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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



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.


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 The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci.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


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.