Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

Selma E Macedo,Dione Mt Alves,David J Bertioli,Ediene G Gouvea,Márcio C Moretzsohn,Vânia Cr Azevedo,Soraya C M Leal-Bertioli

doi:10.1186/1756-0500-5-86

Abstract

BackgroundPeanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm.FindingsA plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD) was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties.ConclusionsThe microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

Highlights

Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries
It has a narrow genetic base due to its recent origin event of tetraploidization [1,2], and this has hindered the application of molecular breeding in this crop
In spite of the number of markers available, the very low polymorphism observed within cultivated germplasm requires large-scale marker screening for the identification of sufficient polymorphic markers even for low density genetic maps in populations derived from cultivated × cultivated crosses

Summary

Introduction

Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Peanut (Arachis hypogaea L.) is an oil crop of great importance in the tropics: in Africa, its production is comparable to all other grain legumes put together, and in Asia it provides about the same number of calories as soya (FAO, 2009). It has a narrow genetic base due to its recent origin event of tetraploidization [1,2], and this has hindered the application of molecular breeding in this crop. We isolated and characterized long repeat AG/ TC SSRs as an effort to develop markers with high polymorphism levels for cultivated peanut [10]

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Results

Conclusion