modern cultivars. However, the frequency of favorable alleles for DH, PH, TGW, and GY were slightly higher in cultivars released post-2000, compared to those released before 2000 (Table 3). DH and PH fell from 108.7 to 106.7 days and 94.0 to 91.8 cm, and TGW and GY increased from 32.2 to 36.4 (g) and 422.4 to 521.5 (g m−2) in pre-2000 compared to post-2000 cultivars, respectively (Table 4).

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