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.)

Authors: WANG, HUI - Shandong Peanut Research Institute; PENMETSA, R - University Of California; YUAN, MEI - Shandong Peanut Research Institute; GONG, LIMIN - Tuskegee University; ZHAO, YONGLI - Fujian Agricultural & Forestry University; Guo, Baozhu; FARMER, ANDREW - National Center For Genome Resources; ROSEN, BENJAMIN - University Of California; GAO, JINLIANG - University Of California; ISOBE, SACHIKO - Kazusa Dna Research Institute; BERTIOLI, DAVID - University Of Brasilia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; COOK, DOUGLAS - University Of California; HE, GUOHAO - Tuskegee University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2012
Publication Date: 3/9/2012
Citation: Wang, H., Penmetsa, R.V., Yuan, M., Gong, L., Zhao, Y., Guo, B., Farmer, A.D., Rosen, B.D., Gao, J., Isobe, S., Bertioli, D.J., Varshney, R.K., Cook, D.R., He, G. 2012. 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.). Biomed Central (BMC) Plant Biology. 12:10.

Interpretive Summary: Cultivated peanut originated in South America, and is grown in tropical and sub-tropical regions across 100 countries on six continents between 40oN and 40oS. Seed dry matter is an important source of digestible protein (25 to 34%), cooking oil (44 to 56%) and vitamins such as thiamine, riboflavin, and niacin, which are particularly important for human nutrition in many developing countries. As a legume, peanuts improve soil fertility by fixing nitrogen, providing up to 60 kg/ha nitrogen to the soil, thus benefiting subsequently planted crops. Cultivated peanut is a tetraploid (2n=4x=40), self-pollinating species with a DNA content of about 2813 Mbp/1C. Very limited genetic variation in peanut has been detected by using molecular markers. As a consequence, there is a significant need to pursue genomic strategies in cultivated peanut, with the specific goal of increasing the availability of useful molecular tools. Therefore, there is a need to expand the density and availability of genetic polymorphisms in peanut, and to survey the status of polymorphic alleles across peanut germplasm. Here we report the identification and characterization of SSRs derived from peanut Bacterial artificial chromosome (BAC) end sequences (BES). These BES-SSR markers were combined with other publicly available peanut SSR markers to construct a new and higher density genetic linkage map with 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM. These SSR based map will aid in the identification of markers linked to genes of interest and map-based cloning.

Technical Abstract: 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), for developing SSR (BES-SSR) markers and 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.