Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virusresistance in common bean

Abstract

BackgroundCommon bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV).ResultsWe physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study.ConclusionsWe demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-903) contains supplementary material, which is available to authorized users.

Bulked sample analysis in genetics, genomics and crop improvement

“…The examples of BSA based on DNA/RNA/ chip are summarized in Table 2. The method has been used to study a dozen of recessive mutants in maize (Liu et al, 2010), leaf rust in wheat (Forrest et al, 2014), sulphur and selenium contents in Arabidopsis thaliana (Becker et al, 2011), salt resistance in cotton (Rodriguez-Uribe et al, 2011), bean common mosaic virus in common bean (Bello et al, 2014), Phytophthora root rot in pepper and photosynthetic traits in poplar (Wang et al, 2014a).…”

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

“…The sequences were blasted against the P. vulgaris proteome using the BLASTP program, with default parameters, in the Phytozome platform (Goodstein et al 2012). Since the genomic positions of the BARCBean6K_3 SNP loci are known (Bello et al 2014), the BEDTools suite (Quinlan and Hall 2010) was used for calculating the distance between common bean aquaporins and BARCBean6K_3 SNP markers. To identify drought-related SNP markers in the BARCBean6K_3 chip, we chose the markers nearest todroughtQTLs identified by Mukeshimana et al (2014).…”

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

“…The physical positions revealed in this study agree with the genetic analysis, which located genes I , Co‐3 , bc‐3 , and Co‐2 in LGs Pv02, Pv04, Pv06, and Pv11, respectively. The dominant I gene was directly mapped on the LG Pv02 and the underlying genomic region was physically located between positions 48.13 to 48.28 Mb in chromosome Pv02 (Bello et al, 2014). The By‐2 gene conferring resistance to Bean yellow mosaic virus , was also located in a similar position (47.99–48.96 Mb) through a genome‐wide association study (Hart and Griffiths, 2015).…”