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An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.

Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - DNA Res. (2014)

Bottom Line: Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number.This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development.The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

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The molecular haplotyping, LD mapping and gene haplotype-specific association analysis in an ABI3VP1 TF gene validating its strong association potential for SW in chickpea. The genotyping of 16 SNPs including one non-synonymous SNP (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this gene (A) among 244 cultivated and 81 wild chickpea accessions constituted seven haplotypes (B). Thirty-seven low seed weight (1.2–3.7 g) accessions represented by single haplotype group 7 (AGAG) and two other haplotypes (GAGC) consisting 24 accessions of high seed weight (13–57.6 g) in the TF gene showed strong association potential for high and low SW differentiation. The seven SNP haplotype-based genotyping information produced higher LD estimates (r2 > 0.60 and P < 0.0001) covering the entire 4,086 bp sequenced region of gene (C). The high (GAGC) and low (AGAG) seed weight-specific haplotypes constituted by four SNPs (shaded with yellow colour in B) in URR of TF gene are depicted (B). (D) The differential expression profiling of ABI3VP1 TF gene in high and low seed weight accessions during seed development compared with the leaf. A superior favourable high seed weight-regulating haplotype (GAGC) with increased transcript expression was identified in the URR of TF gene (D). Each bars represent the mean (±standard error) of three independent biological replicates with two technical replicates for each sample used in quantitative RT–PCR assay. *Significant differences in expression of gene haplotypes at two seed developmental stages of low and high seed weight accessions compared with leaf (LSD-ANOVA significance test at P < 0.01). This figure appears in colour in the online version of DNA Research.
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DSU031F3: The molecular haplotyping, LD mapping and gene haplotype-specific association analysis in an ABI3VP1 TF gene validating its strong association potential for SW in chickpea. The genotyping of 16 SNPs including one non-synonymous SNP (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this gene (A) among 244 cultivated and 81 wild chickpea accessions constituted seven haplotypes (B). Thirty-seven low seed weight (1.2–3.7 g) accessions represented by single haplotype group 7 (AGAG) and two other haplotypes (GAGC) consisting 24 accessions of high seed weight (13–57.6 g) in the TF gene showed strong association potential for high and low SW differentiation. The seven SNP haplotype-based genotyping information produced higher LD estimates (r2 > 0.60 and P < 0.0001) covering the entire 4,086 bp sequenced region of gene (C). The high (GAGC) and low (AGAG) seed weight-specific haplotypes constituted by four SNPs (shaded with yellow colour in B) in URR of TF gene are depicted (B). (D) The differential expression profiling of ABI3VP1 TF gene in high and low seed weight accessions during seed development compared with the leaf. A superior favourable high seed weight-regulating haplotype (GAGC) with increased transcript expression was identified in the URR of TF gene (D). Each bars represent the mean (±standard error) of three independent biological replicates with two technical replicates for each sample used in quantitative RT–PCR assay. *Significant differences in expression of gene haplotypes at two seed developmental stages of low and high seed weight accessions compared with leaf (LSD-ANOVA significance test at P < 0.01). This figure appears in colour in the online version of DNA Research.

Mentions: The sequencing of 4,086 bp cloned amplicon covering the whole CDS and 1 kb URR of a strong SW-regulating ABI3VP1 TF gene (validated by QTL mapping, QTL region-specific association analysis and differential expression profiling) among 244 cultivated (SW-specific association panel) and 81 wild chickpea accessions identified 16 SNP loci (Fig. 3A, Supplementary Table S8). It includes one non-synonymous SNP loci (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this TF gene. The haplotype analysis in ABI3VP1 TF gene combining the genotyping data of 16 SNPs constituted a maximum of seven haplotypes (with PIC varied from 0.68 to 0.97, mean: 0.63) among accessions (Fig. 3B). All these identified seven haplotypes in TF gene were present in five wild species, whereas three haplotypes were shared particularly by 167 desi and 77 kabuli chickpea accessions. It thus suggests that ancient human selection has played a major role in evolution of this SW-influencing TF gene during chickpea domestication.Figure 3.


An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.

Saxena MS, Bajaj D, Das S, Kujur A, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - DNA Res. (2014)

The molecular haplotyping, LD mapping and gene haplotype-specific association analysis in an ABI3VP1 TF gene validating its strong association potential for SW in chickpea. The genotyping of 16 SNPs including one non-synonymous SNP (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this gene (A) among 244 cultivated and 81 wild chickpea accessions constituted seven haplotypes (B). Thirty-seven low seed weight (1.2–3.7 g) accessions represented by single haplotype group 7 (AGAG) and two other haplotypes (GAGC) consisting 24 accessions of high seed weight (13–57.6 g) in the TF gene showed strong association potential for high and low SW differentiation. The seven SNP haplotype-based genotyping information produced higher LD estimates (r2 > 0.60 and P < 0.0001) covering the entire 4,086 bp sequenced region of gene (C). The high (GAGC) and low (AGAG) seed weight-specific haplotypes constituted by four SNPs (shaded with yellow colour in B) in URR of TF gene are depicted (B). (D) The differential expression profiling of ABI3VP1 TF gene in high and low seed weight accessions during seed development compared with the leaf. A superior favourable high seed weight-regulating haplotype (GAGC) with increased transcript expression was identified in the URR of TF gene (D). Each bars represent the mean (±standard error) of three independent biological replicates with two technical replicates for each sample used in quantitative RT–PCR assay. *Significant differences in expression of gene haplotypes at two seed developmental stages of low and high seed weight accessions compared with leaf (LSD-ANOVA significance test at P < 0.01). This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4263302&req=5

DSU031F3: The molecular haplotyping, LD mapping and gene haplotype-specific association analysis in an ABI3VP1 TF gene validating its strong association potential for SW in chickpea. The genotyping of 16 SNPs including one non-synonymous SNP (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this gene (A) among 244 cultivated and 81 wild chickpea accessions constituted seven haplotypes (B). Thirty-seven low seed weight (1.2–3.7 g) accessions represented by single haplotype group 7 (AGAG) and two other haplotypes (GAGC) consisting 24 accessions of high seed weight (13–57.6 g) in the TF gene showed strong association potential for high and low SW differentiation. The seven SNP haplotype-based genotyping information produced higher LD estimates (r2 > 0.60 and P < 0.0001) covering the entire 4,086 bp sequenced region of gene (C). The high (GAGC) and low (AGAG) seed weight-specific haplotypes constituted by four SNPs (shaded with yellow colour in B) in URR of TF gene are depicted (B). (D) The differential expression profiling of ABI3VP1 TF gene in high and low seed weight accessions during seed development compared with the leaf. A superior favourable high seed weight-regulating haplotype (GAGC) with increased transcript expression was identified in the URR of TF gene (D). Each bars represent the mean (±standard error) of three independent biological replicates with two technical replicates for each sample used in quantitative RT–PCR assay. *Significant differences in expression of gene haplotypes at two seed developmental stages of low and high seed weight accessions compared with leaf (LSD-ANOVA significance test at P < 0.01). This figure appears in colour in the online version of DNA Research.
Mentions: The sequencing of 4,086 bp cloned amplicon covering the whole CDS and 1 kb URR of a strong SW-regulating ABI3VP1 TF gene (validated by QTL mapping, QTL region-specific association analysis and differential expression profiling) among 244 cultivated (SW-specific association panel) and 81 wild chickpea accessions identified 16 SNP loci (Fig. 3A, Supplementary Table S8). It includes one non-synonymous SNP loci (T/C) [encoding valine (GTC) to alanine (GCC)] in the B3 functional domain and five regulatory SNPs in the URR of this TF gene. The haplotype analysis in ABI3VP1 TF gene combining the genotyping data of 16 SNPs constituted a maximum of seven haplotypes (with PIC varied from 0.68 to 0.97, mean: 0.63) among accessions (Fig. 3B). All these identified seven haplotypes in TF gene were present in five wild species, whereas three haplotypes were shared particularly by 167 desi and 77 kabuli chickpea accessions. It thus suggests that ancient human selection has played a major role in evolution of this SW-influencing TF gene during chickpea domestication.Figure 3.

Bottom Line: Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number.This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development.The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

Show MeSH
Related in: MedlinePlus