畜禽保种群体遗传多样性的模拟

doi:10.3864/j.issn.0578-1752.2012.18.018

摘要/Abstract

摘要： 【目的】基于微卫星标记特点，采用计算机模拟技术，探讨畜禽保种群遗传多样性的变化过程。【方法】选择30个均匀分布于基因组、具有4—10个等位基因的标记位点，位点间无相互作用；模拟产生的畜禽保种群公母比例为1﹕5、随机交配、各家系随机等量留种、群体规模保持世代恒定，世代间无重叠，群体有效大小分别为Ne=10、20、50、100和200，保种繁殖50个世代，1 000次重复。采用多态性位点数（num-p）、平均等位基因数（Na）、有效等位基因数（Ae）、观测基因杂合度（Ho）、期望杂合度（He）、稀有等位基因数（RA）、缺乏丰富位点数（NRP）作为遗传多样性度量指标。【结果】保种群体的遗传多样性总体趋势随保种世代而逐渐降低，不同群体规模遗传多样性的降低速度差异显著，相比基础群，Ne值越大，num-p、Na、Ae、Ho、He和 RA的下降速率越慢，且当Ne=100和200时，num-p基本维持50个世代不变，RA则分别增加0.86%和2.49倍；而Ne值越大，NRP的增加速率越慢。【结论】遗传漂变导致了群体内遗传多样性的丢失。小群体中遗传漂变导致的遗传多样性丢失速度比大群体更高，发生在闭锁群体水平上的有效群体规模的减少将加快基因漂变速度，从而降低保种群体内的遗传多样性。

关键词: 遗传多样性, 保种, 畜禽品种资源, 计算机模拟

Abstract: 【Objective】The changes of genetic diversity of domestic animals’ genetic resources were studied by using computer simulation based on the characteristics of microsatellite markers.【Method】Thirty mark loci were chosen and they are equally distributed in the whole genome, and each locus has 4-10 alleles, no interactions between these loci. Computer simulation was based on the assumption that there was no gene mutation, selection ratio of male and female is 1﹕5 and random mating was implemented in all generations, the generation was non-overlapping and the number of breeding animals was selected through mating by family in equality, effective population size (Ne) were 10, 20, 50, 100 and 200. The simulation experiment was carried out for 50 generations and 1000 repeats. The number of polymorphic loci (Num-p), allele number (Na), number of effective alleles (Ae), observed heterozygosity (Ho), expected heterozygosity (He), number of rare alleles (RA), number of non-rich polymorphic loci (NRP) were indicators as genetic diversity.【Result】The overall trend of genetic diversity of conservation populations was decreased over generations, and differences were significant as Ne changed. It was seen that larger values of Ne, the more slower descent rate of num-p, Na, Ae, Ho, He, and RA compared with the base population, and num-p basically maintained at 30, RA decreased by 0.86% and 2.49 times as Ne were 100 and 200. Moreover larger, the values of Ne, the slower increase rate of NRP. 【Conclusion】 Decreases in effective population size that occur at a closed population level will increase gene drift and reduce genetic diversity within conservation population.

Key words: genetic diversity, conservation, domestic animal genetic resources, computer simulation

鲁云风, 王茜, 黄文波, 史利华, 吴克亮. 畜禽保种群体遗传多样性的模拟[J]. 中国农业科学, 2012, 45(18): 3849-3858.

LU Yun-Feng, WANG Qian, HUANG Wen-Bo, SHI Li-Hua, WU Ke-Liang. Simulation of Genetic Diversity Variation in Domestic Animal Population Under Conservation[J]. Scientia Agricultura Sinica, 2012, 45(18): 3849-3858.

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参考文献

[1]Anderson S. Animal genetic resources and sustainable livelihoods. Ecological Economics, 2003, 45(3): 331-339.

[2]Frankham R, Ballou J D, Briscoe D A. Introduction to Conservation Genetics. Cambridge, UK: Cambridge University Press, 2002.

[3]Montgomery M E, Woodworth L M, Nurthen R K, Gilligan D M, Briscoe D A, Frankham R. Relationships between population size and loss of genetic diversity: comparisons of experimental results with theoretical predictions. Conservation Genetics, 2000, 1(1): 33-43.

[4]Cervantes I, Meuwissen T H E. Maximization of total genetic variance in breed conservation programmes. Journal of Animal Breeding and Genetics, 2011, 128(6): 465-472.

[5]Food and Agriculture Organization of the United Nations. The State of the World’s Animal Genetic Resources for Food and Agriculture. Guidelines for the Development of Country Reports, 2007.

[6]吴常信. 畜禽遗传资源保存的理论与技术. 家畜生态, 2001, 22(1): 1-4.

Wu C X. Theory and technology of preservation in domestic animal genetic resources. Ecology of Domestic Animal, 2001, 22(1): 1-4. (in Chinese)

[7]何保丽, 鲁绍雄, 连林生. Monte Carlo模拟方法在动物育种中的应用. 黄牛杂志, 2005, 31(4): 43-47.

He B L, Lu S X, Lian L S. Application of Monte Carlo simulation in animal breeding. Journal of yellow cattle science, 2005, 31(4): 43-47. (in Chinese)

[8]王建成, 胡晋, 黄歆贤, 徐盛春. 蒙特卡洛模拟在种质资源研究中的应用探讨. 种子, 2009, 28(1): 59-62.

Wang J C, Hu J, Huang X X, Xu S C. Application of Monte Carlo simulation on germplasm resource research. Seed, 2009, 28(1): 59-62. (in Chinese)

[9]Fraser A S. Simulation of genetic systems by automatic digital computers. I. Introduction. II. Effects of linkage on rates of advance under selection. Australian Journal of Biology Science, 1957, 10: 484-499.

[10]MacCluer J W, Vandeberg J L, Read B, Ryder O A. Pedigree analysis by computer-simulation. Zoo Biology, 1986, 5(2): 147-160.

[11]吴克亮, 吴常信, 杨长锁. 畜禽遗传资源保存的计算机模拟研究. 畜牧兽医学报, 1992, 23(3): 207-212.

Wu K L, Wu C X, Yang C S. Computer simulation on conservation of domestic animal genetic resource. Avta Veterinaria et Zootechnica Sinica, 1992, 23(3): 207-212. (in Chinese)

[12]杨安平, 尚丽蓉, 刘晓宁. 种质资源世代更替中基因漂变的计算机模拟. 杨凌职业技术学院学报, 2003, 2(1): 26-29.

Yang A P, Sang L R, Liu X N. Computer simulation of gene drift in genetic resources during the generation alternations. Journal of Yangling Vocational and Technical College, 2003, 2(1): 26-29. (in Chinese)

[13]Shriver M D, Jin L, Chakraborty R, Boerwinkle E. VNTR Allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics, 1993, 134: 983-993.

[14]Goldstein D B, Linares A R, Cavalli-Sforzaf L L, Feldman M W. An evaluation of genetic distances for use with microsatellite loci. Genetics, 1995, 139: 463-471.

[15]Fernandez J, Toro M A, Caballero A. Managing individual’s contributions to maximize the allelic diversity maintained in small, conserved population. Conservation Biology, 2004, 18: 1358-1367.

[16]Peng B, Kimmel M. Simulations provide support for the common disease-common variant hypothesis. Genetics, 2007, 175(2): 763-776.

[17]van Oosterhout C, Joyce D A, Cummings S M, Blais J, Barson N J, Ramnarine I W, Mohammed R S, Persad N, Cable J. Balancing selection, random genetic drift, and genetic variation at the major histocompatibility complex in two wild population of guppies (Poecilla reticulate). Evolution, 2006, 60(12): 2562-2574.

[18]Epperson B K, Mcrae B H, Scribner K, Cushman S A, Rosenberg M S, Fortin M J, James P M A, Murphy M, Manel S, Legendre P, Dale M R T. Utility of computer simulations in landscape genetics. Molecular Ecology, 2010, 19(17): 3549-3564.

[19]Gowe R S, Robertson A, Latter B D H. Environment and poultry breeding problems. 5. The design of poultry control strains. Poultry Science, 1959, 38(2): 462-471.

[20]吴常信. 动物遗传学. 北京: 高等教育出版社, 2009: 383.

Wu C X. Animal Genetics. Beijing: Higher Education Press, 2009: 383. (in Chinese)

[21]张勤. 动物遗传育种中的计算方法. 北京: 科学出版社, 2007: 125-127.

Zhang Q. Calculation Methods for Animal Genetic and Breeding. Beijing: Science Press, 2007: 125-127. (in Chinese)

[22]Ayala F J, Powell J R, Tracey M L, Mourão C A, Pérez-Salas S. Enzyme variability in the Drosophilla willistoni group. IV. Genic variation in natural populations of Drosophila willistoni. Genetics, 1972, 70: 113-139.

[23]Yeh F C, EI-Kassaby Y A. Enzyme variation in natural populations of Sitka spruce (Piceasitchensis). 1. Genetic variation patterns among trees from 10 IUFRO provenances. Canadian Journal of Forest Research, 1980, 10(3): 415-422.

[24]Nei M. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America, 1973, 70(12): 3321-3323.

[25]Nei M. Estimation of average heterozygosity and genetic distance from a small number of individual. Genetics, 1978, 89(3): 583-590.

[26]Allendorf F W. Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology, 1986, 5(2): 181-190.

[27]Chakraborty R, Fuers P S, Nei M. Statistical studies on protein polymorphism in natural populations. III. Distribution of allele frequencies and the number of alleles per locus. Genetics, 1980, 94(4): 1039-1063.

[28]鲁绍雄, 毛华明, 鲁立刚, 连林生. 随机留种下闭锁群体近交系数和基因杂合度的世代变化. 中国畜牧兽医, 2010, 37(5): 151-156.

Lu S X, Mao H M, Lu L G, Lian L S. Changes of inbreeding coefficient and genic heterozygosity in closed population under random selection. China Animal Husbandry and Veterinary Medicine, 2010, 37(5): 151-156. (in Chinese)

[29]Falconer D S, Mackay T F C. Introduction to Quantitative Genetics. 4th ed., Essex, UK: Longman, 1996: 82-86.

[30]Oldenbroek K. Utilization and Conservation of Farm Animal Genetic Resources. Wageningen, NL: Wageningen Academic Press, 2007: 103-130.

[31]Food and Agriculture Organization of the United Nations. Secondary guidelines for development of national farm animal genetic resources management plans. Management of small populations at risk. Food and Agriculture Organization of the United Nations, 1998. http://dad.fao.org/en/refer/library/guidelin/sml-popn.pdf.

[32]Leroy G. Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses. The Veterinary Journal, 2011, 189(2): 177-182.

[33]Marshall D R, Brown A H D. Optimum Sampling Strategies in Genetic Conservation. Cambridge, UK: Cambridge University Press, 1975: 53-80.

[34]Kaljund K, Jaaska V. No loss of genetic diversity in small and isolated populations of Medicago sativa subsp. Falcate. Biochemical Systematics and Ecology, 2010, 38: 510-520.

[35]Ebrahimi A, Fatahi R, Zamani Z. Analysis of genetic diversity among some Persian walnut genotypes (Juglans regia L.) using morphological traits and SSRs markers. Scientia Horticulturae, 2011, 130(1): 146-151.

[36]Song N, Nwafili S A, Gao T X. Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis. Biochemical Systematics and Ecology, 2011, 39(4/6): 320-327.

[37]Kitada S, Shishidou H, Sugaya T, Kitakado T, Hamasaki K, Kishino H. Genetic effects of long-term stock enhancement programs. Aquaculture, 2009, 290(1/2): 69-79.

[38]Montgomery M E, Woodworth L M, Nurthen R K, Gilligan D M, Briscoe D A, Frankham R. Relationships between population size and loss of genetic diversity: comparisons of experimental results with theoretical predictions. Conservation Genetics, 2000, 1(1): 33-43.

[39]王成树, 李增智. 分子数据的遗传多样性分析方法. 安徽农业大学学报, 2002, 29(1): 90-94.

Wang C S, Li Z Z. Analysis method of genetic diversity using molecular data. Journal of Anhui Aagricultural University, 2002, 29(1): 90-94. (in Chinese)

[40]Nei M, Maruyama T, Chakraborty R. The bottleneck effect and genetic variability in populations. Evolution, 1975, 29(1): 1-10.

[41]Leberg P L. Effects of population bottlenecks on genetic diversity as measured by allozyme electrophoresis. Evolution, 1992, 46(2): 477-494.

[42]Barker J S F. Conservation and management of genetic diversity: a domestic animal perspective. Canadian Journal of Forest Research, 2001, 31(4): 588-595.

[43]Zeng Z B, Cockerham C C. Long-term response to artificial selection with multiple alleles-study by simulations. Theoretical Population Biology, 1990, 37(1): 254-272.

[44]Ayala F J, Kiger J A Jr. Modern Genetics. 2nd ed. California: The Benjamin—Cummings Publishing Company, 1984: 800-850.

[45]Qian W, Ge S, Hong D Y. Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theoretical and Applied Genetics, 2001, 102(2/3): 440-449.

[46]徐玲玲, 岳敏, 吴艳花, 顾为望, 陈振文. 西藏小型猪群体遗传结构分析.中国比较医学杂志, 2009, 19(2): 26-31.

Xu L L, Yue M, Wu Y H, Gu W W, Chen Z W. A population genetic diversity analysis of Tibet minipigs. Chinese Journal of Comparative Medicine, 2009, 19(2): 26-31. (in Chinese)

[47]乔利英, 袁亚男. 微卫星标记遗传多样性的度量指标及影响因素. 中国畜牧兽医, 2010, 37(1): 107-112.

Qiao L Y, Yuan Y N. The measurement indices and influencing factors of microsatellite polymorphisms. China Animal Husbandry and Veterinary Medicine, 2010, 37(1): 107-112. (in Chinese)

[48]Armbruster G, Pfenninger M. Simulated bottlenecks and loss of rare alleles: implications on the conservation genetics of two gastropod species. Journal for Nature Conservation, 2003, 11(2): 77-81.

[49]张胜利, 吴常信. 长期指数选择的遗传效果分析-计算机模拟研究. 遗传学报, 1992, 19(3): 203-211.

Zhang S L, Wu C X. Genetic effect analysis of long-term index selection-computer simulation study. Acta Genetica Sinica, 1992, 19(3): 203-211. (in Chinese)

[50]鲁绍雄, 毛华明, 鲁立刚, 严达伟, 苟潇, 连林生. 不同初始基因频率下闭锁群体遗传漂变的模拟. 江苏农业学报, 2009, 25(5): 991-996.

Lu S X, Mao H M, Lu L G, Yan D W, Gou X, Lian L S. Simulation of genetic drift in closed population under different initial gene frequencies. Jiangsu Journal.of Agricultural Science, 2009, 25(5): 991-996. (in Chinese)

[51]李来祥, 黄乾, 徐成, 段炳志. Monte Carlo模拟在农业综合开发项目风险评价中的应用研究. 安徽农业科学, 2008, 36(8): 3055-3056.

Li L X, Huang Q, Xu C, Duan B Z. Application of Mente Carlo stimulation in risk evaluation of agricultural comprehensive exploration project. Journal of Anhui Agricultural Science, 2008, 36(8): 3055-3056. (in Chinese)

[52]Leroy G, Baumung R. Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding. Animal Genetics, 2010, 42(1): 66-74.

[53]Soulé M E, Gilpin M, Conway W, Foose T. The millennium ark: how long a voyage, how many staterooms, how many passengers? Zoo Biology, 1986, 5(2): 101-113.