广西师范大学学报（自然科学版） ›› 2022, Vol. 40 ›› Issue (4): 180-187.doi: 10.16088/j.issn.1001-6600.2021033101

• 研究论文 • 上一篇    下一篇

基于SSR分析广东罗坑鳄蜥饲养种群的遗传结构

何南1,2, 张小丽1,3, 陈宁1,3, 陈泽柠1,3, 武正军1,3*   

  1. 1. 珍稀濒危动植物生态与环境保护教育部重点实验室(广西师范大学),广西桂林 541006;
    2. 广东曲江罗坑鳄蜥省级自然保护区管理处,广东韶关 512100;
    3. 广西珍稀濒危动物生态学重点实验室(广西师范大学),广西桂林 541006
  • 发布日期:2022-08-05
  • 通讯作者: 武正军(1970—),男(侗族),湖南靖州人,广西师范大学教授,博士。E-mail: wu_zhengjun@aliyun.com
  • 基金资助:
    国家自然科学基金(31760623);广东韶关曲江罗坑省级自然保护区管理处项目;广西大桂山鳄蜥国家级自然保护区管理局项目

Genetic Structure of the Artificial Breeding Shinisaurus crocodilurus in Luokeng Nature Reserve Based on Microsatellite DNA Marker

HE Nan1,2, ZHANG Xiaoli1,3, CHEN Ning1,3, CHEN Zening1,3, WU Zhengjun1,3*   

  1. 1. Key Laboratory of Rare and Endangered Species and Environmental Protection (Guangxi Normal University),Ministry of Education, Guilin Guangxi 541006, China;
    2. Guangdong Qujiang Luokeng Shinisaurus crocodilurus Provincial Nature Reserve Management Office, Shaoguan Guangdong 512100, China;
    3. Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guilin Guangxi 541006, China
  • Published:2022-08-05

PDF (PC)

256

摘要： 鳄蜥Shinisaurus crocodilurus是我国珍稀濒危物种,目前个体数目较少,人工繁殖个体容易发生近亲繁殖现象,因此了解它们的遗传结构有利于避免在饲养条件下发生近亲繁殖。本研究以9对微卫星作为分子标记,对罗坑人工饲养群体的112个鳄蜥进行种群遗传结构分析,结果表明1) 9对SSR位点总共有106个等位基因(Na),均值12。2)Hardy-weinberg平衡检验的数值范围为0.314~0.998,平衡检验系数均大于0.05。3)9个位点的观测杂合度(Ho)波动范围为0.018~0.929,均值0.629,期望杂合度(He)的范围为0.018~0.851,均值0.622。4)利用MEGA软件基于Neis遗传距离构建的邻接进化树(neighbor-joining tree)显示,112个个体划分为2个主支系,第一主支系分成3小支系,第二主支系分成5小支系,分支中的个体亲缘关系较近。5)瓶颈效应检测结果显示,在TPM和SMM模型下,罗坑鳄蜥饲养种群在近期历史上经历了显著的瓶颈效应。在整体水平上,罗坑人工饲养鳄蜥群体遗传多样性贫乏,建议在今后的饲养管理过程中根据邻接进化树将亲缘关系较近的个体分开饲养,避免个体近亲繁殖,维持种群的遗传多样性。

关键词: 罗坑保护区, 鳄蜥, 人工饲养种群, 微卫星, 遗传结构

Abstract: Chinese crocodile lizard Shinisaurus crocodilurus is critically endangered with small population size. Although captive population is increasing, this species is still at risk of inbreeding due to their small population size. Therefore, it’s necessary to understand the genetic structure and relationship of this species to avoid inbreeding. Based on 9 pairs of microsatellite markers, the genetic structure of 112 S. crocodilurus in Luokeng Nature Reserve artificial breeding population was analyzed. The results indicated that: (1) Microsatellite loci detected a total of 106 alleles, with the average of 12 alleles for each loci. (2) Hardy-weinberg exact test are within the range of 0.314-0.998, the balance test coefficient is greater than 0.05. (3) The range of observed heterozygosity (Ho) is 0.018-0.929, with an average of 0.629, and the expected heterozygosity (He) ranges from 0.018 to 0.851, with an average of 0.622. (4) The individual Neighbor-joining tree of S. crocodilurus based on the Nei’s genetic distance showed that they clustered into two clades with three and five lineages in close genetic relationships. (5) Bottleneck effect detection results showed that under the TPM model, the captive population of S. crocodilurus from Luokeng Nature Reserve has experienced bottleneck effect in the recent history. These results indicated that the S. crocodilurus population in Luokeng Nature Reserve had an extremely low genetic diversity. It is recommended to consider genetical relationship in future artificial breeding to avoid inbreeding and keeping the genetic diversity.

Key words: Luokeng Nature Reserve, Shinisaurus crocodilurus, captive population, microsatellite, genetic structure

中图分类号: 

  • S865.3
[1] YANG W Z, DING J, WANG S N, et al. Variation in genetic diversity of tree sparrow (Passer montanus) population in long-term environmental heavy metal polluted areas[J]. Environmental Pollution, 2020, 263(Part B): 114396. DOI: 10.1016/j.envpol.2020.114396.
[2]马静, 安永平, 王彩芬,等. 遗传多样性研究进展[J]. 陕西农业科学, 2010, 56(1): 126-130. DOI: 10.3969/j.issn.0488-5368.2010.01.043.
[3]魏辅文. 我国濒危哺乳动物保护生物学研究进展[J]. 兽类学报, 2016, 36(3): 255-269. DOI: 10.16829/j.slxb.201603001.
[4]ELLEGREN H, GALTIER N. Determinants of genetic diversity[J]. Nature Reviews Genetics, 2016, 17(7): 422-433. DOI: 10.1038/nrg.2016.58.
[5]黄勇杰. 基于线粒体DNA和微卫星标记的务川臭蛙种群遗传结构及分子系统发生研究[D]. 北京: 中国林业科学研究院, 2017.
[6]BEEBEE R. 分子生态学[M]. 张军丽,廖斌,王胜龙,译. 广州: 中山大学出版社, 2009.
[7]LYNCH M. A quantitative-genetic perspective on conservation issues[M]// AISE J, HAMRICK J. Conservation Genetics: Case Histories from Nature. New York: Chapan and Hall, 1996: 471-501.
[8]FANG S G, WAN Q H, FUJIHARA N. Genetic diversity of the giant panda (Ailuropoda melanoleuca) between big and small populations[J]. Journal of Applied Animal Research, 2002, 21(1): 65-74. DOI: 10.1080/09712119.2002.9706358.
[9]RIZVANOVIC M, KENNEDY J D, NOGUS-BRAVO D, et al. Persistence of genetic diversity and phylogeographic structure of three New Zealand Forest beetles under climate change[J]. Diversity and Distributions, 2019, 25(1): 142-153. DOI: 10.1111/ddi.12834.
[10]类延宝, 肖海峰, 冯玉龙. 外来植物入侵对生物多样性的影响及本地生物的进化响应[J]. 生物多样性, 2010, 18(6): 622-630.
[11]HOLDEREGGER R, DI GIULIO M. The genetic effects of roads: a review of empirical evidence[J]. Basic and Applied Ecology, 2010, 11(6): 522-531. DOI: 10.1016/j.baae.2010.06.006.
[12]俞文灏, 吴保锋, 刘勇波. 生境破碎化对动植物遗传多样性的影响研究进展[J]. 应用与环境生物学报, 2019, 25(3): 743-749. DOI: 10.19675/j.cnki.1006-687x.2018.07040.
[13]LIU B, KUANG Y Y, TONG G X, et al. Analysis of genetic diversity on 9 wild stocks of taimen (Hucho taimen) by microsatellite markers[J]. Zoological Research, 2011, 32(6): 597-604. DOI: 10.3724/SP.J.1141.2011.06597.
[14]陈蓉, 吕冉, 程家求, 等. 南京地区圈养黄颊长臂猿核心种群的遗传多样性分析[J]. 野生动物学报, 2020, 41(1): 42-46. DOI: 10.19711/j.cnki.issn2310-1490.2020.01.007.
[15]OUBORG N J. Integrating population genetics and conservation biology in the era of genomics[J]. Biology Letters, 2010, 6(1): 3-6. DOI: 10.1098/rsbl.2009.0590.
[16]LEROY G. Inbreeding depression in livestock species: review and meta-analysis[J]. Animal Genetics, 2014, 45(5): 618-628. DOI: 10.1111/age.12178.
[17]BERGNER L M, JAMIESON I G, ROBERTSON B C. Combining genetic data to identify relatedness among founders in a genetically depauperate parrot, the Kakapo (Strigops habroptilus)[J]. Conservation Genetics, 2014, 15(5): 1013-1020. DOI: 10.1007/s10592-014-0595-y.
[18]CHANG Z F, LUO M F, LIU Z J, et al. Human influence on the population decline and loss of genetic diversity in a small and isolated population of Sichuan snub-nosed monkeys (Rhinopithecus roxellana)[J]. Genetica, 2012, 140(4/5/6): 105-114. DOI: 10.1007/s10709-012-9662-9.
[19]REED D H, BRISCOE D A, FRANKHAM R. Inbreeding and extinction: the effect of environmental stress and lineage[J]. Conservation Genetics, 2002, 3(3): 301-307. DOI: 10.1023/A:1019948130263.
[20]周芸芸. 神农架川金丝猴的遗传多样性及保护研究[D]. 北京: 中央民族大学, 2015.
[21]施禄也, 祁纪伟, 高丹丹, 等. 浅蛤属(Macridiscus)物种特异性线粒体DNA分子标记及其长度多态性和个体内异质性[J]. 北京师范大学学报(自然科学版), 2018, 54(2): 203-207. DOI: 10.16360/j.cnki.jbnuns.2018.02.010.
[22]ZHOU Q, MU K M, NI Z X, et al. Analysis of genetic diversity of ancient Ginkgo populations using SSR markers[J]. Industrial Crops and Products, 2020, 145: 111942. DOI: 10.1016/j.indcrop.2019.111942.
[23]CHOKOE T C, MDLADLA-HADEBE K, MUCHADEYI F, et al. Genetic diversity of South African indigenous goat population from four provinces using Genome-Wide SNP data[J]. Sustainability, 2020, 12(24): 10361. DOI: 10.3390/su122410361.
[24]TSUMURA Y, KIMURA M, NAKAO K, et al. Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia[J]. Tree Genetics & Genomes, 2020, 16(1):19. DOI: 10.1007/s11295-019-1411-0.
[25]刘佳妮, 桂富荣, 李正跃. SSR分子标记技术在入侵昆虫学研究中的运用[J]. 植物保护, 2008,34(3): 7-11. DOI: 10.3969/j.issn.0529-1542.2008.03.002.
[26]Van OPPEN M J H, RICO C, TURNER G F, et al. Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids[J]. Molecular Biology and Evolution, 2000, 17(4): 489-498. DOI: 10.1093/oxfordjournals.molbev.a026329.
[27]PROVAN J, SORANZO N, WILSON N J, et al. A low mutation rate for chloroplast microsatellites[J]. Genetics, 1999, 153(2): 943-947. DOI: 10.1093/genetics/153.2.943.
[28]王家, 周天华. 山白树微卫星特征分析及分子标记开发[J]. 中国实验方剂学杂志, 2019, 25(3): 143-150. DOI: 10.13422/j.cnki.syfjx.20190320.
[29]夏曦中, 车婧, 章志宏, 等. SSR分子标记技术在遗传学实验教学中的应用[J]. 实验技术与管理, 2021, 29(6): 48-50. DOI: 10.3969/j.issn.1002-4956.2012.06.014.
[30]杨万云, 郑军军, 贾博寅, 等. 微卫星分子标记及其在动物遗传育种中的研究进展[J]. 基因组学与应用生物学, 2017, 36(11): 4644-4649. DOI: 10.13417/j.gab.036.004644.
[31]张正义, 邢秀梅, 胡鹏飞, 等. 微卫星标记及其在动物亲缘关系鉴定中的应用[J]. 基因组学与应用生物学, 2018, 37(4): 1406-1412. DOI: 10.13417/j.gab.037.001406.
[32]王萌, 朱思雨, 薛茂盛, 等. 微卫星标记方法在大型猫科动物保护群遗传学研究中的应用与挑战[J]. 野生动物学报, 2019, 40(3): 780-786. DOI: 10.19711/j.cnki.issn2310-1490.20190604.005.
[33]张正义, 邢秀梅, 胡鹏飞, 等. 微卫星标记在动物遗传多样性分析的研究进展[J]. 经济动物学报, 2017, 21(3): 164-168. DOI: 10.13326/j.jea.2017.1191.
[34]王芳, 彭真信, 张金国, 等. 应用微卫星标记分析圈养大熊猫遗传多样性[J]. 生物化学与生物物理进展, 2007, 34(12): 1279-1287. DOI: 10.3321/j.issn:1000-3282.2007.12.009.
[35]修云芳, 刘国伟, 郑舒桓. 圈养小熊猫遗传多样性与种群遗传结构分析[J]. 兽类学报, 2018, 38(4): 393-401. DOI: 10. 16829/j.slxb.150180.
[36]何丽, 张于光, 彭红兰, 等. 利用非损伤性方法评估神农架保护区川金丝猴种群遗传多样性[J]. 生态学报, 2010, 30(16): 4340-4350.
[37]谢海, 陈亮, 黄海燕, 等. 广东罗坑自然保护区鳄蜥的移动格局及其影响因子[J]. 广西师范大学学报(自然科学版), 2017, 35(4): 106-113. DOI: 10.16088/j.issn.1001-6600.2017.04.015.
[38]阳春生, 罗树毅, 李钰慧, 等. 样线法和标志重捕法在鳄蜥种群数量调查中的应用比较[J]. 野生动物学报, 2017, 38(2): 291-294. DOI: 10.19711/j.cnki.issn2310-1490.2017.02.022.
[39]何南, 武正军, 蔡凤金, 等. 鳄蜥的两性异形[J]. 生态学杂志, 2011, 30(1): 7-11. DOI: 10.13292/j.1000-4890.2011.0001.
[40]江海英, 陈金平, 黄铭威, 等. 龟嗜皮菌的快速鉴定及其在鳄蜥皮肤病原检测中的应用[J]. 动物学杂志, 2021, 56(1): 111-118. DOI: 10.13859/j.cjz.202101013.
[41]TANG G S, LIANG X X, YANG M Y, et al. Captivity influences gut microbiota in crocodile lizards (Shinisaurus crocodilurus)[J]. Frontiers in Microbiology, 2020, 11: 550. DOI: 10.3389/fmicb.2020.00550.
[42]贝荣丙. 鳄蜥(Shinisaurus crocodilurus)微卫星文库的构建及遗传结构分析[D]. 桂林: 广西师范大学, 2012.
[43]李洪果, 许基煌, 杜红岩, 等. 基于等位基因最大化法初步构建杜仲核心种质[J]. 林业科学, 2018, 54(2): 42-51. DOI: 10.11707/j.1001-7488.20180205.
[44]SUN L D, GAN J W, JIANG L B, et al. Recursive test of Hardy-Weinberg equilibrium in tetraploids[J]. Trends in Genetics, 2021, 37(6): 504-513. DOI: 10.1016/j.tig.2020.11.006.
[45]HUANG K, MI R, DUNN D W, et al. Performing parentage analysis in the presence of inbreeding and null alleles[J]. Genetics, 2018, 210(4): 1467-1481. DOI: 10.1534/genetics.118.301592.
[46]CHEN B W, COLE J W, GROND-GINSBACH C, et al. Departure from Hardy Weinberg Equilibrium and genotyping error[J]. Frontiers in Genetics, 2017, 8: 167. DOI: 10.3389/fgene.2017.00167.
[47]胡亮, 孙伟, 马月辉. 藏系绵羊群体遗传多样性及遗传结构分析[J]. 畜牧兽医学报, 2019, 50(6): 1145-1153. DOI: 10.11843/j.issn.0366-6964.2019.06.004.
[48]张枫, 张保卫, 唐文乔, 等. 长江口江豚的遗传多样性现状及种群动态[J]. 上海海洋大学学报, 2018, 27(5): 656-665. DOI: 10.12024/jsou.20180302234.
[49]周芸芸, 薛亚东, 张宇, 等. 基于微卫星DNA的神农架川金丝猴遗传结构研究[J]. 生态学报, 2018, 38(4): 1401-1410. DOI: 10.5846/stxb201612192613.
[50]关盛宇, 刘国世, 张鲁. 动物繁殖中的线粒体DNA 遗传“瓶颈效应”[J]. 中国畜牧杂志, 2019, 55(7): 1-4. DOI: 10.19556/j.0258-7033.2019-07-001.
[51]吴华, 胡杰, 万秋红, 等. 梅花鹿的微卫星多态性及种群的遗传结构[J]. 兽类学报, 2008,28(2): 109-116. DOI: 10.16829/j.slxb.2008.02.001.
[52]SPENCER C C, NEIGEL J E, LEBERG P L. Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks[J]. Molecular Ecology, 2000, 9(10): 1517-1528. DOI: 10.1046/j.1365-294x.2000.01031.x.
[1] 罗树毅, 黎永泰, 武正军, 程瑞, 陈耀还, 何家松. 广西大桂山鳄蜥的栖枝高度及其影响因素[J]. 广西师范大学学报（自然科学版）, 2021, 39(5): 182-189.
[2] 程瑞, 何明先, 钟春英, 罗树毅, 武正军. 野生与人工繁育鳄蜥游泳能力比较[J]. 广西师范大学学报（自然科学版）, 2021, 39(1): 79-86.
[3] 何明先, 许淑淋, 李诗林, 罗树毅, 阳春生, 程瑞, 武正军. 人工饲养鳄蜥运动能力及其与身体测量值的关系[J]. 广西师范大学学报（自然科学版）, 2020, 38(1): 120-126.
[4] 谢海，陈亮，黄海燕，何南，刘海洋，武正军. 广东罗坑自然保护区鳄蜥的移动格局及其影响因子[J]. 广西师范大学学报（自然科学版）, 2017, 35(4): 106-113.
[5] 黄华苑, 刘海洋, 何南, 武正军. 利用非损伤法分析鳄蜥粪便激素水平的变化[J]. 广西师范大学学报（自然科学版）, 2014, 32(4): 115-119.
[6] 张永德, 曾兰, 宾石玉, 杜雪松, 杨慧赞, 陈忠, 余艳玲, 林勇. 尼罗罗非鱼选育家系的遗传多样性研究[J]. 广西师范大学学报（自然科学版）, 2014, 32(3): 94-101.
[7] 武正军, 王振兴, 刘海洋, 何南, 于海, 黄乘明. 广东罗坑自然保护区鳄蜥运动能力的热依赖性[J]. 广西师范大学学报（自然科学版）, 2012, 30(3): 276-281.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
版权所有 © 广西师范大学学报（自然科学版）编辑部
地址：广西桂林市三里店育才路15号　邮编：541004
电话：0773-5857325　E-mail: gxsdzkb@mailbox.gxnu.edu.cn
本系统由北京玛格泰克科技发展有限公司设计开发