Bajaj, D and Upadhyaya, H D and Das, S and Kumar, V and Gowda, C L L and Sharma, S and Tyagi, A K and Parida, S K (2016) Identification of candidate genes for dissecting complex branch number trait in chickpea. Plant Science, 245. pp. 61-70. ISSN 0168-9452
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Abstract
The present study exploited integrated genomics-assisted breeding strategy for genetic dissection of complex branch number quantitative trait in chickpea. Candidate gene-based association analysis in a branch number association panel was performed by utilizing the genotyping data of 401 SNP allelic variants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wide association study (GWAS) integrating both genome-wide GBS- (4556 SNPs) and candidate gene-based genotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli accessions (with 350–400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combined PVE) with branch number in chickpea. Of these, seven branch number-associated genes were further validated successfully in two inter (ICC 4958 x ICC 17160)- and intra (ICC 12299 x ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up- and down-regulation (4–5 folds) of the validated seven branch number-associated genes especially in high branch number was apparent as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations. Collectively, this combinatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in seven potential known/candidate genes [PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1), BA1/LAX1 (BARREN STALK1/LIKE AUXIN1), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGA and Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth 2) and lipase] governing chickpea branch number. The useful information generated from this study have potential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars with more number of productive (pods and seeds) branches in chickpea.
| Item Type: | Article |
|---|---|
| Divisions: | RP-Grain Legumes |
| CRP: | CGIAR Research Program on Grain Legumes |
| Uncontrolled Keywords: | Branch Number; Chickpea; Cicer; Desi; GBS; GWAS; Kabuli; QTL; SNP; Genomics; Genomics Assisted Breeding |
| Subjects: | Mandate crops > Chickpea Others > Genetics and Genomics |
| Depositing User: | Mr Ramesh K |
| Date Deposited: | 03 Feb 2016 04:45 |
| Last Modified: | 16 Dec 2016 05:36 |
| URI: | http://oar.icrisat.org/id/eprint/9289 |
| Official URL: | http://dx.doi.org/10.1016/j.plantsci.2016.01.004 |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | UNSPECIFIED |
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