An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea.
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.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.Show MeSH
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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.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.