Open Access Research article

In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

Kenta Shirasawa1*, Padmalatha Koilkonda1, Koh Aoki16, Hideki Hirakawa1, Satoshi Tabata1, Manabu Watanabe2, Makoto Hasegawa2, Hiroyuki Kiyoshima2, Shigeru Suzuki2, Chikara Kuwata2, Yoshiki Naito3, Tsutomu Kuboyama4, Akihiro Nakaya5, Shigemi Sasamoto1, Akiko Watanabe1, Midori Kato1, Kumiko Kawashima1, Yoshie Kishida1, Mitsuyo Kohara1, Atsushi Kurabayashi1, Chika Takahashi1, Hisano Tsuruoka1, Tsuyuko Wada1 and Sachiko Isobe1

Author Affiliations

1 Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan

2 Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan

3 Mitsubishi Chemical Medience Corporation, 4-25-11 Azusawa, Itabashi, Tokyo, 174-0051, Japan

4 College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan

5 Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachidori, Chuo, Niigata, 951-8585, Japan

6 Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka, Sakai, Osaka, 599-8531, Japan

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BMC Plant Biology 2012, 12:80  doi:10.1186/1471-2229-12-80

Published: 6 June 2012



Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers.


The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2%) of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs) for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed.


In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database ( webcite).

DNA marker; Genetic linkage map; Peanut (Arachis hypogaea); QTL analysis; Ratio of oleic/linoleic acid (O/L ratio)