SSR Loci Mining and Development Fluorescent Markers in Camellia sinensis Genome
Microsatellite DNA loci were identified using the MISA online analysis tool based on the published whole genome sequence of Camellia sinensis var.'Shuchazao'in the NCBI database.SSR primers were designed in batch by Primer 3.0 software,some of them were randomly selected to test their effectiveness,high polymorphic primers were screened and verified using fluorescence-labeled capillary electrophoresis technology.The results showed that 659 053 microsatellites DNA loci were detected in whole genome sequences of Camellia sinensis,with a relative abundance of 212 per Mbp.In all of the loci,dinucleotide repeats were identified with the highest number(469 096,accounting for 71.18％),length(8 725 988 bp,accounting for 61.34％),frequency(151.06 per Mbp),and density(2 809.97 bp/Mbp),followed by trinucleotide repeats,with a number,length,frequency,and density of99 716(accounting for 15.13％),2 801 472 bp(accounting for 19.69％),32.11 per Mbp and 902.14 bp/Mbp,res-pectively.The SSR motif types with 6 tandem repeats were the highest(146 844,accounting for 22.28％),followed by the SSR motif types with 7 tandem repeats(87 136,accounting for 13.22％).137 pairs of primers out of200 pairs of random primers were successfully amplified.Among them,82 pairs might have polymorphism.Primer screening was conducted on 8 tea cultivars,and 22 pairs of primers showed polymorphism,with average values of allele num-ber(Na),effective allele number(Ne),Shannon's diversity index(I),observed heterozygosity(Ho),expected heterozygosity(He),fixation index(F),and polymorphism information content(PIC)of 5.091,3.387,1.347,0.591,0.675,0.122,and 0.634,respectively.Among the 22 screened primers,20 pairs were highly polymorphic infor-mation primers(PIC＞0.5)and 2 pairs were polymorphic information primers(0.4＜PIC＜0.5),which had rich poly morphism.Based on the whole genome sequences of Camellia sinensis,polymorphic SSR primers were developed in batch,which can be used as technical references for molecular identification,variety rights protection,and molecular-assisted breeding in germplasm resources of Camellia sinensis.
万方数据
维普
