H2AFZ, RNF4 and NR4A1 loci are associated with boar semen quality by population association studies

Zhao, Liping; Ma, Changping; Song, Huibin; Feng, Yue; Li, Yang; Xia, Xuanyan; Li, Jialian; Li, Fenge

doi:10.1080/10495398.2018.1521825

Cited by 7 publications

(2 citation statements)

References 26 publications

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“…MRPS26 was consistently expressed throughout early embryogenesis with little stage or tissue specificity (Cheong et al., 2020 ). H2AFZ gene had been reported as candidate gene for boar semen quality traits (Zhao et al., 2019 ). UNC5C exerted significant effects on the conception rate in Holsteins (Sugimoto et al., 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep

Zhao,

Xie,

Fang

et al. 2024

Evolutionary Applications

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As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed‐specific traits subject to selection. Here, we conducted whole‐genome resequencing on 206 Hu sheep individuals, each with an approximate 6‐fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1‐5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed‐specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.

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Section: Discussionmentioning

confidence: 99%

Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep

Zhao,

Xie,

Fang

et al. 2024

Evolutionary Applications

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show abstract

“…found that the ITGAV gene is associated with acrosomal responses that may affect semen quality in animals (Palenikova et al., 2021). Previous studies have shown that the H2AZ1 gene has potential as a molecular marker for improving boar semen quality traits (Zhao et al., 2019), while the ITGAV gene plays a crucial role in fertilized egg implantation and embryonic development (Lin et al., 2007). These physiological and biochemical effects may impact pig reproductive traits such as litter size and birth weight.…”

Section: Fields Pietrain Duroc European Wild Boar Overallmentioning

confidence: 99%

Genetic basis of phenotypic convergence in pig terminal sires using pathway‐based selection signature detection methods

Li,

Peng

et al. 2024

Animal Genetics

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The primary purpose of genetic improvement in lean pig breeds is to enhance production performance. Owing to their similar breeding directions, Duroc and Pietrain pigs are ideal models for investigating the phenotypic convergence underlying artificial selection. However, most important economic traits are controlled by a polygenic basis, so traditional strategies for detecting selection signatures may not fully reveal the genetic basis of complex traits. The pathway‐based gene network analysis method utilizes each pathway as a unit, overcoming the limitations of traditional strategies for detecting selection signatures by revealing the selection of complex biological processes. Here, we utilized 13 122 398 high‐quality SNPs from whole‐genome sequencing data of 48 Pietrain pigs, 156 Duroc pigs and 36 European wild boars to detect selective signatures. After calculating FST and iHS scores, we integrated the pathway information and utilized the r/bioconductor graphite and signet packages to construct gene networks, identify subnets and uncover candidate genes underlying selection. Using the traditional strategy, a total of 47 genomic regions exhibiting parallel selection were identified. The enriched genes, including INO80, FZR1, LEPR and FAF1, may be associated with reproduction, fat deposition and skeletal development. Using the pathway‐based selection signatures detection method, we identified two significant biological pathways and eight potential candidate genes underlying parallel selection, such as VTN, FN1 and ITGAV. This study presents a novel strategy for investigating the genetic basis of complex traits and elucidating the phenotypic convergence underlying artificial selection, by integrating traditional selection signature methods with pathway‐based gene network analysis.

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Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends

Sa,

Gòdia,

Lewis

et al. 2024

Animal Reproduction Science

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H2AFZ, RNF4 and NR4A1 loci are associated with boar semen quality by population association studies

Cited by 7 publications

References 26 publications

Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep

Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep

Genetic basis of phenotypic convergence in pig terminal sires using pathway‐based selection signature detection methods

Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends

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