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

Caléo Panhoca De Almeida,Roberto Fritsche-Neto,Sérgio Augusto Morais Carbonell,Caio Cesar Ferrari Barbosa,Alisson Fernando Chiorato,Jean Fausto De Carvalho Paulino,Gabriel De Moraes Cunha Gonçalves,Luciana Lasry Benchimol-Reis,Istvan Rajcan

doi:10.1371/journal.pone.0251745

Caléo Panhoca De Almeida, Roberto Fritsche-Neto + Show 7 more

Open Access

https://doi.org/10.1371/journal.pone.0251745

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Abstract

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.

Highlights

70 species have been described in the Phaseolus genus, only five of which are cultivated; Phaseolus vulgaris L. is considered the most important species in the Phaseolus genus for direct consumption in the human diet [1,2,3]
The boxplot shows the difference in the degree of resistance of the carioca diversity panel (CDP) (Fig 1C), and it shows the smallest phenotypic variation for races 65 and 321
Several studies aiming at the identification of markers associated with ANT resistance loci in common bean have already been conducted, leading to the identification of genotypes showingthe loci of greatest effect

Summary

Introduction

70 species have been described in the Phaseolus genus, only five of which are cultivated; Phaseolus vulgaris L. (bean) is considered the most important species in the Phaseolus genus for direct consumption in the human diet [1,2,3]. 70 species have been described in the Phaseolus genus, only five of which are cultivated; Phaseolus vulgaris L. (bean) is considered the most important species in the Phaseolus genus for direct consumption in the human diet [1,2,3]. In some African and American countries, beans are responsible for providing an average of 15% of total daily calories and 36% of protein content consumed [8]. Most beans are produced by the countries of Asia and the Americas, which together account for approximately 75% of world production. Brazil stands out as one of the largest producer and consumer of beans in the world, and is responsible for 36% of the production on the American continent [9]

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