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

Author
item SHI, CHUN - Agriculture And Agri-Food Canada
item YU, KANGFU - Agriculture And Agri-Food Canada
item XIE, WEILONG - University Of Guelph
item PERRY, GREGORY - University Of Guelph
item NAVABI, ALI - University Of Guelph
item PAULS, K. PETER - University Of Guelph
item Miklas, Phillip - Phil
item FOURIE, DEIDRE - Grain Crops Institute Of South Africa

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/28/2012
Publication Date: 7/14/2012
Citation: Shi, C., Yu, K., Xie, W., Perry, G., Navabi, A., Pauls, K., Miklas, P.N., Fourie, D. 2012. Development of candidate gene markers associated to common bacterial blight resistance in common bean. Theoretical and Applied Genetics. 125:1525-1537.

Interpretive Summary: Common bacterial blight is a devastating seed borne disease of dry bean. Resistance provides control but is difficult to breed for because of quantitative inheritance and influence of environment on disease reaction. A major gene linked with the SU91 marker has been widely used for resistance against this pathogen. The marker is dominant and less informative for marker-assisted breeding purposes than a co-dominant marker. This study describes the development of a co-dominant marker to facilitate selection of this major gene for resistance to common bacterial blight. This study also move us one step closer to identifying the actual gene conferring blight resistance. This work will enable rapid deployment of a gene for development of cultivars with improved blight resistance.

Technical 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 mapbased 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 9 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.