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

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.

Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.)

“…A total of 59 MTAs were identified from 09 different GWA studies for anthracnose in common beans ( Figure 4 and Supplementary Table 4 ). Some of the MQTLs were found to be co-localized with MTAs available from more than one GWA study, for instance, MQTL4.1 co-localized with 40 MTAs reported in eight different GWA studies ( Zuiderveen et al, 2016 ; Wu et al, 2017 ; Banoo et al, 2020 ; VazBisneta and Gonçalves-Vidigal, 2020 ; Vidigal Filho et al, 2020 ; Almeida et al, 2021 ; Bisneta et al, 2021 ; Costa et al, 2021 ). Similarly, MQTL1.3 co-localized with 06 MTAs reported in five different GWA studies ( Perseguini et al, 2016 ; Wu et al, 2017 ; Banoo et al, 2020 ; VazBisneta and Gonçalves-Vidigal, 2020 ; Vidigal Filho et al, 2020 ).…”

“…For this purpose, data from 11 different GWA studies on the most stable and significant MTAs/SNPs were collected. These studies included the following: Burt et al (2015) , Perseguini et al (2016) , Zuiderveen et al (2016) , Wu et al (2017) , Fritsche-Neto et al (2019) , Banoo et al (2020) , VazBisneta and Gonçalves-Vidigal, 2020 , Vidigal Filho et al (2020) , Almeida et al (2021) , Bisneta et al (2021) and Costa et al (2021) .…”

“…However, these control measures may limit yield potential and increase production costs. The development of resistant cultivars is the most efficient, economical, and environmental friendly strategy to circumvent disease outbreaks ( Dillard and Cobb, 1993 ; Almeida et al, 2021 ). Therefore, cultivars with different race-specific or broad spectrum resistance genes conferring resistance against multiple races of the pathogens need to be identified and investigated.…”

“…Numerous QTL mapping studies for ANT disease resistance have also been conducted in different common bean populations ( Geffroy et al, 2008 ; Almeida et al, 2021 ). In addition, genome-wide association studies (GWAS) for ANT resistance have also been conducted, leading to the identification of a large number of marker-trait associations (MTAs) ( Perseguini et al, 2016 ; Zuiderveen et al, 2016 ; Wu et al, 2017 ).…”

Chlorophyll Fluorescence Imaging as a Tool for Evaluating Disease Resistance of Common Bean Lines in the Western Amazon Region of Colombia

“…However, it has been observed that it is possible to identify materials that are disease-resistant in addition to serving as a basis for signal transduction for plant immune defense [ 55 , 56 ]. The common bean originates from two main gene pools and some diseases [ 8 ], due to the process of coevolution, present the same classification and higher degrees of pathogenicity within specific gene pools [ 9 , 57 ]. These studies indicate that plant photosynthesis and immune defense processes are interconnected [ 58 ].…”