title: Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
abstract: To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1-7 seasons and 1-3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Rathore
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Pooran Mal
authors.initials: PM
authors.lastname: Gaur
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Lakshmanan
authors.initials: L
authors.lastname: Krishnamurthy
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India; Guru Gobind Singh Indraprastha University, Delhi, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Roorkiwal
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.affiliation: Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India.
authors.forename: Sushil Kumar
authors.initials: SK
authors.lastname: Chaturvedi
authors.affiliation: Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India.
authors.forename: Partha Sarathi
authors.initials: PS
authors.lastname: Basu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya.
authors.forename: N V P R
authors.initials: NV
authors.lastname: Gangarao
authors.affiliation: Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, Ethiopia.
authors.forename: Asnake
authors.initials: A
authors.lastname: Fikre
authors.affiliation: Egerton University (EU), Egerton, Kenya.
authors.forename: Paul
authors.initials: P
authors.lastname: Kimurto
authors.affiliation: Guru Gobind Singh Indraprastha University, Delhi, India.
authors.forename: Prakash C
authors.initials: PC
authors.lastname: Sharma
authors.affiliation: University of Agricultural Sciences- Bangalore, Bangalore, Karnataka, India.
authors.forename: M S
authors.initials: MS
authors.lastname: Sheshashayee
authors.affiliation: Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tobita
authors.affiliation: Hokkaido University, Sapporo, Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Kashiwagi
authors.affiliation: United Nations University, Yokohama, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Ito
authors.affiliation: DArT Pty. Ltd., Yarralumla, Australia.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Killian
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Rajeev Kumar
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics* / Q000254:growth & development; D055864:Droughts; D005787:Gene Frequency; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D010641:Phenotype; D018517:Plant Roots / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013696:Temperature