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

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 psedouchromosome 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.

Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies

“…Given the genome size of 630 Mb and the genetic linkage map of 680 cM (Lucas et al, 2011;Xu et al, 2011), this approximately equals 1.84 Mb of physical distance. Such level and extent of LD are comparable to those observed in the European barley collection (Rostoks et al, 2006), and the LD decay distance is even shorter than that in a small population of common bean (Phaseolus vulgaris L.) from America, a close relative of asparagus Linkage disequilibrium patterns in asparagus bean P Xu et al bean, where LD decays to 0.1-0.2 within 6-12 cM (McConnell et al, 2010). Collectively, these observations indicate that in inbreeding species including asparagus bean, the LD decay distances are fairly long.…”

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

“…D1468 is associated with several domestication traits including number of pods and days to flowering and maturity (Koinange et al 1996). Locus g776 maps < 2cM from D1468 (McConnell et al 2010).…”

“…A collection of 24 landraces were analysed ( McConnell et al 2010). Two additional Pv08 loci, g776 and D1468, were included.…”

Development and Application of Molecular Markers to Breed Common Bean (Phaseolus vulgaris L.) for Resistance to Common Bacterial Blight (CBB) — Current Status and Future Directions

“…Three hundreds eighteen SNPs were detected from 5,255 bean EST sequences (Melotto et al, 2005). With EST sequence information from two bean genotypes, the Mesoamerican cultivar Negro Jamapa 81 and the Andean cultivar G19833 (Ramirez et al, 2005) , over 1,800 SNPs and indels were detected (McConnell et al, 2010). PCR primers were designed to amplify the BAT93 and Jalo EEP558 fragments and 534 useful fragments with an average size of 500bp were sequenced.…”