基于mtDNA和Y染色体基因片段的塔河马鹿种公鹿遗传多样性分析

doi:10.11843/j.issn.0366-6964.2023.06.019

Abstract

Abstract: This study aimed to explore the genetic diversity and the ancestral types of Tahe red deer at the molecular level. DNA was extracted from fresh blood which was collected at the sawn antler stage, PCR amplification and direct sequencing were performed to analyze AMELY2, DBY, SRY genes on Y chromosome and ND1, COX1, ATP6, ND5, Cytb genes of mtDNA in 38 stud Tahe red deer species. Base composition, nucleotide diversity (Pi), mean nucleotide difference (K), Tajima’D value, haplotype number (H) and haplotype diversity (Hd) were calculated to evaluate the genetic diversity of stud Tahe red deer. The haplotype network diagram was constructed and the genetic distance between haplotypes was calculated. The phylogenetic tree was constructed and white-lipped deer was used as the outgroup to analyze the parental lines of stud Tahe red deer. The results showed that the length of the Y chromosome spliced by comparing the AMELY2, DBY and SRY genes was 3 577 bp, and a total of 17 SNPs polymorphic sites were detected, and 4 haplotypes were defined. The dominant haplotype was Hap-1, accounting for 65.79% of the frequency. The nucleotide diversity and haplotype diversity were 0.001 95 and 0.495 0, respectively, showing a low level of genetic diversity. The phylogenetic tree constructed based on the Y chromosome genes showed the existence of two branches, A and B. After comparison of ND1, COX1, ATP6, ND5 and Cytb genes of mtDNA, the splicing length was 6 160 bp, and a total of 41 SNPs polymorphic sites were detected, and 8 haplotypes were defined. The dominant haplotype was Hap-1, accounting for 47.37% of the frequency. The nucleotide diversity and haplotype diversity were 0.001 54 and 0.699 9, respectively, showing an imbalance of high haplotype diversity and low nucleotide diversity, and the genetic diversity was at a low level. The phylogenetic tree constructed based on mtDNA showed the existence of two branches, I and II. The genetic diversity of stud Tahe red deer is at a low level, and there are two ancestral types in the population of Tahe red deer.

Key words: mtDNA, Y chromosome, stud Tahe red deer, genetic diversity

CLC Number:

S813.3

YANG Sukun, DONG Yimeng, WANG Hongliang, ZHAO Xitang, CHEN Xu, XING Xiumei. Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2402-2413.

References 42

[1]	牛莹莹,张子栋,刘艳华,等.黑龙江穆棱东北红豆杉自然保护区兽类多样性及东北虎猎物资源[J].野生动物学报,2021,42(2):355-362.NIU Y Y,ZHANG Z D,LIU Y H,et al.Mammal Diversity and prey resource of amur tiger in Heilongjiang Muling Japanese yew national nature reserve[J].Chinese Journal of Wildlife,2021,42(2):355-362.(in Chinese)
[2]	李湘涛,彭建生,徐永春,等.《国家重点保护野生动物名录》全解读[J].森林与人类,2021(12):18-45.LI X T,PENG J S,XU Y C,et al.Full interpretation of 《the List of State Key Protected Wildlife》[J].Forest & Humankind,2021(12):18-45.(in Chinese)
[3]	蒋志刚,马勇,吴毅,等.中国哺乳动物多样性[J].生物多样性,2015,23(3):351-364.JIANG Z G,MA Y,WU Y,et al.China's mammalian diversity[J].Biodiversity Science,2015,23(3):351-364.(in Chinese)
[4]	ABABAIKERI B,ABDURIYIM S,TOHETAHONG Y,et al.Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment[J].Front Zool,2020,17:31.
[5]	POLZIEHN R O,STROBECK C.A phylogenetic comparison of red deer and wapiti using mitochondrial DNA[J].Mol Phylogenet Evol,2002,22(3):342-356.
[6]	MAHMUT H,MASUDA R,ONUMA M,et al.Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China:comparison with other Asian,European,and north American populations[J].Zoolog Sci,2002,19(4):485-495.
[7]	LUDT C J,SCHROEDER W,ROTTMANN O,et al.Mitochondrial DNA phylogeography of red deer (Cervus elaphus)[J].Mol Phylogenet Evol,2004,31(3):1064-1083.
[8]	陈长明,吐逊汗·牙合甫,冷朝升,等.浅淡塔里木马鹿的品种选育与结构调整[J].畜牧兽医科技信息,2008(4):116.CHEN C M,TUXUNHAN Y,LENG C S,et al.The breeding and structure adjustment of Tarim red deer[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2008(4):116.(in Chinese)
[9]	MAHMUT H,GANZORIG S,ONUMA M,et al.A preliminary study of the genetic diversity of Xinjiang Tarim red deer (Cervus elaphus yarkandensis) using the microsatellite DNA method[J].Jpn J Vet Res,2001,49(3):231-237.
[10]	帕尔哈提·萨依提.塔里木马鹿遗传资源调查情况[J].当代畜禽养殖业,2015(6):37-38.SAYITI P.Investigation on genetic resources of Tarim red deer[J].Modern Animal Husbandry,2015(6):37-38.(in Chinese)
[11]	姜云.塔里木马鹿驯养史话[J].畜牧兽医科技信息,2014(8):125-126.JIANG Y.On the domestication history of Tarim red deer[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2014(8):125-126.(in Chinese)
[12]	苏莹,鞠贵春,邵元臣,等.利用Y染色体进行鹿科动物的起源和进化分析[J].特产研究,2016,38(1):53-57.SU Y,JU G C,SHAO Y C,et al.Research on Y chromosome molecular genetic diversity and paternal origin of cervidae[J].Special Wild Economic Animal and Plant Research,2016,38(1):53-57.(in Chinese)
[13]	MEADOWS J R S,CEMAL I,KARACA O,et al.Five ovine mitochondrial lineages identified from sheep breeds of the near east[J].Genetics,2007,175(3):1371-1379.
[14]	ESCOUFLAIRE C,CAPITAN A.Analysis of pedigree data and whole-genome sequences in 12 cattle breeds reveals extremely low within-breed Y-chromosome diversity[J].Anim Genet,2021,52(5):725-729.
[15]	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.
[16]	李广祯,马志杰,陈生梅,等.野牦牛及青海地方牦牛品种全线粒体基因组母系遗传多样性、分化及系统发育分析[J].畜牧兽医学报,2022,53(5):1420-1430.LI G Z,MA Z J,CHEN S M,et al.Maternal genetic diversity,differentiation and phylogeny of mitogenome sequence variations of wild yak and local yak breeds in Qinghai[J].Acta Veterinaria et Zootechnica Sinica,2022,53(5):1420-1430.(in Chinese)
[17]	WALLNER B,PALMIERI N,VOGL C,et al.Y chromosome uncovers the recent oriental origin of modern stallions[J].Curr Biol,2017,27(13):2029-2035.e5.
[18]	DENG J,XIE X L,WANG D F,et al.Paternal origins and migratory episodes of domestic sheep[J].Curr Biol,2020,30(20):4085-4095.e6.
[19]	李正杰,周先坤,王浥尘,等.阿坝藏族羌族自治州若尔盖地区藏猪mtDNA D-Loop的遗传多样性分析[J].畜牧兽医学报,2019,50(12):2387-2399.LI Z J,ZHOU X K,WANG Y C,et al.Genetic diversity of Tibetan Pig mitochondrial DNA D-Loop in Ruoergai area of A'ba Tibetan and Qiang autonomous prefecture[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2387-2399.(in Chinese)
[20]	DE A K,SAWHNEY S,BHATTACHARYA D,et al.Origin,genetic diversity and evolution of Andaman local duck,a native duck germplasm of an insular region of India[J].PLoS One,2021,16(2):e0245138.
[21]	唐修君,樊艳凤,贾晓旭,等.基于线粒体控制区的鸡不同杂交组合遗传多样性研究[J].畜牧兽医学报,2021,52(6):1523-1534.TANG X J,FAN Y F,JIA X X,et al.Study on genetic diversity in different hybrid combinations of chickens based on mitochondrial control region[J].Acta Veterinaria et Zootechnica Sinica,2021,52(6):1523-1534.(in Chinese)
[22]	GIOVANNELLI F,MORI E,ZACCARONI M,et al.Genetic insights into an Apennine population of the Italian red deer[J].Mammal Res,2022,67(3):399-406.
[23]	JU Y,LIU H M,HE J M,et al.Genetic diversity of Aoluguya reindeer based on D-loop region of mtDNA and its conservation implications[J].Gene,2020,733:144271.
[24]	董晓宇,单文娟,于丽娟,等.塔里木马鹿(Cervus elaphus yarkandensis)遗传结构及遗传多样性分析[J].生物技术,2010,20(5):16-20.DONG X Y,SHAN W J,YU L J,et al.Structure of the mitochondrial DNA control region and population genetic diversity analysis of Tarim red deer(C.e.yarkandensis)[J].Biotechnology,2010,20(5):16-20.(in Chinese)
[25]	塔依尔江·麦麦提,塔吉古丽·吐热甫,布威海丽且姆·阿巴拜科日,等.环境因子对塔里木马鹿种群遗传多样性的影响[J].野生动物学报,2018,39(4):754-760.TAYERJAN M,TAJIGUL T,BUWEIHAILIQIEMU A,et al.Influence of environmental factors on genetic diversity of Tarim red deer[J].Chinese Journal of Wildlife,2018,39(4):754-760.(in Chinese)
[26]	房瑞新.中国马鹿父系遗传多样性分析[D].哈尔滨:东北林业大学,2021.FANG R X.Paternal genetic diversity of red deer in China[D].Harbin:Northeast Forestry University,2021.(in Chinese)
[27]	苏莹,邢秀梅,邵元臣,等.利用Y染色体AMELY基因分析中国马鹿的遗传多样性[J].中国畜牧兽医,2016,43(3):761-767.SU Y,XING X M,SHAO Y C,et al.Genetic diversity analysis of Cervus elaphus using AMELY gene in Y chromosome[J].China Animal Husbandry & Veterinary Medicine,2016,43(3):761-767.(in Chinese)
[28]	房瑞新,田雪琪,邹晨,等.利用Y染色体SRY基因分析马鹿的父系起源和遗传多样性[J].中国畜牧兽医,2021,48(7):2457-2466.FANG R X,TIAN X Q,ZOU C,et al.Analysis of genetic diversity and paternal type of red deer using SRY gene in Y chromosome[J].China Animal Husbandry & Veterinary Medicine,2021,48(7):2457-2466.(in Chinese)
[29]	苏莹.马鹿群体Y染色体相关基因遗传多样性分析[D].长春:吉林农业大学,2016.SU Y.Using Y chromosome gene analysis the genetic diversity of Malu[D].Changchun:Jilin Agricultural University,2016.(in Chinese)
[30]	董依萌,刘华淼,玉手英利,等.基于SRY基因分析梅花鹿的遗传多样性及父系类型[J].中国畜牧兽医,2019,46(2):489-496.DONG Y M,LIU H M,TAMATA H B,et al.Analysis of genetic diversity and paternal type of sika deer based on SRY gene[J].China Animal Husbandry & Veterinary Medicine,2019,46(2):489-496.(in Chinese)
[31]	王洪亮,任战军,王乐,等.新疆马鹿群体的系统发育[J].西北农业学报,2008,17(6):25-29.WANG H L,REN Z J,WANG L,et al.Molecular phylogeny of wapiti (red deer) populations in Xinjiang[J].Acta Agriculturae Boreali-occidentalis Sinica,2008,17(6):25-29.(in Chinese)
[32]	邓铸疆,任战军,熊建杰,等.西北马鹿群体遗传多样性及系统地位[J].西北农林科技大学学报:自然科学版,2010,38(9):42-46.DENG Z J,REN Z J,XIONG J J,et al.Genetic Diversity and classification status of wapiti (red deer) in northwest of China[J].Journal of Northwest A & F University:Natural Science Edition,2010,38(9):42-46.(in Chinese)
[33]	塔吉古丽·吐热甫.环境因子对塔里木马鹿(Cervus elaphus yarkandensis)遗传多样性的影响[D].乌鲁木齐:新疆大学,2017.TURAP T.Influence of environmental factors on genetic diversity of Tarim red deer(C.e.yarkandensis)[D].Urumqi:Xinjiang University,2017.(in Chinese)
[34]	GRANT W,BOWEN B.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].J Hered,1998,89(5):415-426.
[35]	LAN H,SHI L M.The origin and genetic differentiation of native breeds of pigs in southwest China:an approach from mitochondrial DNA polymorphism[J].Biochem Genet,1993,31(1-2):51-60.
[36]	逯金瑶.基于线粒体基因组探讨紫貂种群遗传结构与进化历史[D].哈尔滨:东北林业大学,2017.LU J Y.Genetic structure and evolutionary history of sable (Martes zibellina L.1758) populations based on the mitochondrial genome[D].Harbin:Northeast Forestry University,2017.(in Chinese)
[37]	刘晓玮,李瑞香,王兴龙,等.基于mtDNA Cytb基因和D-loop区序列的陕西林麝遗传多样性分析[J].中国畜牧兽医,2022,49(4):1352-1363.LIU X W,LI R X,WANG X L,et al.Genetic diversity analysis of Shaanxi Moschus berezovskii based on mtDNA Cytb gene and D-loop region sequence[J].China Animal Husbandry & Veterinary Medicine,2022,49(4):1352-1363.(in Chinese)
[38]	COLLEVATTI R G,VITORINO L C,VIEIRA T B,et al.Landscape changes decrease genetic diversity in the Pallas' long-tongued bat[J].Perspect Ecol Conserv,2020,18(3):169-177.
[39]	BEAGHTON P J,BURT A.Gene drives and population persistence vs elimination:the impact of spatial structure and inbreeding at low density[J].Theor Popul Biol,2022,145:109-125.
[40]	WHITE D J,WOLFF J N,PIERSON M,et al.Revealing the hidden complexities of mtDNA inheritance[J].Mol Ecol,2008,17(23):4925-4942.
[41]	涂剑锋,徐佳萍,王洪亮,等.基于线粒体DNA控制区序列分析我国马鹿5个亚种的遗传分化[J].华北农学报,2018,33(S1):79-83.TU J F,XU J P,WANG H L,et al.Genetic differentiation of five subspecies wapiti in China based on mitochondrial DNA control region sequences[J].Acta Agriculturae Boreali-Sinica,2018,33(S1):79-83.(in Chinese)
[42]	涂剑锋,邢秀梅,刘琳玲,等.基于线粒体控制区全序列的鹿亚科系统发育分析[J].西北农业学报,2012, 21(3):22-26.TU J F,XING X M,LIU L L,et al.A molecular phylogeny of cervinae based on mitochondrial complete control region sequence[J].Acta Agriculturae Boreali-Occidentalis Sinica,2012,21(3):22-26.(in Chinese)

Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 42

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	YANG Qing, GONG Jing, ZHAO Xueyan, ZHU Xiaodong, GENG Liying, ZHANG Chuansheng, WANG Jiying. Comparison of Array and Resequencing in Pig Genetic Structure Studies [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2772-2782.
[2]	ZHANG Renbao, ZHOU Donghui, ZHOU Lisheng, GAO Xiaoxiao, LIU Nan, HE Jianning. Analysis of Genetic Structure of Conservation Population in Jining Gray Goats Based on 70 K SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2836-2847.
[3]	ZHAO Zhenjian, WANG Shujie, CHEN Dong, JI Xiang, SHEN Qi, YU Yang, CUI Shengdi, WANG Junge, CHEN Ziyang, TANG Guoqing. Population Structure and Genetic Diversity Analysis of Neijiang Pigs Based on Low-coverage Whole Genome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2297-2307.
[4]	TAO Xuan, YANG Xuemei, LIANG Yan, LIU Yihui, WANG Yong, KONG Fanjing, LEI Yunfeng, YANG Yuekui, WANG Yan, AN Rui, YANG Kun, Lü Xuebin, HE Zhiping, GU Yiren. Analysis of Genetic Structure of Conservation Population in Yacha Pig Based on SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2308-2319.
[5]	LONG Xi, CHEN Li, WU Pingxian, ZHANG Tinghuan, PAN Hongmei, ZHANG Liang, WANG Jinyong, GUO Zongyi, CHAI Jie. Evaluation of the Genetic Structure and Selection Signatures in Hechuan Black Pigs Conserved Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1854-1867.
[6]	MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1939-1950.
[7]	LIU Jiankui, XU Ye, LIU Chen, YU Hui, YANG Yuan, HE Le, LI Jiarui, DAN Huijuan, DAI Ailing, YANG Xiaoyan, WEI Chunhua. Genomic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in Fujian Province from 2017 to 2021 based on Whole Genome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1579-1589.
[8]	MA Zhijie, WANG Shikang, ZHANG Weizhong, GUO Weixing, ZHAO Haiming, LEI Chuzhao. Y-chromosome Genomic Diversity and Paternal Origins of Qaidam Cattle and Mongolian Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1026-1033.
[9]	GAO Chaoqun, CAO Ranran, DU Wenping, HU Xiaoyu, LEI Yanru, LI Wenting, KANG Xiangtao. Genetic Diversity and Population Structure Analysis of Chinese Native Chicken Breeds using Genome-wide SNPs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 554-562.
[10]	LI Yinxia, YA Shengjiang·Nasier, SAI Like·Duman, QIAN Yong, CAO Shaoxian, WANG Weilie, MENG Chunhua, ZHANG Jun, ZHANG Jianli. Evaluation of Genetic Diversity and Genetic Structure in Kirgiz Sheep Population Based on SNPs Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 572-583.
[11]	QI Lina, LU Xuelin, YANG Kaixuan, ZHOU Jin, LI Xianyu, LIU Ke, ZHANG Wengang, GU Xin, ZHANG Weijian. Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4962-4971.
[12]	HU Ziping, WANG Ligang, ZONG Wencheng, HOU Renda, SU Yanfang, NIU Naiqi, WANG Lixian, WANG Yuan, ZHNAG Longchao. Genetic Structure Analysis of Jianbai Xiang Pig Population Based on Genomic SNP and ROH [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4117-4125.
[13]	LIU Chenlong, LU Dan, ZHOU Quanyong, WAN Mingchun, HAO Xiaodong, ZHANG Xianhe, ZHENG Ruiqiang, JI Huayuan. Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2502-2513.
[14]	YUAN Jiao, XU Guoqiang, ZHOU Xiang, XU Sanping, LI Sheng, LI Wangming, LIU Bang. SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2514-2523.
[15]	MA Lixia, CAO Guowei, ZHU Hongfang, DENG Zhanzhao, CAI Zhengyun, ZHOU Chenghao, HAN Wei, GU Yaling, ZHANG Juan. Analysis of Genetic Variation in a Conserved Population of Jingyuan Chickens Based on RAD-seq [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2104-2117.