Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

Kujur, A and Upadhyaya, H D and Bajaj, D and Gowda, C L L and Sharma, S and Tyagi, A K and Parida, S K (2016) Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea. Scientific Reports, 6 (27968). 01-09. ISSN 2045-2322

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In the present study, molecular mapping of high-resolution plant height QTLs was performed by integrating 3625 desi genome-derived GBS (genotyping-by-sequencing)-SNPs on an ultra-high resolution intra-specific chickpea genetic linkage map (dwarf/semi-dwarf desi cv. ICC12299 x tall kabuli cv. ICC8261). The identified six major genomic regions harboring six robust QTLs (11.5–21.3 PVE), associated with plant height, were mapped within <0.5 cM average marker intervals on six chromosomes. Five SNPs-containing genes tightly linked to the five plant height QTLs, were validated based upon their high potential for target trait association (12.9–20.8 PVE) in 65 desi and kabuli chickpea accessions. The vegetative tissue-specific expression, including higher differential up-regulation (>5-fold) of five genes especially in shoot, young leaf, shoot apical meristem of tall mapping parental accession (ICC8261) as compared to that of dwarf/semi-dwarf parent (ICC12299) was apparent. Overall, combining high-resolution QTL mapping with genetic association analysis and differential expression profiling, delineated natural allelic variants in five candidate genes (encoding cytochrome-c-biosynthesis protein, malic oxidoreductase, NADH dehydrogenase iron-sulfur protein, expressed protein and bZIP transcription factor) regulating plant height in chickpea. These molecular tags have potential to dissect complex plant height trait and accelerate marker-assisted genetic enhancement for developing cultivars with desirable plant height ideotypes in chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, Plant height, QTLs, GBS, SNPs, QTL mapping, Genetics
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 26 Sep 2016 05:56
Last Modified: 26 Sep 2016 05:56
Official URL:
Funders: National Institute of Plant Genome Research (NIPGR), New Delhi, India
Acknowledgement: The authors gratefully acknowledge the financial support by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India. Alice Kujur acknowledges the CSIR (Council of Scientific and Industrial Research) for Senior Research Fellowship award.
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