基于简化基因组测序评价太湖鹅不同保种场的保种效果
|
摘要
旨在评价太湖鹅原种场和国家水禽基因库的保种效果,为进一步更好地对太湖鹅进行保种打下理论依据。利用ddRAD简化基因组测序方法鉴定太湖鹅原始群体(TS)、原种场群体(TC)和基因库群体(TK)的SNP标记,比较分析3个群体的遗传多样性差异,并使用遗传分化系数FST和核苷酸多样性π比值联合筛选选择信号区域及其相关基因,对得到的受选基因进行GO和KEGG功能富集分析。结果发现,与原始群体相比,原种场群体和基因库群体的遗传杂合度均有降低,近交系数上升,且基因库群体与原始群体、原种场群体有中度分化的趋势。原种场群体的脂类代谢相关基因受到了一定程度的选择。结果表明,原种场群体和基因库群体应适当增加保种群数量,避免近交系数上升过快,且基因库群体应加强与原种场群体的基因交流,避免与原始群体、原种场群体的过度分化。
The object of this study was to evaluate the conservation effect of Taihu Goose stock farm and national waterfowl gene bank,and to lay a theoretical foundation for further conservation of Taihu Goose. The simplified genomic sequencing method,ddRAD,was used to identify the SNP markers of the original population(TS),the stock farm population(TC) and the national waterfowl gene bank population(TK) of Taihu Goose. The genetic diversity of the three populations were compared and analyzed. The selected signals and their related genes were screened by using the genetic differentiation coefficient FSTand the ratio of nucleotide diversity(π),and the selected genes were analyzed by functional enrichment methods,such as GO and KEGG. The results showed that compared with the original population,the genetic heterozygosity of TC and TK populations decreased,and the inbreeding coefficient increased. Further more,TK population had a trend of moderate differentiation from the TS and TK populations. The genes related to lipid metabolism in TC population had been selected to some extent. The results indicated that individuals of TC and TK populations should be properly increased to avoid fast increasing of inbreeding coefficient. And TK population should strengthen the gene exchange with TS population,so as to avoid the excessive differentiation with the TS and TC populations.
The object of this study was to evaluate the conservation effect of Taihu Goose stock farm and national waterfowl gene bank,and to lay a theoretical foundation for further conservation of Taihu Goose. The simplified genomic sequencing method,ddRAD,was used to identify the SNP markers of the original population(TS),the stock farm population(TC) and the national waterfowl gene bank population(TK) of Taihu Goose. The genetic diversity of the three populations were compared and analyzed. The selected signals and their related genes were screened by using the genetic differentiation coefficient FSTand the ratio of nucleotide diversity(π),and the selected genes were analyzed by functional enrichment methods,such as GO and KEGG. The results showed that compared with the original population,the genetic heterozygosity of TC and TK populations decreased,and the inbreeding coefficient increased. Further more,TK population had a trend of moderate differentiation from the TS and TK populations. The genes related to lipid metabolism in TC population had been selected to some extent. The results indicated that individuals of TC and TK populations should be properly increased to avoid fast increasing of inbreeding coefficient. And TK population should strengthen the gene exchange with TS population,so as to avoid the excessive differentiation with the TS and TC populations.
引文
[1] Pan Y E,Wang X E,Sun G L,et al. Application of RAD sequencing for evaluating the genetic diversity of domesticated panax notoginseng(araliaceae)[J]. PLo S One,2016,11(11):0166419.
[2] Valdisser P R,Pappas G J,Menezes I D,et al. SNP dis-covery in common bean by restriction-associated DNA(RAD)sequencing for genetic diversity and population structure analysis[J]. Molecular Genetics and Genomics,2016,291(3):1277-1291.
[3]王洋坤,胡艳,张天真. RAD-seq技术在基因组研究中的现状及展望[J].遗传,2014,36(1):41-49.
[4]赵纪萍.基于RAD测序技术的6个中国家兔地方品种的遗传地位研究[D].杨凌:西北农林科技大学,2017.
[5]翟正晓.基于RAD简化基因组测序技术的13种中国地方优良鸡品种SNPs多态性图谱构建及群体遗传学分析[D].上海:上海交通大学,2014.
[6]段修军,董飚,孙国波,等.基于酶切的简化基因组测序在水禽品种进化关系研究中的应用[J].西北农业学报,2015,24(1):13-17.
[7] Mckenna A,Hanna M,Banks E,et al. The genome analysis toolkit:a MapReduce framework for analyzing nextgeneration DNA sequencing data[J]. Genome Research,2010,20(9):1297-1303.
[8] Li H,Handsaker B,Wysoker A,et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[9] See L M,Hassan R,Tan S G,et al. POPGENE,the user-friendly shareware for population genetic analysis[J].Biotechnology,2006,7(2):104-110.
[10] Alexander D H,Novembre J,Lange K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research,2009,19(9):1655-1664.
[11]薛辉,吴孝兵,晏鹏.微卫星标记在分子生态学中的应用及其位点的分离策略[J].应用生态学报,2005,16(2):385-389.
[12]陈红菊,岳永生,樊新忠,等.山东地方鸡种遗传距离与聚类分析方法比较研究[J].畜牧兽医学报,2004,35(1):33-36.
[13]朱文奇,李慧芳,宋卫涛,等.基于线粒体DNA D-loop区序列的我国灰鹅遗传多样性和起源分析[J].生态学杂志,2010,29(3):549-553.
[14]李慧芳,屠云洁,汤青萍,等. 6个中国重点保护地方鹅品种的遗传多样性[J].四川农业大学学报,2005,23(4):466-469.
[15] Randi E,Lucchini V. Organization and evolution of the mitochondrial DNA control region in the avian Genus alectoris[J]. Journal of Molecular Evolution,1998,47(4):449-462.
[16]宋春红,陈红菊,马月辉,等.中国6个地方鸡品种的母系起源[J].畜牧兽医学报,2007,38(7):735-740.
[17]龚道清,张红,张军,等.运用微卫星标记分析11个鸭种(群)的亲缘关系[J].畜牧兽医学报,2005,36(12):1256-1260.
[18]吉文林,钱凯,李慧芳,等.国家水禽基因库七个家鸭群体遗传多样性检测[J].中国家禽,2006,28(24):72-74.
[19]汤青萍,李慧芳,屠云洁,等.中国重点保护地方鸭品种资源的多样性分析[J].西北农林科技大学学报:自然科学版,2007,35(2):47-52.
[20]刘宏祥,王宝维,宋卫涛,等.马踏湖鸭群体遗传结构探讨[J].中国家禽,2015,37(3):57-59.
[21]汤青萍,章双杰,郭军,等.太湖鹅群体遗传多样性研究[J].家畜生态学报,2010,31(1):30-33.
[22]段修军,董飚,王日君,等.太湖鹅微卫星标记与体重的相关性[J].江苏农业学报,2011,27(3):597-601.
[23]王洪志,李国辉,张贤,等.基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状[J].畜牧兽医学报,2017,48(5):818-825.
[24]王得前,陈国宏,吴信生,等.运用微卫星技术分析中国地方鸡品种的亲缘关系[J].扬州大学学报:农业与生命科学版,2003,24(2):1-6.
[25]李慧芳,陈宽维,汤青萍,等.利用微卫星标记分析云南6个地方鸡品种的遗传多样性[J].江苏农业学报,2006,26(1):33-37.
[26]吴兆林,高玉时,童海兵.鹿苑鸡微卫星和AFLP指纹分析[J].中国家禽,2005,9(S):83-85.
[27] Wright S. Evolution and the genetics of populations,Volume 4:variability within and among natural population[M]. Chicago:University of Chicago Press,1978.
[28]赵振华,黎寿丰,吴兆林,等.不同保种方法对地方鸡种的保种效果分析[J].中国家禽,2009,31(14):23-25.
[2] Valdisser P R,Pappas G J,Menezes I D,et al. SNP dis-covery in common bean by restriction-associated DNA(RAD)sequencing for genetic diversity and population structure analysis[J]. Molecular Genetics and Genomics,2016,291(3):1277-1291.
[3]王洋坤,胡艳,张天真. RAD-seq技术在基因组研究中的现状及展望[J].遗传,2014,36(1):41-49.
[4]赵纪萍.基于RAD测序技术的6个中国家兔地方品种的遗传地位研究[D].杨凌:西北农林科技大学,2017.
[5]翟正晓.基于RAD简化基因组测序技术的13种中国地方优良鸡品种SNPs多态性图谱构建及群体遗传学分析[D].上海:上海交通大学,2014.
[6]段修军,董飚,孙国波,等.基于酶切的简化基因组测序在水禽品种进化关系研究中的应用[J].西北农业学报,2015,24(1):13-17.
[7] Mckenna A,Hanna M,Banks E,et al. The genome analysis toolkit:a MapReduce framework for analyzing nextgeneration DNA sequencing data[J]. Genome Research,2010,20(9):1297-1303.
[8] Li H,Handsaker B,Wysoker A,et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[9] See L M,Hassan R,Tan S G,et al. POPGENE,the user-friendly shareware for population genetic analysis[J].Biotechnology,2006,7(2):104-110.
[10] Alexander D H,Novembre J,Lange K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research,2009,19(9):1655-1664.
[11]薛辉,吴孝兵,晏鹏.微卫星标记在分子生态学中的应用及其位点的分离策略[J].应用生态学报,2005,16(2):385-389.
[12]陈红菊,岳永生,樊新忠,等.山东地方鸡种遗传距离与聚类分析方法比较研究[J].畜牧兽医学报,2004,35(1):33-36.
[13]朱文奇,李慧芳,宋卫涛,等.基于线粒体DNA D-loop区序列的我国灰鹅遗传多样性和起源分析[J].生态学杂志,2010,29(3):549-553.
[14]李慧芳,屠云洁,汤青萍,等. 6个中国重点保护地方鹅品种的遗传多样性[J].四川农业大学学报,2005,23(4):466-469.
[15] Randi E,Lucchini V. Organization and evolution of the mitochondrial DNA control region in the avian Genus alectoris[J]. Journal of Molecular Evolution,1998,47(4):449-462.
[16]宋春红,陈红菊,马月辉,等.中国6个地方鸡品种的母系起源[J].畜牧兽医学报,2007,38(7):735-740.
[17]龚道清,张红,张军,等.运用微卫星标记分析11个鸭种(群)的亲缘关系[J].畜牧兽医学报,2005,36(12):1256-1260.
[18]吉文林,钱凯,李慧芳,等.国家水禽基因库七个家鸭群体遗传多样性检测[J].中国家禽,2006,28(24):72-74.
[19]汤青萍,李慧芳,屠云洁,等.中国重点保护地方鸭品种资源的多样性分析[J].西北农林科技大学学报:自然科学版,2007,35(2):47-52.
[20]刘宏祥,王宝维,宋卫涛,等.马踏湖鸭群体遗传结构探讨[J].中国家禽,2015,37(3):57-59.
[21]汤青萍,章双杰,郭军,等.太湖鹅群体遗传多样性研究[J].家畜生态学报,2010,31(1):30-33.
[22]段修军,董飚,王日君,等.太湖鹅微卫星标记与体重的相关性[J].江苏农业学报,2011,27(3):597-601.
[23]王洪志,李国辉,张贤,等.基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状[J].畜牧兽医学报,2017,48(5):818-825.
[24]王得前,陈国宏,吴信生,等.运用微卫星技术分析中国地方鸡品种的亲缘关系[J].扬州大学学报:农业与生命科学版,2003,24(2):1-6.
[25]李慧芳,陈宽维,汤青萍,等.利用微卫星标记分析云南6个地方鸡品种的遗传多样性[J].江苏农业学报,2006,26(1):33-37.
[26]吴兆林,高玉时,童海兵.鹿苑鸡微卫星和AFLP指纹分析[J].中国家禽,2005,9(S):83-85.
[27] Wright S. Evolution and the genetics of populations,Volume 4:variability within and among natural population[M]. Chicago:University of Chicago Press,1978.
[28]赵振华,黎寿丰,吴兆林,等.不同保种方法对地方鸡种的保种效果分析[J].中国家禽,2009,31(14):23-25.