广西稻田养殖金边鲤群体遗传多样性分析
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摘要
为了解广西稻田养殖金边鲤群体的遗传多样性现状,本研究利用10个高度多态微卫星标记,以野生太湖鲤和黑龙江鲤群体,池塘养殖福瑞鲤、兴国红鲤、建鲤群体,广西稻田养殖晒江鲤群体作对照,共7个鲤鱼群体进行群体遗传结构分析。试验结果显示,10个位点共检测到242个等位基因,每个群体的平均等位基因数、期望杂合度、观测杂合度和多态信息含量分别为6～16、0.736～0.900、0.620～0.800和0.689～0.878。9个位点在7个鲤鱼群体中的等位基因频率显著偏离哈迪—温伯格平衡(P<0.05),7个鲤鱼群体遗传多样性丰度由高到低顺序为太湖鲤、黑龙江鲤、建鲤、晒江鲤、福瑞鲤、金边鲤、兴国红鲤。所有群体的遗传分化系数值为0.015～0.141,表明7个鲤鱼群体间存在不同程度的遗传分化,其中金边鲤群体与野生和池塘养殖群体间遗传分化均达中等程度。AMOVA分析显示,群体间的遗传分化占7.15%,而群体内的遗传分化占92.85%,表明鲤鱼群体主要的遗传分化来自于群体内部。7个鲤鱼群体间的遗传距离为0.286～0.977,根据Nei′s遗传距离所绘制的聚类图显示,7个鲤鱼群体被划分为4大支,贝叶斯分析结果与聚类结果相似,其中两个稻田鲤群体遗传结构相似聚为一类。本研究是对金边鲤遗传背景的初探,试验结果表明,金边鲤群体具有较高的遗传多样性和进一步选育的潜力。本研究结果可为稻田养殖鲤品种的选育和遗传改良提供基础遗传学信息。
In this study, genetic diversity and population structure were investigated in 224 samples of 7 strains of common carp including two wild populations(Heilongjiang carp Cyprinus carpio haematoperus, Taihu carp), three pond cultured strains(FFRC strain of common carp C. carpio var. FFRC, Xingguo red carp C. carpio var. singuonensis, Jian carp C. carpio var. jian and two populations(Jinbian carp C. carpio var. Jinbian and Shaijiang carp C. carpio) farmed in rice field by 10 highly polymorphic microsatellite markers to comprehend the genetic information on the local variety of paddy field Jinbian carp in Guangxi. A total of 242 different alleles were detected, with mean number of alleles per population ranging from 6 to 16, mean expected heterozygosity from 0.736 to 0.900 and observed heterozygosity ranging from 0.620 to 0.800. The mean value of polymorphism information content was ranged from 0.689 to 0.878, and nine microsatellite loci were found to deviate significantly(P<0.05) from the Hardy-Weinberg equilibrium after Bonferroni correction in 7 populations. As a whole, the descending order of genetic diversity of 7 common carp populations was expressed as Taihu carp, Heilong river carp, Jian carp, Shaijiang carp, FFRC strain common carp, Jinbian carp and Xingguo red carp, with genetic differentiation coefficient varying from 0.015 to 0.141, indicating that the different degrees of genetic differentiation among the seven populations and the genetic differentiation between Jinbian carp population with the other else populations was medium except Shaijiang carp population. Global analysis of hierarchical gene diversity further revealed that the total genetic variation among populations was 7.15%, whilst variation within populations was estimated to be 92.85%, which showed that the majority of total microsatellite loci variation was appeared to be within populations. The genetic distance among the seven populations was ranged from 0.286 to 0.977, and the phylogenetic tree was constructed based on Nei's standard genetic distance, and the UPGMA algorithm grouped the 7 populations into four major clusters. Bayesian analysis also indicated that these seven common carp populations were clustered into four groups, the two rice field breeding populations being divided into one of the clusters. These findings indicated that Jinbian carp variety paddy field carp population showed a high level of genetic diversity and had some potential for further selective breeding, which provides basic genetic information for breeding and genetic improvement of the new varieties of common carp in paddy fields.
In this study, genetic diversity and population structure were investigated in 224 samples of 7 strains of common carp including two wild populations(Heilongjiang carp Cyprinus carpio haematoperus, Taihu carp), three pond cultured strains(FFRC strain of common carp C. carpio var. FFRC, Xingguo red carp C. carpio var. singuonensis, Jian carp C. carpio var. jian and two populations(Jinbian carp C. carpio var. Jinbian and Shaijiang carp C. carpio) farmed in rice field by 10 highly polymorphic microsatellite markers to comprehend the genetic information on the local variety of paddy field Jinbian carp in Guangxi. A total of 242 different alleles were detected, with mean number of alleles per population ranging from 6 to 16, mean expected heterozygosity from 0.736 to 0.900 and observed heterozygosity ranging from 0.620 to 0.800. The mean value of polymorphism information content was ranged from 0.689 to 0.878, and nine microsatellite loci were found to deviate significantly(P<0.05) from the Hardy-Weinberg equilibrium after Bonferroni correction in 7 populations. As a whole, the descending order of genetic diversity of 7 common carp populations was expressed as Taihu carp, Heilong river carp, Jian carp, Shaijiang carp, FFRC strain common carp, Jinbian carp and Xingguo red carp, with genetic differentiation coefficient varying from 0.015 to 0.141, indicating that the different degrees of genetic differentiation among the seven populations and the genetic differentiation between Jinbian carp population with the other else populations was medium except Shaijiang carp population. Global analysis of hierarchical gene diversity further revealed that the total genetic variation among populations was 7.15%, whilst variation within populations was estimated to be 92.85%, which showed that the majority of total microsatellite loci variation was appeared to be within populations. The genetic distance among the seven populations was ranged from 0.286 to 0.977, and the phylogenetic tree was constructed based on Nei's standard genetic distance, and the UPGMA algorithm grouped the 7 populations into four major clusters. Bayesian analysis also indicated that these seven common carp populations were clustered into four groups, the two rice field breeding populations being divided into one of the clusters. These findings indicated that Jinbian carp variety paddy field carp population showed a high level of genetic diversity and had some potential for further selective breeding, which provides basic genetic information for breeding and genetic improvement of the new varieties of common carp in paddy fields.
引文
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[37] 李建林,李红霞,唐永凯,等.利用微卫星标记分析6个鲤鱼群体的遗传差异[J].福建农业学报,2012,27(9):936-940.
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[2] Ye X,Lv Y,Wei L,et al.The complete mitochondrial genome of Jinbian carp Cyprinus carpio (Cypriniformes:Cyprinidae)[J].Mitochondrial DNA Part B,2018,3(2):1096-1097.
[3] Zheng X,Kuang Y,Lv W,et al.A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits [J].Science China Life Sciences,2013,56(4):351-359.
[4] Yang C,Zhu X,Sun X.Development of microsatellite markers and their utilization in genetic diversity analysis of cultivated and wild populations of the mud carp (Cirrhina molitorella)[J].Journal of Genetics & Genomics,2008,35(4):201-206.
[5] 顾颖,李超,鲁翠云,等.建鲤(Cyprinus carpio var.jian)微卫星DNA亲权鉴定[J].遗传,2012,34(11):1447-1455.
[6] 顾颖,鲁翠云,张晓峰,等.建鲤生长性状QTL区间及其与镜鲤同源性比对[J].中国水产科学,2013,20(6):1148-1156.
[7] Perezenriquez R,Takagi M,Taniguchi N.Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement,based on microsatellite DNA markers [J].Aquaculture,1999,173(1/4):413-423.
[8] 杜晓东,高远镇,邓岳文,等.利用微卫星标记进行马氏珠母贝家系遗传结构分析与系谱认证[J].水产学报,2011,35(12):1795-1804.
[9] Dou Y,Liang X,Yang M,et al.Isolation and characterization of polymorphic EST-SSR and genomic SSR markers in spotted mandarin fish (Siniperca scherzeri Steindachne) [J].Genetics and Molecular Research,2015,14(4):19317-19322.
[10] Sambrook J,Russell D.Molecular cloning:a laboratory manual [M].New York:Cold Spring Harbor Laboratory Press,2001.
[11] Nei M,Li W H.Mathematical model for studying genetic variation in terms of restriction endonucleases[J].Proceedings of the National Academy of Sciences,1979,76(10):5269-5273.
[12] Tamura K,Dudley J,Nei M,et al.MEGA4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0[J].Molecular Biology and Evolution,2007,24(8):1596.
[13] Excoffier L,Laval G,Schneider S.Arlequin (version 3.0):an integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics,2005,1(4A):47-50.
[14] Rice W R.Analyzing tables of statistical tests[J].Evolution,1989,43(1):223-225.
[15] Excoffier L,Smouse P E,Quattro J M.Analysis of molecular variance inferred from metric distances among DNA haplotypes:application to human mitochondrial DNA restriction data [J].Genetics,1992,131(2):479-491.
[16] Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data [J].Genetics,2000,155(2):945-959.
[17] Falush D,Stephens M,Pritchard J K.Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies [J].Genetics,2003,164(4):1567-1587.
[18] 李鸥,赵莹莹,郭娜,等.草鱼种群SSR分析中样本量及标记数量对遗传多度的影响[J].动物学研究,2009,30(2):121-130.
[19] 戴习林,刘洁,李晶晶,等.罗氏沼虾种群SSR分析中样本量及标记量对遗传多样性指标的影响[J].水产学报,2017,41(7):1083-1095.
[20] Brenner S,Elgar G,Sandford R,et al.Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome[J].Nature,1993,366(6452):265-268.
[21] Gastier J M,Pulido J C,Sunden S,et al.Survey of trinucleotide repeats in the human genome:assessment of their utility as genetic markers [J].Human Molecular Genetics,1995,4(10):1829-1836.
[22] Jmh K,Thomas M R,Jcs F,et al.Integration of trinucleotide microsatellites into a linkage map of Citrus[J].Theoretical & Applied Genetics,1997,94(5):701-706.
[23] Ma Z Q,R?der M,Sorrells M E.Frequencies and sequence characteristics of di-,tri-,and tetra-nucleotide microsatellites in wheat[J].Genome,1996,39(1):123-130.
[24] 鲁翠云,张晓丽,顾颖,等.福瑞鲤与豫选黄河鲤选育群体的遗传结构及亲本间遗传距离分布[J].中国水产科学,2016,23(5):1091-1098.
[25] 曾繁振,俞小牧,童金苟.三个鲤品种微卫星丰度与遗传多样性分析[J].水生生物学报,2013,37(5):967-973.
[26] Li D,Kang D,Yin Q,et al.Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinus carpio L.) populations[J].Journal of Genetics and Genomics,2007,34(11):984-993.
[27] 鲁翠云,全迎春,李大宇,等.用鲤鱼EST-SSRs分子标记分析长江黑龙江鲤种群结构[J].农业生物技术学报,2007,15(6):947-952.
[28] Feng L,Xia J H,Bai Z Y,et al.High genetic diversity and substantial population differentiation in grass carp (Ctenopharyngodon idella) revealed by microsatellite analysis[J].Aquaculture,2009,297(1):51-56.
[29] Sun X,Lu C,Liang L.Isolation of microsatellite with enrichment by magnetic beads in grass carp,Ctenopharyngodon idella[J].Journal of Fisheries of China,2005,29(4):482-486.
[30] Ellis J R,Burke J M.EST-SSRs as a resource for population genetic analyses[J].Heredity,2007,99(2):125.
[31] Eujayl I,Sorrells M E,Baum M,et al.Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs [J].Euphytica,2001,119(1/2):39-43.
[32] Eujayl I,Sorrells M E,Baum M,et al.Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat [J].Theoretical and Applied Genetics,2002,104(2):399-407.
[33] Wren J D,Forgacs E,Rd F J,et al.Repeat polymorphisms within gene regions:phenotypic and evolutionary implications[J].American Journal of Human Genetics,2000,67(2):345-356.
[34] 李永强,李宏伟,高丽锋,等.基于表达序列标签的微卫星标记(EST-SSRs)研究进展[J].植物遗传资源学报,2004,5(1):91-95.
[35] Nei M.The bottleneck effect and genetic variability in populations[J].Evolution,1975,29(1):1-10.
[36] Beardmore J A,Mair G C,Lewis R I.Biodiversity in aquatic systems in relation to aquaculture[J].Aquaculture Research,1997,28(10):829-839.
[37] 李建林,李红霞,唐永凯,等.利用微卫星标记分析6个鲤鱼群体的遗传差异[J].福建农业学报,2012,27(9):936-940.
[38] Simmons M,Mickett K,Kucuktas H,et al.Comparison of domestic and wild channel catfish (Ictalurus punctatus) populations provides no evidence for genetic impact[J].Aquaculture,2006,252(2):133-146.
[39] Xu Z,Primacera J H,Penaena L D,et al.Genetic diversity of wild and cultured black tiger shrimp (Penaeus monodon) in the Philippines using microsatellites [J].Aquaculture,2001,199(1):13-40.
[40] Lind C E,Evans B S,Knauer J,et al.Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima)[J].Aquaculture,2009,286(1):12-19.
[41] 韩承慧,马海涛,姜海滨,等.许氏平鲉(Sebastes schlegeli)微卫星标记开发及野生、养殖群体遗传多样性分析[J].海洋与湖沼,2016,47(1):213-220.
[42] 卢彦先,狄明玉,李云峰,等.海蜇微卫星标记开发及自然、养殖群体遗传多样性分析[J].水产科学,2017,36(4):472-479.
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