Saxena, M.S. and Bajaj, D. and Das, S. and Kujur, A. and et al, . (2014) An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea. DNA Research, 21. pp. 695-710.
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Abstract
The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv.ICC4958andCicer reticulatumwild cv.ICC17160)was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6–39.8% R2 at 4.2–15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of theseQTLsshowedpositiveadditivegeneeffects with effectivealleliccontribution fromICC4958,particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL regionspecific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at traitspecific 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
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | chickpea; SSR; SNP; QTLs; transcription factor; wild |
| Author Affiliation: | National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India |
| Subjects: | Crop Improvement |
| Divisions: | Chickpea |
| Depositing User: | Mr T L Gautham |
| Date Deposited: | 13 Aug 2015 04:20 |
| Last Modified: | 13 Aug 2015 04:20 |
| Official URL: | http://dx.doi.org/10.1093/dnares/dsu031 |
| URI: | http://eprints.icrisat.ac.in/id/eprint/13700 |
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