Introgressed Genomic Regions in a Set of Near-Isogenic Lines of Common Bean Revealed by Genotyping-by-Sequencing

Abstract

Genotyping-by-sequencing (GBS) was used to investigate and identify the introgressed genomic regions that corresponded to resistance alleles for anthracnose ( and ), (BCMV), and (BCMNV, and ) in a set of bean near-isogenic lines (NIL). The GBS analysis provided 12,697 single nucleotide polymorphisms (SNPs) although the densities along the chromosomes were not uniform, and some chromosomal regions, such as centromeric or pericentromeric regions, were less tagged. The backcrossing method resulted in the introgression of genomic regions into specific chromosomes. The number of introgressed region-tagging SNPs varied between 1 and 13, representing between 0.33 and 6.88% of the bean genome. The changes detected among the recurrent parent and NIL in chromosomal regions are candidate regions that may contain the introgressed genes. By comparing the NIL derived from the same resistance source, it was possible to delimit in chromosomes Pv02, Pv04, Pv06, and Pv11 the genomic regions containing the resistance genes , , , and . Results allowed verification of the physical positions of the resistance genes and a clearer physical position of the anthracnose resistance genes and . Two nonoverlapping regions were delimited in chromosome Pv11 from common regions in NIL with resistance loci mapped to the Co-2 cluster. Alleles of the loci included within these genomic regions show strong linkage disequilibrium. This knowledge can be used in selection programs involving these regions rich in resistance genes.