Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea

D. Jaganathan; M. Thudi; S. Kale; S. Azam; M. Roorkiwal; P.M. Gaur; P.B.K. Kishor; H. Nguyen; T. Sutton; R.K. Varshney

doi:10.1007/s00438-014-0932-3

Back

Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea

Journal article

Open access

Peer reviewed

Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea

D. Jaganathan, M. Thudi, S. Kale, S. Azam, M. Roorkiwal, P.M. Gaur, P.B.K. Kishor, H. Nguyen, T. Sutton and R.K. Varshney

Molecular Genetics and Genomics, Vol.290(2), pp.559-571

2015

DOI: https://doi.org/10.1007/s00438-014-0932-3

Files and links (2)

pdf

QTL Hotspot.pdfDownload View

Published (Version of Record) Open Access

url

Free to Read *No subscription requiredView

Abstract

To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.

Details

Title: Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea
Authors/Creators: D. Jaganathan (Author/Creator) - Osmania University
M. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
S. Kale (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
S. Azam (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Roorkiwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P.M. Gaur (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P.B.K. Kishor (Author/Creator) - Osmania University
H. Nguyen (Author/Creator) - University of Missouri
T. Sutton (Author/Creator) - Australian Centre for Plant Functional Genomics
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: Molecular Genetics and Genomics, Vol.290(2), pp.559-571
Publisher: Springer
Identifiers: 991005540104707891
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Metrics

7 File views/ downloads

54 Record Views

171 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biochemistry & Molecular Biology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics