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Open Access Research article

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 Wang14, R Varma Penmetsa2, Mei Yuan1, Limin Gong3, Yongli Zhao4, Baozhu Guo5, Andrew D Farmer6, Benjamin D Rosen2, Jinliang Gao2, Sachiko Isobe7, David J Bertioli8, Rajeev K Varshney9, Douglas R Cook2 and Guohao He3*

Author Affiliations

1 Shandong Peanut Research Institute, Qingdao, China

2 University of California, Davis, CA 95616, USA

3 Tuskegee University, Tuskegee, AL 36088, USA

4 Fujian Agricultural and Forestry University, Fuzhou, China

5 USDA-ARS, Tifton, GA 31793, USA

6 National Center of Genome Resources (NCGR), Santa Fe, NM 87505, USA

7 Kazusa DNA Research Institute, Chiba, Japan

8 University of Brasilia, Brasilia, Brazil

9 Intenational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India

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BMC Plant Biology 2012, 12:10  doi:10.1186/1471-2229-12-10

Published: 19 January 2012

Abstract

Background

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. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.

Results

Here, 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 The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.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.

Conclusions

The 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.