Background: Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.Method: A set of 197 Gossypium arboreum acc...Background: Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.Method: A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis.Results: Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G.arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively.Conclusion: The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum.展开更多
Estimation of the size structure of a fish population is often one of the primary objectives of an acoustic/trawl survey.The methods of estimation may be different with different sampling strategies.This paper describ...Estimation of the size structure of a fish population is often one of the primary objectives of an acoustic/trawl survey.The methods of estimation may be different with different sampling strategies.This paper describes the main results as well as the methods used during the acoustic survey of anchovy in the Yellow Sea in February 1999,with emphasis on the estimation of the number at length and biomass at length of the anchovy population surveyed under adoptive sampling strategy.The estimation is done for each transect.Within each transect,the biological sample data is weighted by fish quantity derived from the acoustic density ( s A) of the echo signs that the biological sample represents.This method makes full use of the acoustic data available in a rigorous manner.It is essentially to estimate the size structure of each group of fish aggregation thought to having similar size composition.It is believed that this method may lead to a more accurate estimate of the size structure of a fish population surveyed under adoptive sampling strategy.展开更多
为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测...为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测序数据分析共筛选得到9752个高质量SNP标记用于后续研究;乌饭树5个群体均具有丰富的遗传多样性,平均有效等位基因数为1.523,平均期望杂合度为0.219,平均观测杂合度为0.231,其中江苏溧阳群体的遗传多样性最高。分子方差分析显示整个群体的遗传变异主要来自个体间(65.45%)。群体间遗传分化系数显示5个群体间遗传分化程度高,其中江苏溧阳与江西上犹群体间的遗传分化系数最高,为0.406。系统进化树(邻接法)显示乌饭树种质聚类为3个进化分支,种质的聚集与其地理来源无确定性关系;群体结构分析将乌饭树种质分为3个亚群,主成分分析结果与群体结构的结果类似,不同地区的乌饭树种质在3个亚群中均有分布,显示了乌饭树资源存在着广泛的基因交流。本研究可为今后乌饭树良种选育和资源保护提供参考。展开更多
旨在对西门塔尔牛群体遗传多样性和遗传结构进行分析,为配种方案和遗传改良提供理论依据。本研究对149头西门塔尔牛的全基因组进行了重测序,并利用这些基因组数据获取的高质量单核苷酸多态性(single-nucleotide polymorphisms,SNPs)位点...旨在对西门塔尔牛群体遗传多样性和遗传结构进行分析,为配种方案和遗传改良提供理论依据。本研究对149头西门塔尔牛的全基因组进行了重测序,并利用这些基因组数据获取的高质量单核苷酸多态性(single-nucleotide polymorphisms,SNPs)位点,对其遗传结构、连续纯合片段(runs of homozygosity,ROH)以及其亲缘关系和家系构建等方面进行了深入的分析。结果显示,149头西门塔尔牛平均测序深度为5×,质控后共鉴定到1265356个SNPs位点,平均最小等位基因频率为0.067,平均多态信息含量为0.083,平均观察杂合度为0.121,平均期望杂合度为0.157。亲缘关系G矩阵与状态同源(identical by state,IBS)遗传距离矩阵具有相似的结果,大部分个体间的亲缘关系呈中等水平。在149头西门塔尔牛个体中,共检测到70个基因组ROH,且ROH总长度为127627.935 kb,其中有98.57%的ROH是长度介于在1~5 Mb之间。基于ROH计算得到的近交系数为0.0003,提示近亲繁殖程度不高。此外,进化树分析将这149头西门塔尔牛划分成为22个不同的家系分支。综上所述,西门塔尔牛群体表现出相对丰富的多样性和适度的亲缘关系。在少数个体中观察到近亲繁殖,但种群的整体近亲繁殖水平仍然很低。展开更多
旨在深入了解武雪山羊的群体结构,探究种群内部的遗传变异与分化和种群间的遗传差异及地理分布特征,为该品种的种质资源利用与开发提供重要依据。本研究采集18只武雪山羊(WXG)、9只湘东黑山羊(XDB)、9只合川白山羊(HCW)、9只大足黑山羊(...旨在深入了解武雪山羊的群体结构,探究种群内部的遗传变异与分化和种群间的遗传差异及地理分布特征,为该品种的种质资源利用与开发提供重要依据。本研究采集18只武雪山羊(WXG)、9只湘东黑山羊(XDB)、9只合川白山羊(HCW)、9只大足黑山羊(DZB)、11只马关无角山羊(MGG)以及10只云岭山羊(YLG)的耳组织样本,用于全基因组重测序,平均测序深度约为10×。本研究基于全基因组数据分别利用GCTA、Plink、Admixture、Vcftools及PopLDdecay软件对6个群体进行了主成分分析、系统发育分析、群体遗传结构分析、杂合度分析、群体分化分析以及连锁不平衡分析。主成分分析的结果显示,武雪山羊与湘东黑山羊被聚为同一大类,表明这两个山羊品种遗传背景相似。系统进化分析的结果显示,武雪山羊与其他品种山羊群体单独聚为一支,在进化树上与湘东黑山羊的遗传距离较近。群体遗传结构分析的结果显示,当CV值最小时(K=3),武雪山羊与湘东黑山羊具有相同的遗传组分,说明两个群体间遗传分化指数程度较小,遗传背景相似。杂合度分析的结果显示,武雪山羊的核苷酸多态性(π)较低,观测杂合度(Ho)最低,且低于期望杂合度(He);ROH(runs of homozygosity)分析显示,武雪山羊的ROH数量和长度也明显高于其他品种,且基因组近交系数(F_(ROH))明显高于其他5个群体,这表明武雪山羊在基因组水平上存在明显的纯合片段积累和遗传多样性降低的现象。连锁不平衡分析的结果显示,武雪山羊表现出最高程度的连锁不平衡,进一步证实了该群体较低的遗传多样性。总之,这项研究系统解析了武雪山羊的遗传特性和群体结构,发现武雪山羊与湘东黑山羊遗传背景相似,其群体的遗传多样性较低,且存在一定的近交趋势,结果提示在后续的保种工作中需重点关注群体规模的扩大和近交系数的控制。这些发现不仅为深入了解其遗传背景提供了科学依据,同时为该品种的遗传资源保护与合理开发利用提供了重要理论参考。展开更多
基金supported by the National Natural Science Foundation of China Agriculture(Grant No.2015NWB039)
文摘Background: Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.Method: A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis.Results: Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G.arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively.Conclusion: The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum.
文摘Estimation of the size structure of a fish population is often one of the primary objectives of an acoustic/trawl survey.The methods of estimation may be different with different sampling strategies.This paper describes the main results as well as the methods used during the acoustic survey of anchovy in the Yellow Sea in February 1999,with emphasis on the estimation of the number at length and biomass at length of the anchovy population surveyed under adoptive sampling strategy.The estimation is done for each transect.Within each transect,the biological sample data is weighted by fish quantity derived from the acoustic density ( s A) of the echo signs that the biological sample represents.This method makes full use of the acoustic data available in a rigorous manner.It is essentially to estimate the size structure of each group of fish aggregation thought to having similar size composition.It is believed that this method may lead to a more accurate estimate of the size structure of a fish population surveyed under adoptive sampling strategy.
文摘为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测序数据分析共筛选得到9752个高质量SNP标记用于后续研究;乌饭树5个群体均具有丰富的遗传多样性,平均有效等位基因数为1.523,平均期望杂合度为0.219,平均观测杂合度为0.231,其中江苏溧阳群体的遗传多样性最高。分子方差分析显示整个群体的遗传变异主要来自个体间(65.45%)。群体间遗传分化系数显示5个群体间遗传分化程度高,其中江苏溧阳与江西上犹群体间的遗传分化系数最高,为0.406。系统进化树(邻接法)显示乌饭树种质聚类为3个进化分支,种质的聚集与其地理来源无确定性关系;群体结构分析将乌饭树种质分为3个亚群,主成分分析结果与群体结构的结果类似,不同地区的乌饭树种质在3个亚群中均有分布,显示了乌饭树资源存在着广泛的基因交流。本研究可为今后乌饭树良种选育和资源保护提供参考。
文摘旨在对西门塔尔牛群体遗传多样性和遗传结构进行分析,为配种方案和遗传改良提供理论依据。本研究对149头西门塔尔牛的全基因组进行了重测序,并利用这些基因组数据获取的高质量单核苷酸多态性(single-nucleotide polymorphisms,SNPs)位点,对其遗传结构、连续纯合片段(runs of homozygosity,ROH)以及其亲缘关系和家系构建等方面进行了深入的分析。结果显示,149头西门塔尔牛平均测序深度为5×,质控后共鉴定到1265356个SNPs位点,平均最小等位基因频率为0.067,平均多态信息含量为0.083,平均观察杂合度为0.121,平均期望杂合度为0.157。亲缘关系G矩阵与状态同源(identical by state,IBS)遗传距离矩阵具有相似的结果,大部分个体间的亲缘关系呈中等水平。在149头西门塔尔牛个体中,共检测到70个基因组ROH,且ROH总长度为127627.935 kb,其中有98.57%的ROH是长度介于在1~5 Mb之间。基于ROH计算得到的近交系数为0.0003,提示近亲繁殖程度不高。此外,进化树分析将这149头西门塔尔牛划分成为22个不同的家系分支。综上所述,西门塔尔牛群体表现出相对丰富的多样性和适度的亲缘关系。在少数个体中观察到近亲繁殖,但种群的整体近亲繁殖水平仍然很低。
文摘旨在深入了解武雪山羊的群体结构,探究种群内部的遗传变异与分化和种群间的遗传差异及地理分布特征,为该品种的种质资源利用与开发提供重要依据。本研究采集18只武雪山羊(WXG)、9只湘东黑山羊(XDB)、9只合川白山羊(HCW)、9只大足黑山羊(DZB)、11只马关无角山羊(MGG)以及10只云岭山羊(YLG)的耳组织样本,用于全基因组重测序,平均测序深度约为10×。本研究基于全基因组数据分别利用GCTA、Plink、Admixture、Vcftools及PopLDdecay软件对6个群体进行了主成分分析、系统发育分析、群体遗传结构分析、杂合度分析、群体分化分析以及连锁不平衡分析。主成分分析的结果显示,武雪山羊与湘东黑山羊被聚为同一大类,表明这两个山羊品种遗传背景相似。系统进化分析的结果显示,武雪山羊与其他品种山羊群体单独聚为一支,在进化树上与湘东黑山羊的遗传距离较近。群体遗传结构分析的结果显示,当CV值最小时(K=3),武雪山羊与湘东黑山羊具有相同的遗传组分,说明两个群体间遗传分化指数程度较小,遗传背景相似。杂合度分析的结果显示,武雪山羊的核苷酸多态性(π)较低,观测杂合度(Ho)最低,且低于期望杂合度(He);ROH(runs of homozygosity)分析显示,武雪山羊的ROH数量和长度也明显高于其他品种,且基因组近交系数(F_(ROH))明显高于其他5个群体,这表明武雪山羊在基因组水平上存在明显的纯合片段积累和遗传多样性降低的现象。连锁不平衡分析的结果显示,武雪山羊表现出最高程度的连锁不平衡,进一步证实了该群体较低的遗传多样性。总之,这项研究系统解析了武雪山羊的遗传特性和群体结构,发现武雪山羊与湘东黑山羊遗传背景相似,其群体的遗传多样性较低,且存在一定的近交趋势,结果提示在后续的保种工作中需重点关注群体规模的扩大和近交系数的控制。这些发现不仅为深入了解其遗传背景提供了科学依据,同时为该品种的遗传资源保护与合理开发利用提供了重要理论参考。
