Genetic diversity and population structure in multiple Chinese goat populations using a <scp>SNP</scp> panel

Berihulay, Haile; Li, Y.; Liu, X.; Gebreselassie, Gebremedhin; Islam, Rabiul; Liu, W.; Jiang, Lin; Ma, Yue

doi:10.1111/age.12776

Cited by 32 publications

(20 citation statements)

References 30 publications

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“…Therefore, it is useful to consider our results in the context of the demographic history of the goat population in China. This finding is consistent with our previous study of genetic diversity and population structure, in which it was discussed that the principal component and admixture analysis clearly clustered the population corresponding to their geographic distribution and genetic construction [25]. Comparatively, a decreasing recent Ne was observed for the AC and GF breeds, and their estimated values were closer to 64 and 95 at 13 generations ago, suggesting that these animals were strongly affected by selection pressure or genetic drift which resulted in population decline [44].…”

Section: Discussionsupporting

confidence: 93%

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Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Berihulay

Islam

Jiang

et al. 2019

Animals

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Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

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Section: Discussionsupporting

confidence: 93%

“…In our previous study, we revealed the genetic diversity and population structure of goat populations [25]. Considering this fact, here, we estimated genome-wide linkage disequilibrium and the extent of effective population size in six Chinese goat populations using a 50K SNP panel.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Berihulay

Islam

Jiang

et al. 2019

Animals

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“…This is caused by the differences among breeds, mating schemes, and breed plans. The F -statistic in this population is very low, which is far lower than that reported in other studies ( 37 , 40 ). This indirectly reflects the genetic differentiation among the population.…”

Section: Discussioncontrasting

confidence: 81%

Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

et al. 2021

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Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

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“…Recently, the availability of a medium-density single nucleotide polymorphisms (SNP) panel (8) enabled goat genomic studies at a level of resolution that was not possible with previously used markers, such as microsatellites. Several studies have already used this new SNP array tool to analyze the genetic diversity and population structure of local goat breeds or populations within countries in relation to other cosmopolitan breeds, such as in Italy (9), France (10), Switzerland (11), Spain (12), Pakistan (13), China (14), Canada, and Australia (15). Since the International Goat Genome Consortium (IGGC, http://www.goatgenome.org) was created in 2012, the range of genomic tools and publicly available information for goats has increased immensely (16).…”

Section: Introductionmentioning

confidence: 99%

Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

Pogorevc

Simčić

Khayatzadeh

et al. 2020

Preprint

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BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

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Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel

Cited by 32 publications

References 30 publications

Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

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