Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most ef...

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Autores principales:	Caléo Panhoca de Almeida, Jean Fausto de Carvalho Paulino, Caio Cesar Ferrari Barbosa, Gabriel de Moraes Cunha Gonçalves, Roberto Fritsche-Neto, Sérgio Augusto Morais Carbonell, Alisson Fernando Chiorato, Luciana Lasry Benchimol-Reis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9fd74e2296984247be3bc0526410aea6
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spelling	oai:doaj.org-article:9fd74e2296984247be3bc0526410aea62021-11-25T06:19:07ZGenome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.1932-620310.1371/journal.pone.0251745https://doaj.org/article/9fd74e2296984247be3bc0526410aea62021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251745https://doaj.org/toc/1932-6203Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.Caléo Panhoca de AlmeidaJean Fausto de Carvalho PaulinoCaio Cesar Ferrari BarbosaGabriel de Moraes Cunha GonçalvesRoberto Fritsche-NetoSérgio Augusto Morais CarbonellAlisson Fernando ChioratoLuciana Lasry Benchimol-ReisPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251745 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Caléo Panhoca de Almeida Jean Fausto de Carvalho Paulino Caio Cesar Ferrari Barbosa Gabriel de Moraes Cunha Gonçalves Roberto Fritsche-Neto Sérgio Augusto Morais Carbonell Alisson Fernando Chiorato Luciana Lasry Benchimol-Reis Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
description	Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.
format	article
author	Caléo Panhoca de Almeida Jean Fausto de Carvalho Paulino Caio Cesar Ferrari Barbosa Gabriel de Moraes Cunha Gonçalves Roberto Fritsche-Neto Sérgio Augusto Morais Carbonell Alisson Fernando Chiorato Luciana Lasry Benchimol-Reis
author_facet	Caléo Panhoca de Almeida Jean Fausto de Carvalho Paulino Caio Cesar Ferrari Barbosa Gabriel de Moraes Cunha Gonçalves Roberto Fritsche-Neto Sérgio Augusto Morais Carbonell Alisson Fernando Chiorato Luciana Lasry Benchimol-Reis
author_sort	Caléo Panhoca de Almeida
title	Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
title_short	Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
title_full	Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
title_fullStr	Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
title_full_unstemmed	Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.
title_sort	genome-wide association mapping reveals race-specific snp markers associated with anthracnose resistance in carioca common beans.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/9fd74e2296984247be3bc0526410aea6
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Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans.

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