Gochu Asturcelta猪一个小家系的自接合性研究。

IF 3.6 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Katherine D Arias, Juan Pablo Gutiérrez, Iván Fernández, Isabel Álvarez, Félix Goyache
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引用次数: 0

摘要

背景:尽管有单核苷酸多态性(SNP)阵列数据,但在观察到的纯合性和由亲属间交配引起的纯合(自合性)之间的区分带来了主要困难。由于不同的原因,即孟德尔抽样、群体结构和染色体之间的差异,纯合性估计量显示出很大的变化。因此,确定近亲繁殖如何反映在基因组中仍然是一个问题。本研究的目的是研究基因组信息在评估高度濒危的Gochu Asturcelta猪种遗传多样性方面的有用性。系谱深度从0(始祖)到4个等效离散代(t)不等。计算每个个体的四个纯合性参数(纯合性,FROH;杂合性富集区,FHRR;Li和Horvitz的FLH;以及Yang及其同事的FYAN),根据基础群体(BP;六个个体)的变异性进行调整,并进一步对常染色体进行切刀。计算谱系中每个个体的纯合性(取决于t)和成对纯合性的增加(即父母平均值的增加),并计算五个亚群(队列)的有效群体大小(Ne)。使用系谱参数(个体近亲繁殖、近亲繁殖中的个体增加和Ne)进行比较。结果:平均F为0.120 ± 0.074,经BP校正的平均纯合性范围为0.099 ± 0.081(FLH)至0.152 ± 0.075(财政年度)。夹刀后,平均值略低。成对纯合性的增加往往比纯合性值的相应个体增加高两倍。与系谱估计相比,使用FYAN获得的Ne估计往往具有较低的均方根误差。然而,使用基因组近亲繁殖的FROH和FHRR估计,基于成对纯合性增加的Ne估计具有较低的均方根误差。结论:在育种政策禁止近亲交配的小种群中,表征纯合性的参数可能无法准确描述变异性的损失。BP调整后,FROH和FHRR的表现高度一致。假设纯合性的增加仅取决于谱系深度,可能会导致在谱系浅的人群中低估纯合性。从FROH或FHRR计算的成对纯合性的增加是表征自身合性的一种有前途的方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs.

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs.

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs.

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs.

Background: In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz's, FLH; and Yang and colleague's FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents' mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons.

Results: The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors.

Conclusions: Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.

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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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