Identification of candidate genes for dissecting complex branch number trait in chickpea

Deepak Bajaj; Hari D Upadhyaya; Shouvik Das; Vinod Kumar; C L L Gowda; Shivali Sharma; Akhilesh K Tyagi; Swarup K Parida

doi:10.1016/j.plantsci.2016.01.004

Identification of candidate genes for dissecting complex branch number trait in chickpea

Plant Sci. 2016 Apr:245:61-70. doi: 10.1016/j.plantsci.2016.01.004. Epub 2016 Jan 19.

Authors

Deepak Bajaj¹, Hari D Upadhyaya², Shouvik Das¹, Vinod Kumar³, C L L Gowda², Shivali Sharma², Akhilesh K Tyagi¹, Swarup K Parida⁴

Affiliations

¹ National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
² International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
³ National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India.
⁴ National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India. Electronic address: swarup@nipgr.ac.in.

PMID: 26940492
DOI: 10.1016/j.plantsci.2016.01.004

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 × ICC 17160)- and intra (ICC 12299 × ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up- and down-regulation (4-5 fold) of the validated seven branch number-associated genes especially in high branch number as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations was apparent. 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.

Keywords: Branch number; Chickpea; Cicer; GBS; GWAS; QTL; SNP; desi; kabuli.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breeding
Chromosome Mapping
Cicer / genetics*
Cluster Analysis
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant*
Genetic Association Studies*
Genome-Wide Association Study
Genomics
Genotyping Techniques
Polymorphism, Single Nucleotide / genetics*
Quantitative Trait Loci / genetics
Quantitative Trait, Heritable*
Reproducibility of Results