Development and characterization of whole genome SSR in tetraploid Camellia oleifera
[Objective]Traditional breeding of Camellia oleifera has low efficiency and long cycle,and molecular marker-assisted breeding has become a necessary method to promote the genetic improvement.The overall statistical analysis of the SSR loci of genome provides an effective vehicle,which help to improve the breeding effect and shorten the breeding cycle of C.oleifera.Obtaining high-quality and valuable SSR molecular marker loci by searching and analyzing the distribution pattern and characteristics of SSR loci of tetraploid C.oleifera genome can provide convenient conditions for further research on genetic analysis,molecular marker assisted breeding and fingerprint identification.[Method]Based on the whole genome data of tetraploid C.oleifera,the SSR loci of 1-6 nucleotide repeat types were searched comprehensively and the distribution pattern and characteristics of types of SSR were counted by MISA.SSR primers were designed by Primer 3.0 software.[Result]A total of 6 254 681 SSR loci of different types were found in the whole genome of tetraploid C.oleifera with a total length of 11 069 152 038 bp,and 463 different repeats were identified,a SSR locus appeared at 1.77 kb on average.SSR sites of single nucleotide repeat type were the most,accounting for 62.08%,while SSR sites of hexanucleotide repeat type were the least,accounting for only 0.46%.A and T bases were dominant in SSR sequences of tetraploid C.oleifera genome,while G and C were less in content and have base preference.The SSR sequence length of tetraploid C.oleifera genome ranged from 10 to 187 bp,with an average length of 15.57 bp.Except for single nucleotide repeat types,the SSR sequences with sequence length≥20 bp accounted for 15.75%of all SSR sequences,the SSR length variation of dinucleotide,trinucleotide and tetranucleotide repeats was significantly higher than that of pentanucleotide and hexanucleotide,dinucleotide,trinucleotide and tetranucleotide repeats were the main marker sources for designing SSR primers.Based on the SSR loci mining of tetraploid C.oleifera genome,1 358 248 pairs of primers were developed.[Conclusion]This study is the first attempt to conduct overall statistical analysis on the distribution pattern and characteristics of SSR loci and develop SSR primers in the whole genome of tetraploid C.oleifera,which will provide reference for molecular marker-assisted breeding of C.oleifera.
万方数据
维普
