摘要
甘肃马鹿(Cervus elaphus kansuensis)是中国特有马鹿亚种之一,目前其种群退化比较严重。本研究应用现代分子生物学技术对其SSR和SNP标记特征进行分析,旨在为甘肃马鹿的遗传保护、种群改良、分子辅助育种等奠定基础。本研究采集3只甘肃马鹿快速生长期的鹿茸,对其生长中心进行转录组测序,数据经过滤后分别利用MISA软件和GATK软件对甘肃马鹿SSR和SNP位点进行检索,并分析其特征。结果显示,甘肃马鹿转录组19696条Unigenes中分别检索到4245个SSR位点和298690个SNP位点。SSR包括6种重复类型,主要集中在单碱基、二碱基和三核苷酸重复类型,占总SSR的98.85%,六核苷酸重复数目最少,只有4个,仅占总SSR的0.09%。甘肃马鹿SNP中转换类型多于颠换类型,分别占总SNP的65.77%和34.23%。转换类型中A/G发生频率略高于C/T;颠换类型中A/C发生频率最高,G/T发生频率最低。本研究鉴定了大量甘肃马鹿的SSR和SNP位点,丰富了甘肃马鹿分子标记,对甘肃马鹿种质资源鉴定、种群遗传学研究及保护管理具有重要价值。
Gansu wapiti(Cervus elaphus kansuensis)is one of the endemic red deer species in my country and has the problem of severe degeneration of the population.This study applied modern molecular biology techniques to analyze the characteristics of SSR and SNP markers.The purpose is to lay the foundation for genetic protection,population improvement,and molecular assisted breeding of Gansu wapiti.In this study,velvet antlers of 3 Gansu wapiti were collected and their growth centers were sequenced with RNA-Seq.After data filtering,the SSR and SNP sites of Gansu wapiti were retrieved using MISA and GATK software,and their characteristics were analyzed.The results showed that a total of 4245 SSR loci and 298690 SNP loci were retrieved from 19696 Unigenes in the Gansu wapiti transcriptome.SSR includes six types,mainly concentrated in a single base,two base,and three base repeat types,accounting for 98.85%of the total SSR.The minimum number of SSR is six base repeat types,only 4 loci,accounting for 0.09%of total SSR.In SNP loci of Gansu wapiti,there is more transitions than transversion types,accounting for 65.77%and 34.23%of the total SNP,respectively.The distribution frequency of A/G is slightly higher than C/T in the transition type.A/C accounts for the highest proportion and G/T accounts for the lowest proportion in the transversion type.This study identified a large number of SSR and SNP loci in Gansu wapiti.It enriched the molecular markers of the species and has important value for the identification of germplasm resources,population genetics research,and conservation management of Gansu wapiti.
作者
陈艳霞
张振祥
肖荣荣
张彤
侯磊年
张姗姗
Chen Yanxia;Zhang Zhenxiang;Xiao Rongrong;Zhang Tong;Hou Leinian;Zhang Shanshan(Gansu Engineering Laboratory of Applied Mycology,Hexi University,Zhangye,734000;Institute of Qilian Mountain Ecology,Hexi University,Zhangye,734000;College of Life Science and Engineering,Hexi University,Zhangye,734000)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2021年第9期2976-2987,共12页
Genomics and Applied Biology
基金
河西学院科研创新与应用校长基金项目(XZ2018008)
河西学院博士科研启动基金项目共同资助
