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

Abstract

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.

Key words: breeder sika deer, Y chromosome, genetic diversity, paternal origin

CLC Number:

S825.2

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.

References

[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)

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

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