基于基因组重测序的藏羚Y染色体多态性遗传位点筛选
Genome-Sequencing-Based Screening of Polymorphic Genetic Loci in the Y Chromosome of Pantholops hodgsonii
王舒闻 1王东 2成若通 1陈玉莹 1李佳宾 1陈一博 1陈家瑞 1魏青1
作者信息
- 1. 青海大学生态环境工程学院,西宁 810016
- 2. 中国科学院西北高原生物研究所,高原生物适应与进化重点实验室,西宁 810008;青海师范大学地理科学学院,西宁 810008
- 折叠
摘要
藏羚Pantholops hodgsonii是藏羚属Pantholops现存的唯一物种,由于Y染色体基因较保守,基于近缘物种的Y染色体多态性遗传位点筛选受到了很大的限制.本研究对15份藏羚新鲜组织样品进行基因组重测序,生物信息分析筛选出Y染色体雄性特异区(MSY)对应的scaffolds,对部分SNP及SSR位点进行多态性验证.共比对出44个scaffolds,以其中序列最长、候选变异位点最多且最完整的KE113803.1为参考,对其中190个SNP变异位点设计引物进行验证,共获得45条MSY DNA序列,其中15对引物扩增到的11 898 bp DNA序列中检测到27个SNP位点;同时对KE113803.1中除单核苷酸重复以外的134个SSR位点设计引物并验证多态性,筛选出56个Y-SSR位点,其中5个具有多态性.本研究结果为后续分析藏羚Y染色体遗传多样性及父系遗传奠定了良好基础.
Abstract
The screening of polymorphic genetic loci in Y chromosome is fundamental to study the genetic diversity of Y chromosome and paternal inheritance in animals.Tibetan antelope(Pantholops hodgsonii)is the sole extant species of the genus Pantholops with relatively conservative Y-chromosome genes,and screening for the polymorphisms of Y chromo-some based on the closely related species is greatly limited.In this study,15 fresh tissue samples of P.hodgsonii were sub-jected to genome resequencing,followed by bioinformatic analyses to screen the polymorphic SNP and SSR loci in the male specific region of Y chromosome.The results showed that 44 scaffolds belonging to the male-specific region of Y chromo-some were identified.The scaffold KE113803.1,which has the longest sequence and the most complete candidate vari-ants,were selected to validate the 190 SNP variants by using PCR.Finally,45 DNA sequences of the male specific region of Y chromosome were obtained,and of which 27 SNP sites were detected in the 11 898 bp DNA sequences amplified by us-ing 15 pairs of primers.Primers were also designed to amplify the 134 candidate SSR loci other than single nucleotide re-peats in KE113803.1 and to verify the polymorphism.A total of 56 male specific SSR loci of P.hodgsonii were screened and 5 SSR loci were found to be polymorphic.The 27 polymorphic Y-SNP loci and 5 polymorphic Y-SSR loci obtained in this study provide a good basis for further exploring the genetic diversity of Y chromosome and paternal inheritance of P.hodgsonii population.
关键词
藏羚/基因组重测序/Y染色体/SNP/SSRKey words
Pantholops hodgsonii/genome resequencing/Y chromosome/SNP/SSR引用本文复制引用
基金项目
青海省自然科学基金青年项目(2020-ZJ-958Q)
中国科学院-青海省人民政府三江源国家公园联合研究专项(LHZX-2020-01)
青海大学生态环境工程学院生态学世界一流学科研究生科技创新项目(2023-stxy-Y13)
出版年
2024
NETL
NSTL
维普
万方数据