Transcriptome profiling, SSR markers development and genetic diversity analysis of Ixora germplasms

• The pigment regulatory mechanisms of I. coccinea 'Apric Gold' and I. paruiflora were clarified through transcriptome sequencing. 31 key differential genes related to chlorophyll, carotenoid and anthocyanin synthesis pathways were identified, providing core targets for the study of flower color molecular regulatory mechanisms. • Efficient development of SSR markers for Ixora transcriptome and verification of their practicality: 7734 simple repetitive sequences were selected from the transcriptome, and 9432 qualified SSR loci were identified. 12 pairs of effective primers were successfully developed, providing an efficient molecular tool for the identification of Ixora resources. • Systematic revelation of genetic diversity and population structure characteristics of 55 dragon flower varieties: 67 alleles were detected using the developed SSR markers, with a mean polymorphism information content (PIC) range of 0.6121. The collected germplasms were clearly classified into 4 groups, which providing a scientific basis for germplasm classification and genetic relationship identification. Ixora is a traditional Chinese medicinal herb, which also has ornamental values. Transcriptome sequencing was used to analyze the regulation of the pigment difference of I. coccinea 'Apric Gold' and I. paruiflora . A total of 31,676 unigenes were annotated. 18,856 DEGs, 9228 up-regulated genes and 9628 down-regulated genes were obtained. EF-1α gene was used as an internal reference gene. Expression patterns of 31 genes associated with the biosynthesis of chlorophyll, carotenoids and anthocyanins were significantly different. 7734 simple repeat sequences were screened out, with an occurrence frequency of 10.84 %, and 9432 eligible SSR sites were identified, with an occurrence probability of 13.22 %. Repeat types were mainly dinucleotide repeats, accounting for 49.07 % of the total. 12 primer pairs were successfully developed and used to analyze the genetic diversity of 55 Ixora genus germplasms. A total of 67 alleles were detected. The polymorphism information content (PIC) ranged from 0.0926 to 0.8376. The results of the population structure analysis were highly consistent with the phylogenetic and PCoA analysis. 55 Ixora germplasms could be classified into 4 groups. AMOVA analysis showed that the groups mainly consisted of 74.06 % of within-population variation, 25.94 % of among-population variation, and Fixation Index was 0.2594. The results provided theoretical basis for analyzing the molecular mechanism of pigment regulation, evaluating the genetic diversity of Ixora genus, and promoted the molecular breeding and development of germplasms of Ixora .