Genome-wide identification of SSR markers for Curcuma alismatifolia Gagnep., and their potential for wider application in this genus

Abstract

The genus Curcuma, containing over 120 species, have considerable ornamental, edible and medicinal value. Due to the persistent lack of efficient genomic SSR markers, the conservation and identification of Curcuma genetic resources have faced substantial challenges in practical applications. To date, there are few systematic researches on whole-genome mining of SSR locus in the genus Curcuma. Herein, we performed the first deep identification of genome-wide SSR markers based on the whole-genome data of C. alismatifolia. A total of 257,032 SSR loci were identified with an average density of 216.1–367.3 SSRs/Mb within each chromosome. Mononucleotide repeat loci were most abundant, accounting for 55.1 % of all SSRs, with dinucleotide and trinucleotide repeats accounting for 22.6 % and 20.3 %, respectively. Moreover, 38 polymorphic genomic SSRs (g-SSR) were screened from the synthesized 280 primer pairs, with an average allele number (Na) and polymorphic information content (PIC) of 15.342 and 0.775 per locus, respectively. These markers had excellent cross-species transferability with an overall efficiency of 97.5 % in 21 Curcuma species. According to the cluster and structure analyses, the 178 Curcuma accessions were devided into three major clades correspongding to their origins, hybrid affinities and use values. Finally, a total of 66 Curcuma core collections were preserved, with no significant difference in genetic diversity between the core and entire collections by the t-test. A combination of numbers and letters was employed to establish DNA barcodes for 66 core collections. This study provides valuable molecular markers for wild-collection and conservation, genetic diversity analysis and marker-assisted selection breeding of Curcuma.