Record Details

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

NIPGR Digital Knowledge Repository (NDKR)

View Archive Info
 
 
Field Value
 
Title Identification of candidate genes for dissecting complex branch number trait in chickpea
 
Creator Bajaj, Deepak
Upadhyaya, Hari D.
Das, Shouvik
Kumar, Vinod
Gowda, C.L.L.
Sharma, Shivali
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Branch number
Chickpea
Cicer
desi
GBS
GWAS
kabuli
QTL
SNP
 
Description Accepted date: 15 January 2016
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.
The authors gratefully acknowledge the financial support by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India. Shouvik Das acknowledges the Department of Biotechnology (DBT), Government of India for Senior Research Fellowship award. We are thankful to the editor and reviewer for critically evaluating the manuscript and providing constructive comments.
 
Date 2016-02-22T07:28:46Z
2016-02-22T07:28:46Z
2016
 
Type Article
 
Identifier Plant Science, 245: 61-70
0168-9452
http://172.16.0.77:8080/jspui/handle/123456789/624
http://www.sciencedirect.com/science/article/pii/S0168945216300048
10.1016/j.plantsci.2016.01.004
 
Language en_US
 
Publisher Elsevier B.V.