In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut
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
BMC Plant Biology 2012, 12:80 doi:10.1186/1471-2229-12-80Published: 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 (http://marker.kazusa.or.jp webcite).