The Development And Application Of SNPs In Tea Plant (Camellia Sinensis)

Tea (Camellia sinensis), which originate from China, was one of the most popularbeverages in the world. In a long span of natural selection and evolution, the tea plantcontains various germplasms, which has a great potential to select elite individuals. However,it belongs to woody perennials. The traditional breeding program was time consuming. Thus,the molecular marker assisted breeding has attracted more interest.In this paper, we mined SNPs from Camellia sinensis derived ESTs. Then, primers weredesigned to amplify these SNPs in the genome DNA from tea plant. And the directsequencing method was used to confirm these SNPs in amplicons. For the purpose of reducethe cost of genotyping. Some SNPs were converted into CAPS and dCAPS markers. At last,these markers were used to analysis the genetic diversity of tea plant. The main results ofthis research are as follows:1) Eight hundred and eighteen candidate SNPs were mined from ESTs, thus the diversityof SNPs was average one SNP per172bp. One hundred and twenty three primer pairs weredesigned. The direct sequencing method was used to confirm these SNPs in genome DNA. Atotal of165SNPs were identified, including162substitution type of SNPs and3InDels.Thus, the diversity of SNPs was average one SNP per90bp, and one SNP per97bp and oneper68bp in coding and non-coding regions, respectively.2) A total of39SNPs was converted into CAPS markers. Eight SNPs were successfullyconverted to dCAPS markers (72.7%); two dCAPS markers which have polymorphisms inparents exhibited a separate ratio of1:1in the F1population.3) Ten primer pairs were chose to analysis the genetic diversity of17individuals in threevarietas of tea. The results show that, in C. sinensis var. assamica the density was1SNP/78bp, in C. sinensis and C. sinensis var. pubilimba were nearly1SNP/95bp. In JingguDabaicha the frequence was1SNPs/506bp and in Yuanjiang Zhujiecha it was1SNP/156bp.The haplotype number was ranging from4to16. The haplotype diversity was between0.412and0.916.The nucleotide polymorphism was between0.00119and0.01179.4) Fourteen CAPS markers and5dCAPS markers were used to analysis25cultivars, then17markers shown polymorphisms. The expected heterozygosity and observedheterozygosity were0.0435-0.516and0.0435-0.9167, respectively. The PIC value wasbetween0.0425and0.497. The genetic distance was between0.038-0.5067. thus thesemarkers would be useful in germplasm identification and genetic diversity research in teaplant.