High resolution mapping of Co Ind gene from common bean landrace KRC 5 possessing resistance to Colletotrichum lindemuthianum races

Abstract

The common bean landrace KRC-5, native to Kinnaur region of Himachal Pradesh is known to possess resistance against different races of Colletotrichum lindemuthianum. In this study, an attempt has been made to fine map the resistance locus in common bean landrace KRC-5 and to convert RAPD marker linked to the resistance gene into specific SCAR marker. In addition, the effectivity of the R-gene was tested against 24 physiological races of C. lindemuthianum. The segregation studies on F2 and F2:9 mapping population obtained from Jawala x KRC-5 cross against races 3 and 211 showed a good fit of 3R:1S and 1R:1S ratio, thus confirmed the presence of a single dominant gene in landrace KRC-5. To fine map the gene, a set of 576 molecular markers comprising of SSRs and RAPDs was used for polymorphism survey. One hundred and thirty six markers found polymorphic on parents failed to distinguish the resistant and susceptible bulks in bulked segregant analysis (BSA). Therefore to accomplish the fine mapping, ddRAD sequencing based strategy using 40 RIL individuals including parents was applied to identify SNP based markers. From ddRAD 1,15,578 SNP markers were identified on 11 common bean linkage groups and finally 1,979 SNPs were retained for linkage map development using JoinMap software. In addition 28 anchored SSRs and two SCARs were also genotyped on 40 individuals (RILs and parents) used for ddRAD to validate the linkage of identified SNPs on bean chromosomes. The genotyping of 219 F2:9 RIL individuals with SCAR marker ScOPR15408 and previously developed SCAR (ScOPF6522) showed their linkage with R-gene at 2 cM distance on the opposite sides of R-locus. Linkage map developed by using 2,009 markers including 1,979 SNPS, 28 anchored SSRs and 2 SCAR markers (linked to R-gene) showed the distribution of different markers on 11 linkage groups of common bean genome spanning 618 cM distance. The tentative position of R-gene (Co-Ind) present in landrace KRC-5 was marked on chromosome 10 along with two SCAR markers flanking the target gene and other SNP markers. However the exact position of R-gene can only be established after genotyping whole population with associated SNPs. In gene strength analysis, the landrace KRC-5 was found resistant to 17 races of C. lindemuthianum and hence could be effectively used in molecular breeding programmes. newline newline newline