1. Prioritization of candidate genes in 'QTL-hotspot' region for drought tolerance in chickpea (Cicer arietinum L.)
- Author
-
Sandip M. Kale, Jacqueline Batley, Henry T. Nguyen, Mohan A. V. S. K. Katta, Deepa Jaganathan, Pooran M. Gaur, Charles Chen, Vanika Garg, Dadakhalandar Doddamani, Tim Sutton, Pradeep Ruperao, P. B. Kavi Kishor, Mahendar Thudi, Himabindu Kudapa, Manish Roorkiwal, David Edwards, Rajeev K. Varshney, and Ramu Punna
- Subjects
Candidate gene ,Genotype ,Genetic Linkage ,Quantitative Trait Loci ,Drought tolerance ,Population ,Adaptation, Biological ,Genomics ,Single-nucleotide polymorphism ,Quantitative trait locus ,Biology ,Genes, Plant ,Polymorphism, Single Nucleotide ,Article ,Chromosome Breakpoints ,Quantitative Trait, Heritable ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetic linkage ,Inbreeding ,education ,Recombination, Genetic ,Genetics ,education.field_of_study ,Multidisciplinary ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,food and beverages ,Cicer ,Droughts ,Genetic marker ,Genome, Plant ,Genome-Wide Association Study - Abstract
A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea.
- Published
- 2015
- Full Text
- View/download PDF