Fine mapping of the “QTL-hotspot” region for drought tolerance in Chickpea (Cicer arietinum L.)

Jaganathan, D (2016) Fine mapping of the “QTL-hotspot” region for drought tolerance in Chickpea (Cicer arietinum L.). PHD thesis, Osmania University,Hyderabad.

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Supervisors NameSupervisors ID
Varshney, R KICRISAT(Patancheru)
Kavi Kishor, P BDepartment of Genetics, Osmania University, Hyderabad


Chickpea (Cicer arietinum L.) is the third most important grain legume cultivated in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50% production losses in chickpea. In order to understand the basics of drought tolerance, two recombinant inbred line (RIL) mapping populations (ICC 4958 × ICC 1882 and ICC 283 × ICC 8261) segregating for root traits were developed and a promising “QTL-hotspot” region was reported on these populations. With an objective to fine map this region, two approaches were adopted, i) genotyping-by sequencing (GBS) and ii) skim sequencing. GBS approach enabled identification of 828 single nucleotide polymorphism (SNP) markers. A high-density genetic map was developed, comprising 1,007 marker loci including 49 SNP markers in the “QTL-hotspot” region and spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data generated earlier, re-estimated the “QTL-hotspot” from 29 cM to 14 cM. In addition, these 49 SNPs were converted into cleaved amplified polymorphic sequence (CAPS)/derived CAPS (dCAPS) markers which can be used in marker assisted breeding. An ultra-high-density bin map was developed using 53,223 SNPs obtained through skim sequencing approach and its analysis with the phenotyping data, split the “QTL-hotspot” region into two sub-regions namely “QTL-hotspot_a” of 139.22 kb with 15 genes and “QTL-hotspot_b” of 153.36 kb with 11 genes. To validate and find more recombination in these regions, a large mapping population was developed. Flanking SNP markers of the two regions were converted to KASPar assays and screened on 1,911 F2 lines. Progeny testing on F2:3 lines revealed the role of “QTL-hotspot_a” in controlling 100-SDW. A total of 15 candidate genes were reported in this region. In summary, the refined region will help in precise introgression of the “QTL-hotspot” in breeding program for yield improvement under drought conditions and the reported genes can be used for further cloning studies to dissect the molecular basis of drought tolerance in chickpea.

Item Type: Thesis (PHD)
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, Drought, Production,Tolerance, Phenotyping
Subjects: Mandate crops > Chickpea
Depositing User: Mr T L Gautham
Date Deposited: 14 Oct 2016 09:45
Last Modified: 14 Oct 2016 09:45
Acknowledgement: UNSPECIFIED
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