Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

Wang, Kai; Wu, Pingxian; Wang, Shujie; Ji, Xiang; Dong, Chen; Jiang, Anan; Xiao, Weihang; Gu, Yiren; Jiang, Yanzhi; Zeng, Yangshuang; Xu, Xu; Li, Xuewei; Tang, Guoqing

doi:10.1186/s12863-021-00977-0

Cited by 10 publications

(6 citation statements)

References 44 publications

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“…Among them, the SV locus with the highest F ST was MSRB3 on chromosome 5, which was previously reported to have a key role in pig ear size [ 46 ]. MYH8 has been reported to be associated with muscle development and meat quality traits [ 47 ], and NR1D2 is responsible for adipogenesis and lipid accumulation in the myocardium [ 48 , 49 ]. The KIT locus is a key gene in determining coat color in different pig breeds [ 50 ].…”

Section: Resultsmentioning

confidence: 99%

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Zong,

Wang,

Zhao

et al. 2023

J Animal Sci Biotechnol

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Background During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. Results Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

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Section: Resultsmentioning

confidence: 99%

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Zong,

Wang,

Zhao

et al. 2023

J Animal Sci Biotechnol

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“…Our results indicated that the mutant T allele results in a non-synonymous substitution leading to reduced alveolar macrophage and further attenuated host defense, which was supported by in vitro Mhp infection experiments in cell culture. Besides, we also identified several swept genes with coding mutations, like ALS2, EXOC2, PRDM15, and SEMA3B/E, which played an essential role in muscle growth, fat deposition, and neuronal development 8,[38][39][40] . Altogether, these functional coding variants constitute valuable information for future pig breeding.…”

Section: Discussionmentioning

confidence: 99%

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

Yi,

Liu,

Yao

et al. 2023

Preprint

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Selection signatures that contribute to phenotypic diversity, especially morphogenesis in pigs, remain to be further elucidated. To reveal the regulatory role of genetic variations in phenotypic differences between Eastern and Western pig breeds, we performed a systematic analysis based on seven high-quality de novo assembled genomes, 1,081 resequencing data representing 78 domestic breeds, 162 methylomes, and 162 transcriptomes of skeletal muscle from Tongcheng (Eastern) and Landrace (Western) pigs at 27 developmental stages. Selective sweep uncovers different genetic architectures behind divergent selection directions for the Eastern and Western breeds. Notably, two loci showed functional alterations by almost fixed missense mutations. By integrating time-course transcriptome and methylome, we revealed differences in developmental timing during myogenesis between Eastern and Western breeds. Genetic variants under artificial selection have critical regulatory effects on progression patterns of heterochronic genes like GHSR and BDH1, by the interaction of local DNA methylation status, particularly during embryonic development. Altogether, our work not only provides valuable resources for understanding pig complex traits, but also contributes to human biomedical research.

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“…The Ningxiang pigs, classified as an obese-type breed, are renowned for their abundant fat content and excellent meat quality. In this study, we identified genes ZNF280D [41], PLIN1 [42], PAPPA2 [43], SLC5A4 [44], and CABIN1 [45], which were found to be associated with BFT in pigs, and CCPG1 [46], ATP1B1 [47], and CABS1 [16], which demonstrated associations with reproductive performance in boars. Additionally, we identified some genes that simultaneously influence multiple traits.…”

Section: Identification Of Roh Islands Candidate Genes and Qtlmentioning

confidence: 89%

A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond

Yin,

Li,

Yang

et al. 2023

IJMS

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Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1–5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.

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Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

Cited by 10 publications

References 44 publications

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond

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