Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence

Abstract

Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-012-9774-z) contains supplementary material, which is available to authorized users.

Inter- and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR markers

“…Taking as a basis the PCA and the cluster analysis with ISSR and SSR markers, both species were clearly separated. The separation of C. pubescens varieties from C. annuum is probably due to C. annuum, C. baccatum, C. chinense and C. frutescens showing interspecific compatibility to each other, unlike C. pubescens (Shirasawa et al, 2013). The cluster analysis with ISSR shows a separation.…”

“…This may be due to cross SSRs transferability, by conservation of gene coding regions within related species. Such an effect has been demonstrated in various cultivars including Capsicum (Shirasawa et al, 2013), so that the nucleotide sequences in coding regions of Capsicum species are substantially preserved. Successful amplification of SSR primer pairs in different species suggests its usefulness in similar studies with other species of Capsicum and its possible use for producing DNA species-specific and accession-specific markers, while allowing identification of the genetic relationship among other Capsicum species (Ince et al, 2009).…”

“…This genus grows preferentially on plains and originated in Central and South America (Ahmed, 2013) and includes approximately 25 species, five of which are cultivated to a greater or lesser degree worldwide (Patel et al, 2011). The domesticated species include C. annuum, Capsicum baccatum, Capsicum chinense, Capsicum frutescens and Capsicum pubescens (Shirasawa et al, 2013).…”

“…In general, EST-SSRs show greater transferability between species/genera because the coding regions of genes are more suitable to be preserved among related species/genus (Shirasawa et al, 2013).…”

Genetics and Genomics of Cultivated Eggplants and Wild Relatives

“…A general problem in the construction of genetic maps is that different types of molecular markers tend to map in a specific regions of the genome (Jeuken et al, 2001;Fukuoka et al, 2012;Shirasawa et al, 2013;Nunome et al, 2009). Our use of a wide variety of molecular markers including those used in previous eggplant genetic maps (Nunome et al, 2009;Wu et al, 2009;Barchi et al, 2012;Fukuoka et al, 2012) allowed us to achieve better representation of the eggplant genome, which is important for effective molecular breeding and synteny studies in the future.…”