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Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

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 nuc...

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Autores principales: Kale, Sandip M, Jaganathan, Deepa, Ruperao, Pradeep, Chen, Charles, Punna, Ramu, Kudapa, Himabindu, Thudi, Mahendar, Roorkiwal, Manish, Katta, Mohan AVSK, Doddamani, Dadakhalandar, Garg, Vanika, Kishor, P B Kavi, Gaur, Pooran M, Nguyen, Henry T, Batley, Jacqueline, Edwards, David, Sutton, Tim, Varshney, Rajeev K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609953/
https://www.ncbi.nlm.nih.gov/pubmed/26478518
http://dx.doi.org/10.1038/srep15296
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author Kale, Sandip M
Jaganathan, Deepa
Ruperao, Pradeep
Chen, Charles
Punna, Ramu
Kudapa, Himabindu
Thudi, Mahendar
Roorkiwal, Manish
Katta, Mohan AVSK
Doddamani, Dadakhalandar
Garg, Vanika
Kishor, P B Kavi
Gaur, Pooran M
Nguyen, Henry T
Batley, Jacqueline
Edwards, David
Sutton, Tim
Varshney, Rajeev K
author_facet Kale, Sandip M
Jaganathan, Deepa
Ruperao, Pradeep
Chen, Charles
Punna, Ramu
Kudapa, Himabindu
Thudi, Mahendar
Roorkiwal, Manish
Katta, Mohan AVSK
Doddamani, Dadakhalandar
Garg, Vanika
Kishor, P B Kavi
Gaur, Pooran M
Nguyen, Henry T
Batley, Jacqueline
Edwards, David
Sutton, Tim
Varshney, Rajeev K
author_sort Kale, Sandip M
collection PubMed
description 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.
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spelling pubmed-46099532015-10-29 Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.) Kale, Sandip M Jaganathan, Deepa Ruperao, Pradeep Chen, Charles Punna, Ramu Kudapa, Himabindu Thudi, Mahendar Roorkiwal, Manish Katta, Mohan AVSK Doddamani, Dadakhalandar Garg, Vanika Kishor, P B Kavi Gaur, Pooran M Nguyen, Henry T Batley, Jacqueline Edwards, David Sutton, Tim Varshney, Rajeev K Sci Rep Article 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. Nature Publishing Group 2015-10-19 /pmc/articles/PMC4609953/ /pubmed/26478518 http://dx.doi.org/10.1038/srep15296 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Kale, Sandip M
Jaganathan, Deepa
Ruperao, Pradeep
Chen, Charles
Punna, Ramu
Kudapa, Himabindu
Thudi, Mahendar
Roorkiwal, Manish
Katta, Mohan AVSK
Doddamani, Dadakhalandar
Garg, Vanika
Kishor, P B Kavi
Gaur, Pooran M
Nguyen, Henry T
Batley, Jacqueline
Edwards, David
Sutton, Tim
Varshney, Rajeev K
Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title_full Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title_fullStr Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title_full_unstemmed Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title_short Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)
title_sort prioritization of candidate genes in “qtl-hotspot” region for drought tolerance in chickpea (cicer arietinum l.)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609953/
https://www.ncbi.nlm.nih.gov/pubmed/26478518
http://dx.doi.org/10.1038/srep15296
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