Development of 15 genic-ssr markers in oil-tea tree (Camellia oleifera) based on transcriptome sequencing

Abstract

Oil-tea tree is one of the most important woody edible oil plants; however, lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of developing seeds and characterized microsatellites from transcriptome sequences to identify valuable markers for C. oleifera molecular genetics research. A total of 69,798 unigenes were identified, in which 6,949 putative SSR motifs from 6,042 SSR-containing unique putative transcripts were discovered. Twenty-nine primer pairs corresponding to 29 unigene loci were designed, of which 15 polymorphic genic-SSR markers were developed in 18 varieties and characterized by capillary electrophoresis. The number of alleles per locus (Na) ranged from 2 to 14, the expected heterozygosity (He) ranged from 0.374 to 0.876, and the polymorphism information content (PIC) values ranged from 0.498 to 0.887, respectively. Cross-species amplification was also conducted in 15 varieties of C. japonica. All 15 markers successfully amplified PCR products with expected size in C. japonica and exhibited polymorphisms. The 15 polymorphic genic- SSR markers will have potential for applications in genetic diversity evaluation, molecular fingerprinting identification, comparative genome analysis, and genetic mapping in the C. oleifera and C. japonica.

Assessment of morphological and genetic variability through genic microsatellite markers for essential oil in Sandalwood (Santalum album L.)

“…In this study, expected heterozygosity (He) was ranged 0.78-0.88 with an average 0.85 per loci (Tables 3, 4), which indicated their high level of polymorphic nature. Similarly, the expected heterozygosity ranged from 0.374 to 0.876 in Oil tea tree (Camellia oleifera) by 15 genic SSR markers (Jia et al 2014). In this study, diversity in S. album was higher, although measures of heterozygosity and rare alleles were higher in Karnataka and Telangana trees compared with those in Kerala.…”

Genetic relationships in a germplasm collection of Camellia japonica and Camellia oleifera using SSR analysis

“…This could improve C. japonica germplasm management. There are three reports on SSR markers for C. japonica, but 1) only three SSR markers for C. japonica were developed and used for genotyping 22 individuals from a Japanese population (Ueno and Tsumura, 2009); 2) Jia et al (2014) only reported the development of 15 genic-SSR markers for cultivar 'Huashou' of C. oleifera, and its ability to successfully amplify PCR products with expected size and polymorphisms in 15 cultivars of C. japonica and 18 cultivars of C. oleifera, there is no report on genetic relationships among different cultivars, and there cultivars are different from the genotypes in this study; and 3) Jia et al (2015) only reported cross-species transferability rates of 52-genic SSR markers in C. chekangoleosa and C. japonica based on SSR markers, which was developed from 20 cultivars of C. oleifera. These SSR markers and cultivars of C. oleifera are also different from the genotypes in this study, and there is also no report on genetic relationship between cultivars of C. oleifera and C. japonica.…”

“…Recently, developed 15 genic-SSR markers for C. oleifera were developed based on transcriptome sequencing. These successfully amplified PCR products with expected size and polymorphisms in 15 cultivars of C. japonica (Jia et al, 2014). Fifty-two SSRs developed from transcriptome sequencing revealed polymorphism in 20 cultivars of C. oleifera, with number of alleles per locus ranging from 2 to 15 and expected heterozygosity values from 0.269 to 0.888.…”

Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

“…In Camellia flavida , 38 polymorphic microsatellite loci were identified based on the transcriptome sequencing and polymorphic alleles between C. flavida and C. nitidissima were revealed [ 52 ]. In C. oleifera , molecular markers were also developed and 6949 putative SSR motifs were discovered from a seed transcriptome from which 15 polymorphic genic-SSR markers were verified [ 53 ].…”