Journal of Guangxi Normal University(Natural Science Edition) ›› 2022, Vol. 40 ›› Issue (4): 180-187.doi: 10.16088/j.issn.1001-6600.2021033101

Previous Articles     Next Articles

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)

572

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

CLC Number: 

  • 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] LUO Shuyi, LI Yongtai, WU Zhengjun, CHENG Rui, CHEN Yaohuan, HE Jiasong. Influencing Factors of Perch Height of Shinisaurus crocodilurus in Daguishan Mountain, China [J]. Journal of Guangxi Normal University(Natural Science Edition), 2021, 39(5): 182-189.
[2] CHENG Rui, HE Mingxian, ZHONG Chunying, LUO Shuyi, WU Zhengjun. Comparison of Swimming Ability between Wild and Captive Breeding Shinisaurus crocodilurus [J]. Journal of Guangxi Normal University(Natural Science Edition), 2021, 39(1): 79-86.
[3] HE Mingxian, XU Shulin, LI Shilin, LUO Shuyi, YANG Chunsheng,CHENG Rui, WU Zhengjun. Correlation between Locomotor Performance and Body Measurements of Captive Breeding Shinisaurus crocodilurus [J]. Journal of Guangxi Normal University(Natural Science Edition), 2020, 38(1): 120-126.
[4] XIE Hai，CHEN Liang，HUANG Haiyan，HE Nan，LIU Haiyang，WU Zhengjun. Research on Movement Pattern and the Influencing Factors of Shinisaurus crocodilurus in the Luokeng Nature Reserve， Guangdong, China [J]. Journal of Guangxi Normal University(Natural Science Edition), 2017, 35(4): 106-113.
[5] HUANG Hua-yuan, LIU Hai-yang, HE Nan, WU Zheng-jun. Preliminary Noninvasive Analysis of Fecal Hormone in the Chinese Crocodile Lizard (Shinisaurus crocodilurus Ahl) [J]. Journal of Guangxi Normal University(Natural Science Edition), 2014, 32(4): 115-119.
[6] ZHANG Yong-de, ZENG Lan, BIN Shi-yu, DU Xue-song, YANG Hui-zan, CHEN Zhong, YU Yan-ling, LIN Yong. Genetic Diversity Analysis of Nile Tilapia Breeding Families [J]. Journal of Guangxi Normal University(Natural Science Edition), 2014, 32(3): 94-101.
[7] LIU Zhao-hui, LU Yong-bin, ZHANG Qi-wei, LIU Yan-hua, TANG Shao-Qing. Fine-scale Spatial Genetic Structure Analysis of Abies ziyuanesis Population in Dayuan,Hunan,China [J]. Journal of Guangxi Normal University(Natural Science Edition), 2013, 31(4): 140-144.
[8] WU Zheng-jun, WANG Zhen-xing, LIU Hai-yang, HE Nan, YU Hai, HUANG Cheng-ming. Thermal Dependence of Locomotor Performance for Shinisaurus crocodilurus in the Luokeng Nature Reserve,Guangdong,China [J]. Journal of Guangxi Normal University(Natural Science Edition), 2012, 30(3): 276-281.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Copyright © Journal of Guangxi Normal University(Natural Science Edition), All Rights Reserved.
Tel: 0773-5857325　E-mail: gxsdzkb@mailbox.gxnu.edu.cn
Powered by Beijing Magtech Co. Ltd