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

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).Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n？=？4x？=？40) composed of A and B genomes that are derived from two diploids, most likely A. duranensis (A genome) and A. ipa？nsis (B genome). On the basis of branching habit, the presence/absence of flowers on the main stem, alternate vs. sequential branching, fruit and seed traits, and maturity, A. hypogaea has been categorized into two subspecies: hypogaea and fastigiata; six botanical varieties: hypogaeahirsutafastigiatavulgarisaequatoriana, and peruviana; and four agronomic types: Virginia, Spanish, Valencia, and Southeast-runner [1,2]. As the nuclear DNA content in peanut is calculated to be 5.914？pg/2？C [3], the genome size is estimated to be approximately 2.8 Gb based on an assumption that 1？pg of DNA is equivalent to 980？Mb [4]. Because of its allotetraploidy and large genome size, genom