利用Y染色体基因分析梅花鹿种公鹿的遗传多样性和父系起源

doi:10.11843/j.issn.0366-6964.2018.02.007

畜牧兽医学报 ›› 2018, Vol. 49 ›› Issue (2): 282-290.doi: 10.11843/j.issn.0366-6964.2018.02.007

利用Y染色体基因分析梅花鹿种公鹿的遗传多样性和父系起源

周永娜, 刘华淼, 鞠妍, 张然然, 王磊, 董世武, 邢秀梅*

中国农业科学院特产研究所特种经济动物分子生物重点实验室, 长春 130112

收稿日期:2017-07-28 出版日期:2018-02-23 发布日期:2018-02-23
通讯作者: 邢秀梅,研究员,主要从事特种经济动物种质资源保护与遗传育种研究,E-mail:xingxiumei2004@126.com
作者简介:周永娜(1992-),女,河南新乡人,硕士生,主要从事梅花鹿种质资源保护与遗传育种研究,E-mail:yongnazhou@qq.com
基金资助:
中国农业科学院科技创新工程（CAAS-ASTIP-201X-ISAPS）

Genetic Diversity and Paternal Origin of Breeder Sika Deer Based on Y Chromosome Genes

ZHOU Yong-na, LIU Hua-miao, JU Yan, ZHANG Ran-ran, WANG Lei, DONG Shi-wu, XING Xiu-mei*

Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Animal and Plant Sciences of Chinese Academy of Agriculture Sciences, Changchun 130112, China

Received:2017-07-28 Online:2018-02-23 Published:2018-02-23

摘要/Abstract

摘要：

旨在利用Y染色体基因研究梅花鹿种公鹿的遗传多样性和父系起源，为梅花鹿的保种育种工作提供数据支持。对171只双阳、敖东、四平、东丰、兴凯湖、长白山和东大梅花鹿种公鹿Y染色体上的AMELY、DBY、USP9Y、SRY基因的5个片段进行PCR扩增，对PCR产物进行直接测序和生物信息学分析。结果表明，5个基因片段共筛选到8个突变位点，AMELY1、AMELY2、DBY、USP9Y、SRY基因片段分别有3、2、1、1、1个突变位点。利用DNASP5.1软件共定义了10种单倍型，分别为H1、H2、H3、H4、H5、H6、H7、H8、H9、H10，其中H1是优势单倍型，占梅花鹿种公鹿群体的49.1%，H5和H10为东丰梅花鹿种公鹿独有，H9是最原始的单倍型。171只梅花鹿种公鹿的单倍型多样性为0.696 80，核苷酸多样性为0.000 36。NJ系统进化树和structure群体结构分析结果表明，梅花鹿种公鹿有3个父系类型，分别为Y1、Y2和Y3，除双阳梅花鹿种公鹿和四平梅花鹿种公鹿均来自Y3，其余梅花鹿种公鹿群体均为多父系类型。表明我国梅花鹿种公鹿Y染色体具有较高的单倍型多样性和极低的核苷酸多样性。

Abstract:

The objective of this study was to investigate the genetic diversity and paternal origin of breeder sika deer by Y chromosome genes, and provide data support for the protection and breeding of sika deer. AMELY, DBY, USP9Y, SRY gene fragments on Y chromosome of 171 breeder sika deer (Shuangyang, Aodong, Siping, Dongfeng, Xingkaihu, Changbaishan, Dongda breeder sika deer) were amplified by PCR, and the PCR products were sequenced directly and analyzed by bioinformatics. The results showed that 8 SNPs were screened from 5 gene fragments, and AMELY1, AMELY2, DBY, USP9Y, SRY gene fragments had 3, 2, 1, 1, 1 mutation sites, respectively. Ten haplotypes (H1, H2, H3, H4, H5, H6, H7, H8, H9 and H10) were defined by DNASP5.1. H1 was the dominant haplotype, accounting for 49.1% of all breeder sika deer. H5 and H10 were unique to Dongfeng breeder sika deer. H9 was the ancestral haplotype. Haplotype diversity and nucleotide diversity of 171 breeder sika deer were 0.696 80 and 0.000 36, respectively. The results of NJ phylogenetic tree and structure population analysis showed that breeder sika deer had 3 paternal types (Y1, Y2 and Y3). Shuangyang and Siping breeder sika deer had a single paternal type(Y3), the other 5 breeder sika deer populations had multiple paternal types. The results indicate that Y chromosome of Chinese breeder sika deer have high haplotype diversity and very low nucleotide diversity.

中图分类号:

S825.2

周永娜, 刘华淼, 鞠妍, 张然然, 王磊, 董世武, 邢秀梅. 利用Y染色体基因分析梅花鹿种公鹿的遗传多样性和父系起源[J]. 畜牧兽医学报, 2018, 49(2): 282-290.

ZHOU Yong-na, LIU Hua-miao, JU Yan, ZHANG Ran-ran, WANG Lei, DONG Shi-wu, XING Xiu-mei. Genetic Diversity and Paternal Origin of Breeder Sika Deer Based on Y Chromosome Genes[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(2): 282-290.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.xmsyxb.com/CN/10.11843/j.issn.0366-6964.2018.02.007

https://www.xmsyxb.com/CN/Y2018/V49/I2/282

参考文献

[1] IMMEL U D, KLEIBER M, KLINTSCHAR M. Y chromosome polymorphisms and haplotypes in South Saxony-Anhalt (Germany)[J]. Forensic Sci Int, 2005, 155(2-3):211-215.
[2] SEO Y, TAKAMI Y, NAKAYAMA T, et al. Y chromosome DNA polymorphisms and their haplotypes in a Japanese population[J]. Leg Med, 1999, 1(3):145-149.
[3] UNDERHILL P A, PASSARINO G, LIN A A, et al. Maori origins, Y-chromosome haplotypes and implications for human history in the Pacific[J]. Hum Mutat, 2001, 17(4):271-280.
[4] 常振华, 卫利选, 张润锋, 等. 中国黄牛Y-SNPs遗传多样性与起源研究[J]. 畜牧兽医学报, 2011, 42(11):1537-1542.
CHANG Z H, WEI L X, ZHANG R F, et al. Genetic diversity and origin based on Y-SNPs in Chinese cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2011, 42(11):1537-1542.(in Chinese)
[5] SU B, XIAO C J, DEKA R, et al. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas[J]. Hum Genet, 2000, 107(6):582-590.
[6] LI R, XIE W M, CHANG Z H, et al. Y chromosome diversity and paternal origin of Chinese cattle[J]. Mol Biol Rep, 2013, 40(12):6633-6636.
[7] LI R, WANG S Q, XU S Y, et al. Novel Y-chromosome polymorphisms in Chinese domestic yak[J]. Anim Genet, 2014, 45(3):449-452.
[8] ZHANG G, VAHIDI S M F, MA Y H, et al. Limited polymorphisms of two Y-chromosomal SNPs in Chinese and Iranian sheep[J]. Anim Genet, 2012, 43(4):479-480.
[9] NIEMI M, BLÄUER A, ISO-TOURU T, et al. Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland:comparison with contemporary sheep breeds[J]. Genet Sel Evol, 2013, 45:2.
[10] ZHANG M, PENG W F, YANG G L, et al. Y chromosome haplotype diversity of domestic sheep (Ovis aries) in northern Eurasia[J]. Anim Genet, 2014, 45(6):903-907.
[11] WALLNER B, VOGL C, SHUKLA P, et al. Identification of genetic variation on the horse Y chromosome and the tracing of male founder lineages in modern breeds[J]. PLoS One, 2013, 8(4):e60015.
[12] BRANDARIZ-FONTES C, LEONARD J A, VEGA-PLA J L, et al. Y-chromosome analysis in retuertas horses[J]. PLoS One, 2013, 8(5):e64985.
[13] HAN H Y, ZHANG Q, GAO K X, et al. Y-single nucleotide polymorphisms diversity in Chinese indigenous horse[J]. Asian-Australas J Anim Sci, 2015, 28(8):1066-1074.
[14] RAMÍREZ O, OJEDA A, TOMÀS A, et al. Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds[J]. Mol Biol Evol, 2009, 26(9):2061-2072.
[15] CLIFFE K M, DAY A E, BAGGA M, et al. Analysis of the non-recombining Y chromosome defines polymorphisms in domestic pig breeds:ancestral bases identified by comparative sequencing[J]. Anim Genet, 2010, 41(6):619-629.
[16] 王兆龙. 实验动物贵州白香猪母系及父系遗传检测[D]. 贵州:贵州大学, 2009.
WANG Z L. Matrilineal and patrilineal genetic detection on laboratory animalization of Guizhou white Xiang pig[D]. Guizhou:Guizhou University, 2009. (in Chinese)
[17] 吴华, 胡杰, 方盛国, 等. 中国圈养梅花鹿的遗传多样性和遗传结构[J]. 动物学杂志, 2006, 41(4):41-47.
WU H, HU J, FANG S G, et al. Genetic diversity and genetic structure of domestic Sika deer in China[J]. Chinese Journal of Zoology, 2006, 41(4):41-47. (in Chinese)
[18] 李欢霞. 梅花鹿线粒体基因组全序列测定及种群遗传结构分析[D]. 镇江:江苏科技大学, 2012.
LI H X. The sequencing of the mitochondrial complete genome of Sika deer (Cervus nippon) and genetic structure among populations[D]. Zhenjiang:Jiangsu University of Science and Technology, 2012. (in Chinese)
[19] 周盼伊. 利用Y染色体基因分析家养梅花鹿的父系类型[D]. 北京:中国农业科学院, 2016.
ZHOU P Y. Using the Y chromosome gene analysis the paternal type of Cervus nippon[D]. Beijing:Chinese Academy of Agricultural Sciences, 2016. (in Chinese)
[20] TAMURA K, STECHER G, PETERSON D, et al. MEGA6:molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12):2725-2729.
[21] LIBRADO P, ROZAS J. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11):1451-1452.
[22] FELSENSTEIN J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution, 1985, 39(4):783-791.
[23] PRITCHARD J K, STEPHENS M, DONNELLY P. Inference of population structure using multilocus genotype data[J]. Genetics, 2000, 155(2):945-959.
[24] TAJIMA F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3):585-595.
[25] OIDA S, NAGANO T, YAMAKOSHI Y, et al. Amelogenin gene expression in porcine odontoblasts[J]. J Dent Res, 2002, 81(2):103-108.
[26] SESSION D R, LEE G S, WOLGEMUTH D J. Characterization of D1Pas1, a mouse autosomal homologue of the human AZFa region DBY, as a nuclear protein in spermatogenic cells[J]. Fertil Steril, 2001, 76(4):804-811.
[27] LEE K H, SONG G J, KANG I S, et al. Ubiquitin-specific protease activity of USP9Y, a male infertility gene on the Y chromosome[J]. Reprod Fertil Dev, 2003, 15(1-2):129-133.
[28] WHITFIELD L S, LOVELL-BADGE R, GOODFELLOW P N. Rapid sequence evolution of the mammalian sex-determining gene SRY[J]. Nature, 1993, 364(6439):713-715.
[29] 李讨讨, 马友记, 赵兴绪. SOX9基因调控雄性哺乳动物生殖活动的研究进展[J].畜牧兽医学报,2017, 48(6):971-978.
LI T T, MA Y J, ZHAO X X. Research progress on reproduction regulation of SOX9 gene in male mammals[J]. Acta Veterinaria et Zootechnica Sinica, 2017, 48(6):971-978.(in Chinese)

利用Y染色体基因分析梅花鹿种公鹿的遗传多样性和父系起源

Genetic Diversity and Paternal Origin of Breeder Sika Deer Based on Y Chromosome Genes

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 9

编辑推荐

Metrics

本文评价

[1]	张然然, 荣敏, 董依萌, 王天骄, 邢秀梅. 不同生长时期梅花鹿鹿茸代谢组分析[J]. 畜牧兽医学报, 2022, 53(12): 4518-4526.
[2]	唐丽昕, 王天骄, 刘华淼, 张然然, 邢秀梅. 梅花鹿与欧洲马鹿染色体水平基因组的比较研究[J]. 畜牧兽医学报, 2021, 52(2): 376-388.
[3]	董世武, 王天骄, 刘华淼, 王磊, 唐丽昕, 邢秀梅. 基于GBS技术对梅花鹿、马鹿及其杂交后代基因组SNP特征的分析[J]. 畜牧兽医学报, 2019, 50(12): 2422-2430.
[4]	张然然, 刘华淼, 王洪亮, 李洋, 邢秀梅. 基于label-free技术的梅花鹿(Cervus nippon)茸角蛋白组分比较[J]. 畜牧兽医学报, 2019, 50(10): 2005-2012.
[5]	张然然, 王磊, 李洋, 徐佳萍, 邢秀梅. 基于代谢组学技术的鹿血与鹿茸血鉴别研究[J]. 畜牧兽医学报, 2018, 49(7): 1533-1539.
[6]	张然然, 刘华淼, 王磊, 周永娜, 唐福全, 夏述忠, 邢秀梅. 基于Label-free技术的鹿角与鹿骨蛋白组分比较[J]. 畜牧兽医学报, 2017, 48(12): 2286-2292.
[7]	王磊, 张然然, 刘华淼, 刘汇涛, 周永娜, 董世武, 邢秀梅. 马鹿鹿茸不同部位差异蛋白质组学分析[J]. 畜牧兽医学报, 2017, 48(8): 1401-1415.
[8]	刘华淼, 鞠妍, 张然然, 邢秀梅. 基于蛋白质组学技术的鹿茸不同部位差异蛋白筛选[J]. 畜牧兽医学报, 2017, 48(4): 618-626.
[9]	张然然，刘华淼，邵元臣，周盼伊，苏莹，王磊，邢秀梅. 不同生长时期梅花鹿鹿茸差异蛋白质组学分析[J]. 畜牧兽医学报, 2016, 47(3): 493-501.