薄壳山核桃转录组中的SSR位点信息分析

Analysis of SSR Information in Carya illinoinensis Transcriptome

通过对薄壳山核桃转录组数据的分析,开发新的薄壳山核桃分子标记,为研究薄壳山核桃的遗传多样性、分子标记辅助育种提供科学依据。利用ESTtrimmer和cross-match对转录组测序获得的Unigene进行过滤,除去冗杂序列;利用MISA对无冗余Unigene进行SSR搜索,并应用Primer3进行SSR引物设计。从搜索序列中发现了10 303个SSR,分布于9 871条Unigenes中,出现频率为18.31%,分布密度为1/4.06 kb。二核苷酸和单核苷酸是主要重复类型,分别占SSR总数的44.27%和40.64%;优势重复基元为A/T、AG/CT和AAC/GTT,分别占单核苷酸的39.66%、二核苷酸的35.22%和三核苷酸的4.90%。88.86%的基序长度集中在10~20 bp。成功设计了5 547对SSR引物。通过对薄壳山核桃高通量转录组序列的SSR信息的研究,表明薄壳山核桃转录组SSR位点出现频率高、分布密度大,具有较高的多态性潜能,能提供丰富的重复类型,可以为研究薄壳山核桃的遗传多样性、分子标记辅助育种、遗传图谱绘制等方面提供有效的理论依据。

In order to develop new molecular markers of Carya illinoinensis, SSR markers were developed based on transcriptome data. This study lay foundations for studies of genetic diversity and molecular marker assisted breeding of C. illinoinensis. The Unigenes obtained from transcriptome sequencing were removed miscellaneous sequences by ESTtrimmer and cross-match. MISA was used to search SSR without redundant Unigene, and the SSR primer was designed by using primer3. We found that 10 303 SSRs distributed in 9 871 Unigenes were detected, accounting for 18.31% of all the Unigenes. The average distribution distance of the transcriptomic SSRs is about 1/4.06 kb. The dinucleotide and mononucleotide are the major repetitive types, accounting for 44.27% and40.64% of all the SSRs, respectively. The dominating motifs were A/T in mononucleotide repeats, AG/CT in dinucleotide repeats, and AAC/GTT in trinucleotide repeats, accounting for 39.66%, 35.22% and 4.90%,respectively. 88.86 percent of the motif length is centered in 10~20 bp. 5 547 pairs of SSR primers were successfully designed. The results showed that the SSR loci of the pecan transcriptome were higher in frequency,rich in type, large in density and higher in polymorphism potential. There is great potential for genetic diversity,molecular marker assisted breeding and genetic mapping.