Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.).

Hui Wang,Limin Gong,David J Bertioli,Rajeev K Varshney,Mei Yuan,Baozhu Guo,Yongli Zhao,R Varma Penmetsa,Sachiko Isobe,Andrew D Farmer,Douglas R Cook,Jinliang Gao,Guohao He,Benjamin D Rosen

doi:10.1186/1471-2229-12-10

Abstract

BackgroundCultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.ResultsHere, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton.ConclusionsThe SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.

Highlights

Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein
Sequencing and annotation of Bacterial artificial chromosome (BAC) clone ends 3,784 resistance gene homolog (RGH)-containing BAC clones of A. hypogaea cv Tifrunner were identified by means of hybridization with a set of peanut disease resistance gene probes, representing ~580 unique nucleotide binding (NB) domains (Rosen, He and Cook unpublished data)
These BAC clones were sequenced from their ends to yield 3,905 BAC end sequences (BES) representing 3.5 Mbp of the cultivated Tifrunner genome sequence

Summary

Introduction

Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting. Low genetic diversity among cultivated accessions likely derives from the origin of tetraploid peanut in a single, relatively recent allopolyploid event that is thought to have involved genotypes of the wild diploid species Arachis duranensis and Arachis ipaensis [11,12,13,14,15]. There is a significant need to pursue genomic strategies in cultivated peanut, with the specific goal of increasing the availability of useful molecular tools

Methods

Results

Conclusion