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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

Population structure of association mapping pannel based on unlinked SNP marker. (A) Plot of the scaled average logarithm of the probability of data likelihood [LnP (D)] and delta K (ΔK) with K allowed to range from 2 to 15. (B) Membership co-efficient (Q-value) where each horizontal line represents one wheat line and partitioned into seven sub-populations.
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Figure 1: Population structure of association mapping pannel based on unlinked SNP marker. (A) Plot of the scaled average logarithm of the probability of data likelihood [LnP (D)] and delta K (ΔK) with K allowed to range from 2 to 15. (B) Membership co-efficient (Q-value) where each horizontal line represents one wheat line and partitioned into seven sub-populations.

Mentions: The number of subgroups (K) were estimated based on the rate of change in the log probability of data between successive K-values. In the plot of K against ΔK, a break in the slope was observed at K = 7 followed by flattening of the curve (Figure 1). This indicated that the cultivars could be divided into seven sub-groups. Group I included post-Green Revolution cultivars selected for irrigated areas, group II included post-Green Revolution cultivars adapted for rainfed areas, group III were landraces and their derivatives, group IV were derivatives of Green-Revolution cultivars, group V included Green Revolution cultivars adapted from CIMMYT, group VI were post-Green Revolution cultivars from CIMMYT, and group VII included elite cultivars with an Inqalab-91 background. Almost 65% of the population showed admixture trend, whereas only 35% originated from a single genetic background. Linkage disequilibrium (LD) analysis performed on all entries indicated the highest LD in the B genome, followed by D and then A genomes. The B genome had the highest LD in chromosome 1B due to the 1B.1R translocation. LD decay rate for the B genome was 25 cM followed by D (20 cM) and A genomes (7 cM). The frequency of physically linked locus pairs in significant LD was 31% overall (r2 = 0.2), among which the D genome had the highest proportion of marker pairs in LD (41%), followed by B (35%) and A (25%) genome. The estimated average r2 for unlinked loci was 0.024. Chromosome 6D had the maximum number of marker pair in LD (73%), followed by 2D (48%) and 1B (46%). LD decreased with increasing genetic distance between marker loci. In all three cases, the r2 declined within 12 cM below critical values. In GWAS, there are two ways to account for confounding effect of population structure: (i) statistically accounting population structure, and (ii) carefully selection of the association mapping panel to reduce the range of phenology. We employed first strategy because the number of cultivars released in Pakistan were not sufficient for further selection based on phenology.


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)

Population structure of association mapping pannel based on unlinked SNP marker. (A) Plot of the scaled average logarithm of the probability of data likelihood [LnP (D)] and delta K (ΔK) with K allowed to range from 2 to 15. (B) Membership co-efficient (Q-value) where each horizontal line represents one wheat line and partitioned into seven sub-populations.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Population structure of association mapping pannel based on unlinked SNP marker. (A) Plot of the scaled average logarithm of the probability of data likelihood [LnP (D)] and delta K (ΔK) with K allowed to range from 2 to 15. (B) Membership co-efficient (Q-value) where each horizontal line represents one wheat line and partitioned into seven sub-populations.
Mentions: The number of subgroups (K) were estimated based on the rate of change in the log probability of data between successive K-values. In the plot of K against ΔK, a break in the slope was observed at K = 7 followed by flattening of the curve (Figure 1). This indicated that the cultivars could be divided into seven sub-groups. Group I included post-Green Revolution cultivars selected for irrigated areas, group II included post-Green Revolution cultivars adapted for rainfed areas, group III were landraces and their derivatives, group IV were derivatives of Green-Revolution cultivars, group V included Green Revolution cultivars adapted from CIMMYT, group VI were post-Green Revolution cultivars from CIMMYT, and group VII included elite cultivars with an Inqalab-91 background. Almost 65% of the population showed admixture trend, whereas only 35% originated from a single genetic background. Linkage disequilibrium (LD) analysis performed on all entries indicated the highest LD in the B genome, followed by D and then A genomes. The B genome had the highest LD in chromosome 1B due to the 1B.1R translocation. LD decay rate for the B genome was 25 cM followed by D (20 cM) and A genomes (7 cM). The frequency of physically linked locus pairs in significant LD was 31% overall (r2 = 0.2), among which the D genome had the highest proportion of marker pairs in LD (41%), followed by B (35%) and A (25%) genome. The estimated average r2 for unlinked loci was 0.024. Chromosome 6D had the maximum number of marker pair in LD (73%), followed by 2D (48%) and 1B (46%). LD decreased with increasing genetic distance between marker loci. In all three cases, the r2 declined within 12 cM below critical values. In GWAS, there are two ways to account for confounding effect of population structure: (i) statistically accounting population structure, and (ii) carefully selection of the association mapping panel to reduce the range of phenology. We employed first strategy because the number of cultivars released in Pakistan were not sufficient for further selection based on phenology.

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