Breeding and Genetics of Pig

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2024) | Viewed by 2390

Special Issue Editors


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Guest Editor
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: genomics; genome selection; GWAS; molecular genetics; multi-omics; pig

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Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou, China
Interests: mobilome; genome; transposable elements; transposon; retrotransposon; evolution; exaptation/domestication; horizontal transfer; gene transfer; gene editing
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Competence Area Genetics and Genomics, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
Interests: animal genomics; transcriptome; epigenome; animal health; animal welfare
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In this Special Issue, we delve into the fascinating realm of pig breeding and genetics, exploring the advancements and breakthroughs that have revolutionized the industry. From identifying desirable traits to enhancing productivity, this collection of articles offers valuable insights into the science behind pig breeding and the genetic factors that contribute to their diversity. Whether you are a researcher, farmer, or simply curious about the intricacies regarding pig genetics, this Special Issue will certainly provide a comprehensive overview of this study area. Contributions in the format of original research papers and review manuscripts will be welcome in this Special Issue.

Dr. Longchao Zhang
Prof. Dr. Chengyi Song
Prof. Dr. Klaus Wimmers
Guest Editors

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Keywords

  • genomics
  • genome selection
  • GWAS
  • molecular genetics
  • multi-omics
  • pig

Published Papers (3 papers)

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13 pages, 1166 KiB  
Article
Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing
by Wenjun Li, Xudong Wu, Decai Xiang, Wei Zhang, Lingxiang Wu, Xintong Meng, Jinlong Huo, Zongjun Yin, Guowen Fu and Guiying Zhao
Genes 2024, 15(2), 233; https://doi.org/10.3390/genes15020233 - 12 Feb 2024
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Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in [...] Read more.
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1–5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs. Full article
(This article belongs to the Special Issue Breeding and Genetics of Pig)
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10 pages, 408 KiB  
Article
Comparison of Growth Performance, Carcass Properties, Fatty Acid Profile, and Genes Involved in Fat Metabolism in Nanyang and Landrace Pigs
by Jinzhou Zhang, Shuaitao Meng, Heming Wang, Chuankuan Zhang, Zhe Sun, Luyao Huang and Zhiguo Miao
Genes 2024, 15(2), 186; https://doi.org/10.3390/genes15020186 - 30 Jan 2024
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Abstract
This study compared the growth, carcass properties, fatty acid profile, lipid-producing enzyme activity, and expression pattern of genes involved in fat metabolism in Nanyang and Landrace pigs. In the study, 32 Nanyang (22.16 ± 0.59 kg) and 32 Landrace barrows (21.37 ± 0.57 [...] Read more.
This study compared the growth, carcass properties, fatty acid profile, lipid-producing enzyme activity, and expression pattern of genes involved in fat metabolism in Nanyang and Landrace pigs. In the study, 32 Nanyang (22.16 ± 0.59 kg) and 32 Landrace barrows (21.37 ± 0.57 kg) were selected and divided into two groups, each with eight pens and four pigs per pen. The trial period lasted 90 days. The findings showed that the Nanyang pigs had lower average daily weight gain and lean percentage and higher average backfat thickness and lipogenic enzyme activities, including for acetyl-CoA carboxylase, glucose-6-phosphate dehydrogenase, malic enzyme, and fatty acid synthase, than the Landrace pigs. A total of 14 long-chain fatty acids were detected using HPLC-MS, in which it was found that the levels of C14:0, C18:1n-9, C20:1n-9, C20:4n-6, and MUFA were up-regulated and C18:2n-6, C18:3n-3, PUFA n6, n3/n6, and total PUFA were down-regulated in the Nanyang pigs. Moreover, the mRNA levels for genes involved in fat metabolism, ME1, FAS, and LPL, were higher and the expression of SREBP1 mRNA was lower in the Nanyang pigs. Our results suggest genetic differences between the pig breeds in terms of growth, carcass traits, lipogenic enzyme activities, fatty acid profile, and the mRNA expression of genes involved in fat metabolism in subcutaneous fat tissue, which may provide a basis for high-quality pork production. Further studies are needed to investigate the regulation of lipid metabolism. Full article
(This article belongs to the Special Issue Breeding and Genetics of Pig)
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7 pages, 1848 KiB  
Brief Report
Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes
by Xudong Wu, Decai Xiang, Wei Zhang, Yu Ma, Guiying Zhao and Zongjun Yin
Genes 2024, 15(5), 623; https://doi.org/10.3390/genes15050623 - 14 May 2024
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Abstract
Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which have difficulty adapting to the modern swine industry. However, the genome-wide mutational differences between these pig breeds [...] Read more.
Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which have difficulty adapting to the modern swine industry. However, the genome-wide mutational differences between these pig breeds are yet to be evaluated. Therefore, this study aimed to evaluate genomic variation and identify breed-specific SNPs in Danish LW pigs. Here, 43 LW, 15 Diqing Tibetan (DQZ), and 15 Diannan small-ear (DN) pigs whose genomes were re-sequenced with 5× depth were selected. This was followed by a conjoined analysis of our previous resequencing data of 24 Anqing six-end white (AQ) and six Asian wild (SS) pigs. In total, 39,158,378 SNPs and 13,143,989 insertion–deletions were obtained in all breeds. The variation number of LW pigs was the lowest, with 287,194 breed-specific and 1289 non-synonymous SNPs compared with Chinese breeds. Functional analysis of the breed-specific non-synonymous SNPs indicated that these mutations were mainly associated with the reproductive performance, feed intake, and feed conversion ratio of LW pigs. These findings provide a theoretical basis for genetic improvements in the Chinese swine industry. Full article
(This article belongs to the Special Issue Breeding and Genetics of Pig)
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