Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis

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

BACKGROUND

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 x G19833.

RESULTS

We 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.

CONCLUSIONS

Class 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.

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

Background

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.

Results

We 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.

Conclusions

Class 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.

FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut

In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.