Development of candidate gene markers associated to common bacterial blight resistance in common bean

Abstract

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Two major CBB-resistant quantitative trait loci (QTL), linked to the sequence characterized amplified region markers BC420 and SU91, are located at chromosomes 6 and 8, respectively. Using map-based cloning approach, four bacterial artificial chromosome (BAC) clones from the BC420-QTL locus and one BAC clone containing SU91 were sequenced by Roche 454 technique and subsequently assembled using merged assemblies from three different programs. Based on the quality of the assembly, only the sequences of BAC 32H6 and 4K7 were used for candidate gene marker (CGM) development and candidate gene (CG) selection. For the BC420-QTL locus, 21 novel genes were predicted in silico by FGENESH using Medicago gene model, whereas 16 genes were identified in the SU91-QTL locus. For each putative gene, one or more primer pairs were designed and tested in the contrasting near isogenic lines. Overall, six and nine polymorphic markers were found in the SU91- and BC420-QTL loci, respectively. Afterwards, association mapping was conducted in a breeding population of 395 dry bean lines to discover marker-trait associations. Two CGMs per each locus showed better association with CBB resistance than the BC420 and SU91 markers, which include BC420-CG10B and BC420-CG14 for BC420_QTL locus, and SU91-CG10 and SU91-CG11 for SU91_QTL locus. The strong associations between CBB resistance and the CGs 10 and 14 from BC420_QTL locus and the CGs 10 and 11 from SU91_QTL locus indicate that the genes 10 and 14 from the BC420 locus are potential CGs underlying the BC420_QTL locus, whereas the genes 10 and 11 from the SU91 locus are potential CGs underlying the SU91_QTL locus. The superiority of SU91-CG11 was further validated in a recombinant inbred line population Sanilac × OAC 09-3. Thus, co-dominant CGMs, BC420-CG14 and SU91-CG11, are recommended to replace BC420 and SU91 for marker-assisted selection of common bean with resistance to CBB.

A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes

“…The SU91 marker was not found in the G19833 sequence. However, a SU91-associated region in the G19833 sequence was selected using the c00126p592970 and c00322p82935 markers, which were previously mapped to the SU91 QTL in HR45 (Figure 1C, Xie et al, unpublished results; Shi et al, 2012). It starts at 58,994,870 bp and ends at 59,444,870 bp.…”

“…Unique genes from OAC-Rex with homology to P. acutifolius ESTs are indicated by green asterisks above the contigs. For the chromosome 8 figure, the positions of two additional gene-based markers (CG10 and CG11, Shi et al, 2012) are also denoted by purple triangles. Additionally, the location of the identified CBB-QTL from the region surrounding the SU91 marker in a OAC-Rex X Sanilac population is indicated by the embedded chart, normalized to the markers on chromosome 8 (Xie et al, unpublished results).…”

“…No contigs were found within the region from 59,511,657 to 59,661,425 bp, due to the presence of a large number of unknown (N) nucleotides ( P. vulgaris v0.9, DOE-JGI and USDA-NIFA, http://www.phytozome.net/commonbean). A previous characterization of a 65 kb HR45 BAC contig library (32H6), containing the SU91 marker resulted in the development of additional molecular markers (CG10 and CG11) for this region (Shi et al, 2012; Figure 1C) that were used to identify the corresponding region in G19833 and OAC-Rex (G19833 c8:59,333,799-59,396,160 and 232701:94178-160157 bp, respectively).…”

“…Although these resistance gene candidates are outside the main QTL for the resistance trait on chromosome 8, it is known that CBB-resistance is conditioned by several interacting loci (Gepts et al, 2008). At best, the major QTL usually account for 20–40% of the variation for resistance (Shi et al, 2012) leaving the possibility that more loci with small additive effects contribute to the full resistance observed in OAC Rex. The propensity of resistance gene clusters to contain unique genes in OAC-Rex, as seen in chromosome 8 (Figures 4, 10) could represent one mechanism for the introgression of new genetic material from an interspecific hybridization.…”

“…In particular, OAC-Rex, which was registered as the first bacterial blight resistant cultivar in Canada in 2002 (Michaels et al, 2006), derives its resistance from the P. acutifolius line PI 440795. Resistance loci have been associated with molecular markers Pv -CTT001 (GI:169360), SU91 (GI:156072919), BNG71 and BNG21 in OAC Rex (Tar'an et al, 2001; Shi et al, 2012; Durham et al, 2013). …”