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

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Relation http://oar.icrisat.org/9724/
 
Title Fine mapping of the “QTL-hotspot” region for
drought tolerance in Chickpea (Cicer arietinum L.)
 
Creator Jaganathan, D
 
Subject Chickpea
 
Description 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.
 
Date 2016
 
Type Thesis
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/9724/1/Deepa_.pdf
Jaganathan, D (2016) Fine mapping of the “QTL-hotspot” region for drought tolerance in Chickpea (Cicer arietinum L.). PhD thesis, Osmania University,Hyderabad.