摘要
旨在对甘薯耐盐转录组中潜在的SSR和SNP位点进行挖掘及特征分析,以完善甘薯分子标记。试验以不同耐盐甘薯品种的转录组序列为基础,利用MISA、GATK软件分析了转录本中的SSR和SNP信息。结果显示,研究共获得SSR位点33192个,分布在24323条Unigenes中,出现频率为21.11%。其中,6271条Unigenes含有超过1个以上的SSR位点。SSR类型以单核苷酸重复SSR和双核苷酸重复SSR为主。在重复基元中,A/T和AG/CT所占的比例最高,为优势基元。在157252条Unigenes中共挖掘到SNP位点7691906个,分布密度为0.08个/bp。其中转换类型有4729922个,颠换类型有2961984个。在所有突变类型中,C/T和A/G含量最高,分别为占总数的32.34%和29.15%。综上所述,甘薯转录组具有较丰富的SSR和SNP标记,多态性较高,可为甘薯抗逆品种筛选、种质培育等研究奠定理论基础。
The aims are to mine and analyze the potential SSR and SNP loci in sweet potato transcriptome under salt stress,and enrich the molecular markers of sweet potato.Based on the transcriptome sequences of different salt tolerant sweet potato varieties,the SSR and SNP were analyzed by MISA and GATK software.The results showed that,a total of 33192 SSR loci were identified in 24323 Unigenes with a frequency of 21.11%.6271 Unigenes contained more than one SSR locus.Mono-nucleotide repeat SSR and di-nucleotide repeat SSR were the main types.The two repeat motifs,A/T and AG/CT,had the highest proportion and were the dominant motifs of sweet potato SSR.After searching SNP loci in 157252 Unigenes,7691906 SNP loci were identified with a distribution density of 0.08 SNP per bp.The predicted SNPs included 4729922 transitions and 2961984 transversions.C/T and A/G were the main types,accounting for 32.34%and 29.15%of all the SNPs.Taken together,the transcriptome of sweet potato has abundant SSR and SNP markers with high polymorphism,and the study could lay a theoretical basis for the selection of stress resistant varieties and germplasm cultivation of sweet potato.
作者
张小红
彭琼
鄢铮
ZHANG Xiaohong;PENG Qiong;YAN Zheng(Fuzhou Institute of Agricultural Sciences,Fuzhou 350018,Fujian,China)
出处
《农学学报》
2022年第11期55-61,共7页
Journal of Agriculture
基金
福建省科技计划项目“淀粉型甘薯良种的创制及高效简约化栽培技术集成”(2019N0036)
“植物生理实验平台提升与应用”(2019N0037)。