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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVED FOOD QUALITY IN DRY BEANS USING GENETIC AND MOLECULAR APPROACHES

Location: Sugarbeet and Bean Research

Title: Saturation of an intra-gene pool linkage map: toward unified consensus linkage map in common bean

Authors
item Gelaeano, Carlos -
item Fernandez, Andrea -
item Franco-Herrera, Natalia -
item Cichy, Karen
item Mclean, Phillip -
item Vanderleyden, Jos -
item Beebe, Steve -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 1, 2011
Publication Date: December 8, 2011
Citation: Gelaeano, C.H., Fernandez, A.C., Franco-Herrera, N., Cichy, K.A., McClean, P.E., Vanderleyden, J., Beebe, S.E. 2011. Saturation of an intra-gene pool linkage map: toward unified consensus linkage map in common bean. PLoS One. 6(12):e28135.

Interpretive Summary: Chromosomal maps are useful to identify genomic regions and genes associated with phenotypic traits of interest. The more information available defining points on the maps, the more useful the map is for genetic studies. In this study, we saturated the map of the population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. There have been numerous chromosome maps developed in common bean under different genetic backgrounds. Combining these individual maps in to a single map will greatly increase the utility of the map. In this study maps of three populations were combined to a single consensus map. The constructed map consisted of a total of 1,010 markers, with a total map length of 2,041 cM across all 11 bean chromosomes. This map was then aligned with soybean genome sequence since soybean is the most closely related species with a completed genome sequence and an abundance of genetic and genomic information. A total of 772 markers sequences were compared with the soybean genome and a total of 44 conserved regions were located within the bean consensus map. The common bean consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the common bean genome and to fill the number of gaps on individual maps. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic region to identify genes of interest.

Technical Abstract: Map-based cloning to find genes of interest and marker assisted selection (MAS) requires good genetic maps with high reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers in including SSR, SNP, and gene-based markers. On average the polymorphism rate was of 7.7 % due the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. In order to increase the marker saturation and to improve the marker order, a consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93×JALO EEP558 (BJ). Using a graph theory of direct acyclic graph (DAG), a consensus map was constructed and consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83 % were single locus markers. The locus order on the consensus map correlated highly with maps based on a single population. Finally, a synteny analysis was carried out using our high saturated consensus maps with soybean pseudochromosome assembly. A total of 772 markers sequences were compared with the soybean genome, and the two highest hits were selected based on the duplicate polyploidy history of soybean. A total of 44 syntenic block were defined. Chromosome Pv06Pv06 present the most diverse pattern of synteny with seven syntenic blocks, and the Pv09Pv09k shows the most consistent relations with soybean with just two syntenic blocks. Additionally, a collinear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the common bean genome and to fill the number of gaps on individual maps. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic region to identify closely linked polymorphic markers for indirect selection or for map-based cloning.

Last Modified: 7/12/2014