title: Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.).
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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Sandip M
authors.initials: SM
authors.lastname: Kale
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.|Osmania University, Department of Genetics, Hyderabad, 500007, India.
authors.forename: Deepa
authors.initials: D
authors.lastname: Jaganathan
authors.affiliation: The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.|University of Queensland, School of Agriculture and Food Science, Queensland, 4072, Australia.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Ruperao
authors.affiliation: Oklahoma State University, Department of Biochemistry and Molecular Biology, Stillwater, 74074, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Chen
authors.affiliation: Cornell University, Biotechnology Building, Ithaca, 14853, USA.
authors.forename: Ramu
authors.initials: R
authors.lastname: Punna
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Roorkiwal
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Mohan Avsk
authors.initials: MA
authors.lastname: Katta
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Dadakhalandar
authors.initials: D
authors.lastname: Doddamani
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Vanika
authors.initials: V
authors.lastname: Garg
authors.affiliation: Osmania University, Department of Genetics, Hyderabad, 500007, India.
authors.forename: P B Kavi
authors.initials: PBK
authors.lastname: Kishor
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
authors.forename: Pooran M
authors.initials: PM
authors.lastname: Gaur
authors.affiliation: University of Missouri, National Center for Soybean Biotechnology and Division of Plant Sciences, Columbia, 65211, USA.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
authors.affiliation: The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.affiliation: South Australian Research and Development Institute, Adelaide, 5001, Australia.|University of Adelaide, Australia and School of Agriculture, Adelaide, 5064, Australia.
authors.forename: Tim
authors.initials: T
authors.lastname: Sutton
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.|The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics* / Q000378:metabolism*; D055864:Droughts; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008040:Genetic Linkage; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D007178:Inbreeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics*