枇杷花转录组SSR位点信息分析

Analysis of SSR Loci Information of Flower Transcriptome in Loquat

通过对枇杷花转录组数据的分析,开发新的枇杷分子标记,为研究枇杷的遗传多样性、分子标记辅助育种提供科学依据。本研究采用MIcroSAtellite(MISA)和Blast2GO对无冗余Unigene进行SSR搜索、筛选、识别及富集分析,并采用Primer 3进行SSR引物设计。搜索发现44622个SSR位点分布于28617个Unigene中,SSR位点出现的频率为47.51%,平均分布距离为4.87 kb。单核苷酸和二核苷酸重复是枇杷花转录组中SSR的主要重复类型,分别占总SSR的52.09%和32.83%;优势重复基元为A/T和AG/CT,分别占单核苷酸的50.94%和二核苷酸的26.70%,65.79%的基序长度集中在12~20 bp。基因GO功能分类表明,含有SSR位点的28617个枇杷花转录组基因被富集到3个Ontology类别的51个GO Term中,Biological process涉及的GO Term最多,有21个。成功设计34301对SSR序列引物,成功率为76.87%。通过分析表明,枇杷花转录组SSR位点出现频率高、分布密度大,具有良好的多态性潜能,能提供丰富的重复类型,可为研究枇杷的数量性状基因座定位、分子标记辅助育种、基因组进化、遗传多样性研究等提供科学依据。

In order to provide scientific basis for studying the genetic diversity and molecular marker-assisted breeding of loquat,new molecular markers of loquat were developed by analyzing flower transcriptome data.In this study,MIcroSAtellite(MISA)and Blast2 GO were used for SSR searching,screening,identification,and analysis of non-redundant unigenes,and Primer 3 was used for SSR primer design.A search found that 28617 unigenes contained 44622 SSR loci,and the frequency of occurrence of SSR loci was 47.51%,and the total average distribution distance was 4.87 kb.Single-nucleotide and dinucleotide repeats were the main repeat types of SSR in the loquat flower transcriptome that the SSR of single-nucleotide and dinucleotide repeats accounted for52.09%and 32.83%of the total SSR,respectively.The dominant repeat motifs were A/T and AG/CT,which accounted for 50.94%and 26.70%of the single-nucleotide repeats and dinucleotide respectively,and the 65.79%length of motif was concentrated in 12~20 bp.Gene Ontology(GO)functional classification showed that28617 loquat flower transcriptome unigenes containing SSR loci were enriched in 51 GO terms of the 3 GO categories,and the biological process category involved the most GO terms(21).Primers for 34301 SSR sequences were successfully designed,with a success rate of 76.87%.It is shown by the analysis that the flower transcriptome SSR loci had high frequency,high distribution density,and high polymorphism potential and could provide abundant repeat types.These could provide scientific basis for studying qua ntitative trait loci mapping,molecular marker-assisted breeding,genome evolution,genetic diversity analysis.