在中国家鸡保护计划中管理基因组多样性

IF 3.6 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Mengmeng Zhang, Shiwei Wang, Ran Xu, Yijun Liu, Han Zhang, Mengxia Sun, Junyan Wang, Zhexi Liu, Keliang Wu
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引用次数: 0

摘要

有效保护和利用农场动物是实现粮食可持续增产的基础。就地保护和异地保护是目前保护中国家鸡品种遗传完整性的两种主要策略。然而,这些保护种群的基因组多样性和种群结构尚未得到比较。我们从中国三个家鸡品种的原生境和非原生境保护种群中收集了361个个体,并采用基因分型测序(GBS)技术对其进行了基因分型。首先,我们使用基于杂合度、基因组近交和连锁不平衡的不同参数估计了这些种群的基因组多样性,并应用主成分分析(PCA)、邻接树和ADMIXTURE分析了种群结构。我们发现,与原地保护种群相比,在受控环境中维持的小型原地保护种群保留的遗传多样性较少。此外,我们还发现同一品种的原地保护种群和异地保护种群之间存在遗传分化。接下来,我们使用三种统计方法(固定指数(FST)、核苷酸多样性(Pi)和跨种群扩展单倍型同源性(XP-EHH))分析了选择的特征,以研究原地保护种群和非原地保护种群之间分化的遗传足迹。我们的结论是,在这些小种群中,分化可能是由遗传漂移或来自原始种群的突变造成的。在京优鸡种群中观察到的分化可能反映了动物从原产地迁移到异地保护的新地点时对温度和湿度环境变化的适应。三个中国家鸡品种的保护计划在一定程度上保持了其基因组多样性。与就地保护的种群相比,在受控环境中进行异地保护的小型种群所保留的遗传多样性较少。此外,出于保护目的将种群从原产地转移到另一地点会导致遗传分化,而遗传分化可能是由遗传漂变或适应引起的。这项研究为进一步优化中国家鸡品种的原地和异地保护计划提供了依据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Managing genomic diversity in conservation programs of Chinese domestic chickens
Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (FST), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation. Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.
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来源期刊
Genetics Selection Evolution
Genetics Selection Evolution 生物-奶制品与动物科学
CiteScore
6.50
自引率
9.80%
发文量
74
审稿时长
1 months
期刊介绍: Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.
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