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: A set of 839 including 470 genic and genomic SSR markers (Supplementary Fig. S2) and 369 TF gene-derived SNP markers (Supplementary Fig. S3) showing polymorphism between parental accessions were genotyped in 229 individuals of a RIL mapping population (ICC 4958 × ICC 17160) to construct an inter-specific genetic linkage map in chickpea. The linkage analysis using the markers showing significant Mendelian segregation ratio (1:1) mapped 834 markers (including 468 SSR and 366 SNP markers) on eight LGs (LG1–LG8) of chickpea (Fig. 1) according to their physical positions (bp) on respective chromosomes (Supplementary Fig. S1). The constructed genetic map comprising eight LGs spanned a total map length of 949.42 cM with an average inter-marker distance of 1.138 cM (Supplementary Table S5). The map length covered by each LG varied from 71.57 cM (62 markers) in LG8 to 157.80 cM (162 markers) in LG4. The most saturated LG was LG4 (average inter-marker distance of 0.974 cM), whereas LG1 was least saturated (1.647 cM) (Supplementary Table S5). Assuming ∼740 Mb genome size of chickpea, the 834 marker-based genetic linkage map had mean marker density of one marker per 887.3 kb. Interestingly, 76 major hot-spot regions were identified on eight LGs of genetic map in which more than two markers were mapped and clustered within 1 cM genetic distance.Figure 1.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.