Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Xu, Zhi-Hong; Mei, Shuqi; Zhou, Jiawei; Qiao, Mu; Sun, Hua; Li, Zipeng; Li, Lianghua; Dong, Binke; Oyelami, Favour Oluwapelumi; Wu, Jianliang; Peng, Xianwen

doi:10.3389/fgene.2021.720081

Cited by 15 publications

(11 citation statements)

References 42 publications

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“…The Xidu black pig is a composite breed, with about 50% Hubei white, 25% Meishan, and 25% Enshi black pig inheritance ( 17 ). It has good meat quality, making it a good subject for this study ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Qiao

et al. 2022

Front. Nutr.

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Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r2 = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.

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Section: Introductionmentioning

confidence: 99%

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Qiao

et al. 2022

Front. Nutr.

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“…The primary goal of this study is to investigate the population structure and genetic diversity so as to provide better conservation strategies for TC pigs. Numerous studies have shown that multi-dimensional scaling (MDS) and phylogenetic tree analyses are effective methods for the investigation of population structure, that the proportion of polymorphic loci (P N ), minor allele frequency (MAF), heterozygosity, and nucleotide diversity (Pi) in combination with linkage disequilibrium (LD) and effective population size (Ne) levels are good indicators reflecting the genetic diversity of the population, and that runs of homozygosity (ROH) and ROH island analyses can reveal the inbreeding of the genome ( Cai et al, 2020 ; Xu et al, 2021 ). Owing to the rapid development of molecular biology in recent years, a variety of markers and DNA sequences of different species can be determined easily at low cost.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip

Yuan

Zhou

et al. 2022

Front. Genet.

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Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.

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“…The following criteria and thresholds were used to define the ROH: a sliding window of 50 SNPs, a maximum missingness of 1 allele, a minimum length of 25,000 bp, at least 30 homozygous SNPs included in the ROH, a minimum density of 1 SNP per 1000 kilobases, and a minimum length of 1 Mb. The algorithm of ROH is extensively described by Xu et al [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Assessing the Genomics Structure of Dorper and White Dorper Variants, and Dorper Populations in South Africa and Hungary

Wanjala

Astuti

Bagi

et al. 2023

Biology

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Dorper sheep was developed for meat production in arid and semi-arid regions under extensive production systems in South Africa. Two variants with distinct head and neck colors were bred during their development process. White Dorper have a white coat while Dorper have a black head and neck. Both variants have grown in popularity around the world. Therefore, understanding the genomic architecture between South African Dorpers and Dorper populations adapted to other climatic regions, as well as genomic differences between Dorper and White Dorper variants is vital for their molecular management. Using the ovine 50K SNP chip, this study compared the genetic architecture of Dorper variants between populations from South Africa and Hungary. The Dorper populations in both countries had high genetic diversity levels, although Dorper in Hungary showed high levels of inbreeding. White Dorpers from both countries were genetically closely related, while Dorpers were distantly related according to principal component analysis and neighbor-joining tree. Additionally, whereas all groups displayed unique selection signatures for local adaptation, Dorpers from Hungary had a similar linkage disequilibrium decay. Environmental differences and color may have influenced the genetic differentiation between the Dorpers. For their molecular management and prospective genomic selection, it is crucial to understand the Dorper sheep’s genomic architecture, and the results of this study can be interpreted as a step in this direction.

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Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Cited by 15 publications

References 42 publications

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip

Assessing the Genomics Structure of Dorper and White Dorper Variants, and Dorper Populations in South Africa and Hungary

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