Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.

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 r...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Mahendar Thudi, Hari D Upadhyaya, Abhishek Rathore, Pooran Mal Gaur, Lakshmanan Krishnamurthy, Manish Roorkiwal, Spurthi N Nayak, Sushil Kumar Chaturvedi, Partha Sarathi Basu, N V P R Gangarao, Asnake Fikre, Paul Kimurto, Prakash C Sharma, M S Sheshashayee, Satoshi Tobita, Junichi Kashiwagi, Osamu Ito, Andrzej Killian, Rajeev Kumar Varshney
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2014
Materias:
R
Q
Acceso en línea:https://doaj.org/article/d2b17c3e9fe847499bdb795a2857715e
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:d2b17c3e9fe847499bdb795a2857715e
record_format dspace
spelling oai:doaj.org-article:d2b17c3e9fe847499bdb795a2857715e2021-11-18T08:20:36ZGenetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.1932-620310.1371/journal.pone.0096758https://doaj.org/article/d2b17c3e9fe847499bdb795a2857715e2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24801366/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203To 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.Mahendar ThudiHari D UpadhyayaAbhishek RathorePooran Mal GaurLakshmanan KrishnamurthyManish RoorkiwalSpurthi N NayakSushil Kumar ChaturvediPartha Sarathi BasuN V P R GangaraoAsnake FikrePaul KimurtoPrakash C SharmaM S SheshashayeeSatoshi TobitaJunichi KashiwagiOsamu ItoAndrzej KillianRajeev Kumar VarshneyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 5, p e96758 (2014)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Mahendar Thudi
Hari D Upadhyaya
Abhishek Rathore
Pooran Mal Gaur
Lakshmanan Krishnamurthy
Manish Roorkiwal
Spurthi N Nayak
Sushil Kumar Chaturvedi
Partha Sarathi Basu
N V P R Gangarao
Asnake Fikre
Paul Kimurto
Prakash C Sharma
M S Sheshashayee
Satoshi Tobita
Junichi Kashiwagi
Osamu Ito
Andrzej Killian
Rajeev Kumar Varshney
Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
description 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.
format article
author Mahendar Thudi
Hari D Upadhyaya
Abhishek Rathore
Pooran Mal Gaur
Lakshmanan Krishnamurthy
Manish Roorkiwal
Spurthi N Nayak
Sushil Kumar Chaturvedi
Partha Sarathi Basu
N V P R Gangarao
Asnake Fikre
Paul Kimurto
Prakash C Sharma
M S Sheshashayee
Satoshi Tobita
Junichi Kashiwagi
Osamu Ito
Andrzej Killian
Rajeev Kumar Varshney
author_facet Mahendar Thudi
Hari D Upadhyaya
Abhishek Rathore
Pooran Mal Gaur
Lakshmanan Krishnamurthy
Manish Roorkiwal
Spurthi N Nayak
Sushil Kumar Chaturvedi
Partha Sarathi Basu
N V P R Gangarao
Asnake Fikre
Paul Kimurto
Prakash C Sharma
M S Sheshashayee
Satoshi Tobita
Junichi Kashiwagi
Osamu Ito
Andrzej Killian
Rajeev Kumar Varshney
author_sort Mahendar Thudi
title Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
title_short Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
title_full Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
title_fullStr Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
title_full_unstemmed Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
title_sort genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches.
publisher Public Library of Science (PLoS)
publishDate 2014
url https://doaj.org/article/d2b17c3e9fe847499bdb795a2857715e
work_keys_str_mv AT mahendarthudi geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT haridupadhyaya geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT abhishekrathore geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT pooranmalgaur geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT lakshmanankrishnamurthy geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT manishroorkiwal geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT spurthinnayak geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT sushilkumarchaturvedi geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT parthasarathibasu geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT nvprgangarao geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT asnakefikre geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT paulkimurto geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT prakashcsharma geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT mssheshashayee geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT satoshitobita geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT junichikashiwagi geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT osamuito geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT andrzejkillian geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
AT rajeevkumarvarshney geneticdissectionofdroughtandheattoleranceinchickpeathroughgenomewideandcandidategenebasedassociationmappingapproaches
_version_ 1718421891724607488