Integrating genetic and physical positions of the anthracnose resistance genes described in bean chromosomes Pv01 and Pv04

Abstract

A complex landscape of anthracnose resistance genes ( Co- ) located at the telomeric regions of the bean chromosomes Pv01 and Pv04 has been reported. The aim of this work was to investigate the genetic and physical positions of genes conferring resistance to races 6, 38, 39, 357, 65, and 73 as well as the relationships among the resistance genes identified herein and the previously described Co- genes in these telomeric regions. The linkage analysis using a genetic map of 497 SNPs from the recombinant inbred line population Xana/BAT93 revealed that the gene conferring resistance to race 65 in cultivar Xana ( Co-1 65-X ) was located in the Co-1 cluster, at the distal end of chromosome Pv01. The fine mapping of Co-1 65-X indicated that it was positioned between the physical positions 49,512,545 and 49,658,821 bp. This delimited physical position agrees with the positions of the previously mapped genes Co- 1 4 , Co-x , Co-14 , Co-1 HY , and Co-Pa . Responses to races 6, 38, 39, and 357 in BAT93 exhibited co-segregation suggesting that the same gene, or very closely linked genes, were involved in the control. The linkage analysis showed that the resistance gene to race 38 in the genotype BAT93 ( Co-3 38-B ) was located at the beginning of chromosome Pv04, in the genetic position of the Co-3 cluster, and was flanked by markers with physical positions between 1,286,490 and 2,047,754 bp. Thus, the genes Co-3, Co-9, Co-10, Co-16, and Co-3 38-B , found in this work, form part of the same anthracnose resistance cluster at the beginning of chromosome Pv04, which is consistent with the discontinuous distribution of typical R genes annotated in the underlying genomic region. Resistance loci involved in the response to race 73 in the genotypes Xana (R) and BAT93 (R) were mapped to the same positions on clusters Co-1 and Co-3, respectively. The positioning of the resistance genes in the bean genome based on fine linkage mapping should play an important role in the characterization and differentiation of the anthracnose resistance genes. The assignment of Co- genes to clusters of race specific genes can help simplify the current scenario of anthracnose resistance.

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

“…The common bean genome also contains NBS-LRR regions that are distributed across all chromosomes ( Ferrier-Cana et al, 2003 ; Richard et al, 2017 ; Wu et al, 2017 ) and a recent GWAS study showed associations between these NBS-LRR regions with anthracnose resistance ( Wu et al, 2017 ). Anthracnose resistance genes Co-3 and its alleles, Co-16 are mapped to common bean Pv04 and this study also found association of SNPs on Pv04 with anthracnose resistance to races 3, 87, and 503 ( Geffroy et al, 1999 ; David et al, 2008 ; Coimbra-Gonçalves et al, 2016 ; Murube et al, 2019 ). The Co-3 4 locus was previously mapped on the 3.36-Mb genomic position but it was recently mapped to the region between 0.49 to 0.58 Mb on Pv04 ( Valentini et al, 2017 ) which indicates shift in the physical positions with better mapping tools ( Kelly and Bornowski, 2018 ).…”

Integration of anthracnose resistance loci and RLK and NBS‐LRR‐encoding genes in the Phaseolus vulgaris L. genome

“…In addition to these genes, the borders contain genes encoding LRR. The second region contains 13 annotated genes, one of which encodes a protein kinase and another which encodes a protein related to the biotic stress response (Murube et al., 2019). In the interval region considered to build an integrated map, we observed the presence of 29 NBS‐LRRs and four kinases (Figure 4).…”

New Andean source of resistance to anthracnose and angular leaf spot: Fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar

“…To identify sources of resistance against the ANT pathogen, a panel of 14 Andean cultivars were screened for their reactions to ten Mesoamerican (9,64,65,73,89,445,453,1545,2047, and 3481) and six Andean (2,7,19,23,39, and 55) races of C. lindemuthianum ( Table 1). The genomic locations of the known Co genes in each cultivar, except for Jalo Vermelho, Jalo Pintado 2, and CDRK (Table 1), have been previously reported [25,28,29,30,31,32,53]. We observed that five genotypes known to carry alleles at the Co-1 locus (MDRK, Kaboon, Perry Marrow, AND 277, and Widusa) showed different spectra of ANT resistance (Table 1), supporting the hypothesis that they indeed carry different alleles of Co-1 or additional unidentified Co loci.…”

“…The candidate region containing the CoPv01 CDRK and PhgPv01 CDRK loci in linkage group Pv01 is located close to one of the most important clusters of ANT resistance genes in the common bean genome [32]. The Pv01 cluster includes the following ANT disease-resistance genes: Co-1, Co-1 HY , Co-1 4 ; Co-x, Co-Pa, Co-AC, and Co-1 X [23,25,28,29,30,31,53,68]. The CoPv01 CDRK /PhgPv01 CDRK loci was found in a genomic region flanked by the markers ss715645251 (50,301,532 bp) and ss715645248 (50,546,925 bp) on Pv01 (Fig 1).…”

“…The resistance gene in the Xana cultivar, named Co-1 X , was mapped between the markers SNP01_483 and SNP01_490, located in a 153 Kb region from 50,223,771 and 50,377,556. A total of 17 candidate genes were identified in this region, which also covers part of the Co-1 HY and Co-x region [53].…”