Development of SNP markers and construction of DNA fingerprint in tea-oil Camellia germplasms based on simplified genome sequencing
[Objective]To establish a rapid and accurate method for identification of the major-cultivated tea-oil seedlings in Guangxi,we screened the single nucleotide polymorphism(SNP)sites,developed the SNP markers and drew the fingerprint map based on simplified genome sequencing.[Method]Two replicates of 12 tea-oil Camellia germplasms were used as samples.The library was constructed using double digest restriction site-associated sequencing(ddRADseq)and the filtered data was mapped to the released reference genome data of Camellia oleifera var."Nanyongensis"using BWA.GATK was used for SNP site screening,ANNOVAR software was used for SNP site annotation,STRUCTURE software was used for population analysis,and PLINK was used for principal component analysis.Using R language,conditional random screening(CRS)was used to select the simplest SNP combinations that could distinguish tea-oil Camellia germplasms.[Result]The sequencing data was of good quality and could be used for the development and screening of SNP molecular marker sites.After sequence alignment with the reference genome,a total of 622 064 SNP sites were obtained,among which 40 147 SNP sites were without genotype deletion.Furthermore,there were 2 094 SNP sites with polymorphism information content(PIC)value greater than 0.35,184 of which were with no base variations from 60 bp upstream to 60 bp downstream of the SNP sites.Finally,15 core SNP sites that could distinguish 12 tea-oil Camellia germplasms were screened out,and the fingerprint map was figured out.[Conclusion]The method about SNP marker development and fingerprint illustration for Guangxi main tea-oil Camellia germplasms was established based on simplify genome sequencing,providing theoretical and technical assistance for distinguishing the germplasms fast and accurately,ultimately normalizing the tea-oil Camellia seedling market and promoting the sound development of tea-oil Camellia industry.
NETL
NSTL
万方数据
