Evolutionary insights into porcine genomic structural variations based on a novel‐constructed dataset from 24 worldwide diverse populations

Gong, Haiming; Liu, Weiwei; Wu, Zhongzi; Zhang, Mingpeng; Sun, Yingchun; Ling, Ziqi; Xiao, Shijun; Ai, Huashui; Xin, Yuyun; Yang, Bin; Huang, Lusheng

doi:10.1111/eva.13455

Cited by 4 publications

(4 citation statements)

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“…Moreover, insertional variants in particular have rarely been included in SV studies due to their complex genotyping process, and the phenotypic impact of insertional variants remains largely unknown. While transposon insertion identification depends on reference sequences, which facilitates subsequent genotyping, and a previous study has confirmed that approximately 80% of the variation in the pig genome overlaps with transposable elements [ 15 ], which provided an opportunity to investigate the contribution of insertional variants to the phenotype in the present study. Therefore, we performed GWAS on four SV types in the pig genome, providing new insights into the contribution of different SV types to the phenotype.…”

Section: Discussionmentioning

confidence: 77%

“…Therefore, using SVs as markers for directly performing GWAS is expected to identify causal loci affecting phenotypes. There have been several previous studies on SVs in the pig genome, but SV-based GWAS in the pig genome have been rarely reported [ 13 – 15 ]. The Large White × Min pig resource population provides an opportunity to deepen the understanding of the potential and biological role of SVs as markers for association studies.…”

Section: Discussionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 77%

Section: Discussionmentioning

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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“…Moreover, the quantification of introgressed genetic material between Chinese and European pigs, as well as the effect on the phenotypes, remains an unanswered question to date. Structural variations (SVs) are also recognized as an essential mutational force in shaping the genomic landscape during pig domestication (Li et al 2017;Jiang et al 2023), with recent findings indicating a marked stratification of SVs between Chinese and European breeds, potentially associated with breed-defining characteristics (Gong et al 2022). The role and impact of introgressed SVs in the history of genetic material exchange between Chinese and European breeds merit further investigation through population-based detection methods.…”

Section: Introductionmentioning

confidence: 99%

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

Qiu,

Liu,

Huang

et al. 2023

Preprint

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Historically, Chinese indigenous pigs were introduced to Europe centuries ago with the aim of enhancing economically important traits in European breeds. In recent decades, there has been a reciprocal introduction of European commercial breeds to China for indigenous pig breeding. Our study investigated the genomes of 418 pigs, revealing a genomics landscape of bi-directional introgression patterns between Chinese and European pig populations. We noted a common occurrence of incomplete linkage disequilibrium between structural variations (SVs) and adjacent single-nucleotide polymorphisms (SNPs) in our population, suggesting that conventional SNP-based analyses might not adequately capture the effect of SVs. Therefore, we examine both the roles of population-level SNPs and SVs in bi-directional introgression patterns, and highlight a show case centered around theBMP2gene. We identified introgressed haplotypes and SVs originating from Southern Chinese indigenous pigs, dispersing widely across various European pig breeds. Concurrently, we noted that the introgressed European haplotypes and SVs have attained high frequencies in Northern Chinese indigenous breeds, likely contributing to improvements in body size. In summary, these findings underscore the significant role of introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.

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“…In pigs, CNVs have been extensively characterized ( 12 , 14 – 16 ) and have been found to be associated with a variety of traits such as coat color ( 17 , 18 ), fatty acid composition ( 19 ), and growth and reproductive traits ( 20 – 22 ). However, to the best of our knowledge, associations between CNVs and microbial traits have not been documented in livestock.…”

Section: Introductionmentioning

confidence: 99%

Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs

et al. 2023

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Evolutionary insights into porcine genomic structural variations based on a novel‐constructed dataset from 24 worldwide diverse populations

Abstract: Huanfa Gong and Weiwei Liu contributed equally to this study.

Cited by 4 publications

References 100 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

Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs

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