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BMC Plant Biol. 2012; 12: 80.
Published online Jun 6, 2012. doi:  10.1186/1471-2229-12-80
PMCID: PMC3404960
In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut
Kenta Shirasawa,corresponding author1 Padmalatha Koilkonda,1 Koh Aoki,1,6 Hideki Hirakawa,1 Satoshi Tabata,1 Manabu Watanabe,2 Makoto Hasegawa,2 Hiroyuki Kiyoshima,2 Shigeru Suzuki,2 Chikara Kuwata,2 Yoshiki Naito,3 Tsutomu Kuboyama,4 Akihiro Nakaya,5 Shigemi Sasamoto,1 Akiko Watanabe,1 Midori Kato,1 Kumiko Kawashima,1 Yoshie Kishida,1 Mitsuyo Kohara,1 Atsushi Kurabayashi,1 Chika Takahashi,1 Hisano Tsuruoka,1 Tsuyuko Wada,1 and Sachiko Isobe1
1Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
2Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizennocho, Midori, Chiba, 266-0006, Japan
3Mitsubishi Chemical Medience Corporation, 4-25-11 Azusawa, Itabashi, Tokyo, 174-0051, Japan
4College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
5Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachidori, Chuo, Niigata, 951-8585, Japan
6Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuencho, Naka, Sakai, Osaka, 599-8531, Japan
corresponding authorCorresponding author.
Kenta Shirasawa: shirasaw/at/kazusa.or.jp; Padmalatha Koilkonda: padmalathakk/at/gmail.com; Koh Aoki: kaoki/at/plant.osakafu-u.ac.jp; Hideki Hirakawa: hh/at/kazusa.or.jp; Satoshi Tabata: tabata/at/kazusa.or.jp; Manabu Watanabe: m.wtnb38/at/pref.chiba.lg.jp; Makoto Hasegawa: m.hsgw12/at/pref.chiba.lg.jp; Hiroyuki Kiyoshima: h.kyshm/at/pref.chiba.lg.jp; Shigeru Suzuki: s.szk248/at/pref.chiba.lg.jp; Chikara Kuwata: c.kwt/at/pref.chiba.lg.jp; Yoshiki Naito: Naitou.Yoshiki/at/mx.medience.co.jp; Tsutomu Kuboyama: kuboyama/at/mx.ibaraki.ac.jp; Akihiro Nakaya: nakaya/at/bri.niigata-u.ac.jp; Shigemi Sasamoto: sasamoto/at/kazusa.or.jp; Akiko Watanabe: watanabe/at/kazusa.or.jp; Midori Kato: mamidori/at/kazusa.or.jp; Kumiko Kawashima: kawasima/at/kazusa.or.jp; Yoshie Kishida: kishida/at/kazusa.or.jp; Mitsuyo Kohara: kohara/at/kazusa.or.jp; Atsushi Kurabayashi: katsushi/at/kazusa.or.jp; Chika Takahashi: ctakaha/at/kazusa.or.jp; Hisano Tsuruoka: thisano/at/kazusa.or.jp; Tsuyuko Wada: twada/at/kazusa.or.jp; Sachiko Isobe: sisobe/at/kazusa.or.jp
Received February 15, 2012; Accepted June 6, 2012.
Abstract
Background
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.
Results
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.
Conclusions
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 (http://marker.kazusa.or.jp).
Keywords: DNA marker, Genetic linkage map, Peanut (Arachis hypogaea), QTL analysis, Ratio of oleic/linoleic acid (O/L ratio)
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