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Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)

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Abstract

Molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris, common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana, genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana. Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris. Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican × Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current pseduochromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred.

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Acknowledgments

This project was funded by the USDA Cooperative State Research, Education and Extension Service: National Research Initiative, Plant Genome Program. We would also like to thank Dr. Paul Gepts for supplying us with genotype information on the markers from the core BAT93 × Jalo EEP558 RI linkage map.

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Authors and Affiliations

  1. Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58105, USA

    Melody McConnell, Sujan Mamidi, Rian Lee, Shireen Chikara & Phillip McClean

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105, USA

    Melody McConnell, Sujan Mamidi, Rian Lee, Shireen Chikara & Phillip McClean

  3. Dipartimento di Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy

    Monica Rossi & Roberto Papa

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  1. Melody McConnell
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Correspondence to Phillip McClean.

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McConnell, M., Mamidi, S., Lee, R. et al. Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet 121, 1103–1116 (2010). https://doi.org/10.1007/s00122-010-1375-9

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