Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers

Juana M Córdoba,Matthew W Blair,Carolina Chavarro,Jessica A Schlueter,Scott A Jackson

doi:10.1186/1471-2164-11-436

Abstract

BackgroundCommon bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833.ResultsWe searched for simple sequence repeats (SSRs) in the 89,017 BAC-end sequences (BES) from the physical map and genetically mapped any polymorphic BES-SSRs onto the genetic map. Among the BES it was possible to identify 623 contig-linked SSRs, most of which were highly AT-rich. A subgroup of 230 di-nucleotide and tri-nucleotide based SSR primer pairs from these BACs was tested on the mapping parents with 176 single copy loci and 114 found to be polymorphic markers. Of these, 99 were successfully integrated into the genetic map. The 99 linkages between the genetic and physical maps corresponded to an equal number of contigs containing a total of 5,055 BAC clones.ConclusionsClass II microsatellites were more common in the BES than longer class I microsatellites. Both types of markers proved to be valuable for linking BAC clones to the genetic map and were successfully placed across all 11 linkage groups. The integration of common bean physical and genetic maps is an important part of comparative genome analysis and a prelude to positional cloning of agronomically important genes for this crop.

Highlights

Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a bacterial artificial chromosome (BAC) library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833
These microsatellites were named using a combination of the series name BMb with a sequential number, and organized according to the contig or singletons they were derived from, their repetition type and the motif they contained (See Additional File 1: Information about the BMb microsatellite loci used for primer pair development)
Uniform distribution of BAC-end sequences (BES)-microsatellite locus (SSR) loci across the common bean genome In the genetic mapping phase of this project, we found the BES-SSR loci to be distributed across all linkage groups with no significant bias towards any specific chromosome a slightly larger number of BESSSR loci were found on linkage groups b02d and b08f

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833. Consumeracceptability and genetic diversity has made common bean the most widely grown legume for direct human consumption, with a worldwide distribution and presence in tropical, subtropical and temperate countries and many different environments. Microsatellite loci can be classified according to their motif or to the number of repeats they contain: SSRs can be perfect having only one repeat type, or imperfect characterized by having repetitions interrupted by one or more nucleotides differing from the ones of the repetition. Microsatellites have been used for molecular characterization of cultivated and wild accessions as well as for genetic diversity analysis and anchoring of genetic maps (for example [8,9,10,11])

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