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Theoretical and Applied Genetics

, Volume 125, Issue 7, pp 1525–1537 | Cite as

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

  • Chun Shi
  • Kangfu Yu
  • Weilong Xie
  • Gregory Perry
  • Alireza Navabi
  • K. Peter Pauls
  • Phillip N. Miklas
  • Deidré Fourie
Original Paper

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.

Keywords

Quantitative Trait Locus Bacterial Artificial Chromosome Common Bean Bacterial Artificial Chromosome Clone Bulk Segregation Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors acknowledge the financial supports from the Ontario Bean Produces’ Marketing Board, Ontario Coloured Bean Growers’ Association, Agriculture and Agri-Food Canada, Ontario Research Fund, and the technical assistance provided by Terry Rupert, Barbara Harwood, Bailing Zhang, and Samantha Krueger.

Supplementary material

122_2012_1931_MOESM1_ESM.doc (30 kb)
Supplementary material 1 (DOC 30 kb)

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Copyright information

© Her Majesty the Queen in Right of Canada 2012

Authors and Affiliations

  • Chun Shi
    • 1
  • Kangfu Yu
    • 1
  • Weilong Xie
    • 2
  • Gregory Perry
    • 2
  • Alireza Navabi
    • 1
    • 2
  • K. Peter Pauls
    • 2
  • Phillip N. Miklas
    • 3
  • Deidré Fourie
    • 4
  1. 1.Greenhouse and Processing Crops Research CentreAgriculture and Agri-Food CanadaHarrowCanada
  2. 2.Department of Plant AgricultureUniversity of GuelphGuelphCanada
  3. 3.Vegetable and Forage Crop Production UnitU.S. Department of AgricultureProsserUSA
  4. 4.ARC Grain Crops InstitutePotchefstroomRepublic of South Africa

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