Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea)

BACKGROUND: The genus Arachis includes Arachis hypogaea (cultivated peanut) and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop A. hypogaea microsatellite loci and to evaluate the transferability of these markers to other Arachis species. RESULTS: Thirteen loci were isolated and characterized using 16 accessions of A. hypogaea. The level of variation found in A. hypogaea using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild Arachis species showed that almost all wild species had similar repeated sequence to the one observed in A. hypogaea. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to A. hypogaea and the number of repeats found in its microsatellite loci. CONCLUSION: These results show that microsatellite primer pairs from A. hypogaea have multiple uses. A higher level of variation among A. hypogaea accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of A. hypogaea showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in Arachis species

A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome

<p>Abstract</p> <p>Background</p> <p><it>Arachis hypogaea </it>(peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for <it>A. hypogaea </it>is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of <it>Arachis</it>, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability.</p> <p>Results</p> <p>In this work, we constructed a B-genome linkage map, which will complement the previously published map for the A-genome of <it>Arachis</it>, and produced an entire framework for the tetraploid genome. This map is based on an F₂population of 93 individuals obtained from the cross between the diploid <it>A. ipaënsis </it>(K30076) and the closely related <it>A. magna </it>(K30097), the former species being the most probable B genome donor to cultivated peanut. In spite of being classified as different species, the parents showed high crossability and relatively low polymorphism (22.3%), compared to other interspecific crosses. The map has 10 linkage groups, with 149 loci spanning a total map distance of 1,294 cM. The microsatellite markers utilized, developed for other <it>Arachis </it>species, showed high transferability (81.7%). Segregation distortion was 21.5%. This B-genome map was compared to the A-genome map using 51 common markers, revealing a high degree of synteny between both genomes.</p> <p>Conclusion</p> <p>The development of genetic maps for <it>Arachis </it>diploid wild species with A- and B-genomes effectively provides a genetic map for the tetraploid cultivated peanut in two separate diploid components and is a significant advance towards the construction of a transferable reference map for <it>Arachis</it>. Additionally, we were able to identify affinities of some <it>Arachis </it>linkage groups with <it>Medicago truncatula</it>, which will allow the transfer of information from the nearly-complete genome sequences of this model legume to the peanut crop.</p