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Genetics and Genomics of Pig Breeding

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

Deadline for manuscript submissions: closed (15 February 2024) | Viewed by 16712

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Dr. Kang Xu

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Guest Editor

Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
Interests: pig breeding; genomics; genetic marker; meat quality
Special Issues, Collections and Topics in MDPI journals

Dr. Kejun Wang

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Guest Editor

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
Interests: animal pan-genome; animal genetics; gene mapping; trait dissection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to its great application value, the selective breeding of pigs has been carried out since the beginning of the 20th century by identifying the genetic foundations for economic traits. The completion of multiple pig genome projects has constructed a comprehensive list of pig genes. Moreover, a large number of genes and loci have been discovered in pigs. However, years of extensive research have demonstrated that not many major genes or loci can be used for breeding. The genetic mechanisms and genomics of pigs are still the focus.

Therefore, this Special Issue will focus on the genetic mechanisms of economic traits, such as reproductive performance, growth rate, intestinal digestibility (feed to meat ratio), meat-producing performance, meat quality, disease resistance, and others, among different porcine varieties or strains. Moreover, we will analyze the genetic mechanisms and molecular regulatory networks of pig economic traits at the level of DNA, RNA, proteins, and chromatin using multiple methods, such as transcriptomics, proteomics, metabolomics, monocytomics, and multi-omics joint analysis.

In addition, mining new candidate genes and detecting the genetic loci for the economic traits will also be considered. Meanwhile, the role and contribution of the genes and molecular makers for the formation of economic traits will be discussed.

Finally, the application of the genes and loci in marker-assisted selection and the genome-wide selection of pigs will be of great concern.

Dr. Kang Xu
Dr. Kejun Wang
Guest Editors

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Keywords

pig genome
pig breeding
multi-omics
economic traits
molecular maker

Published Papers (11 papers)

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Research

16 pages, 3311 KiB

Open AccessArticle

Differences in Immune Characteristics and Related Gene Expression in Spleen among Ningxiang, Berkshire Breeds and Their Hybrid Pigs

by Gang Song, Yuebo Zhang, Hu Gao, Yawei Fu, Yue Chen, Yulong Yin and Kang Xu

Genes 2024, 15(2), 205; https://doi.org/10.3390/genes15020205 - 04 Feb 2024

Viewed by 849

Abstract

To investigate the differential immunology in Ningxiang and Berkshire pigs and their F₁ offspring (F₁ offspring), physiological and biochemical indicators in the plasma and spleen were analyzed. Then, transcriptomic analysis of the spleen identified 1348, 408, and 207 differentially expressed genes (DEGs) in comparisons of Ningxiang vs. Berkshire, Berkshire vs. F₁ offspring, and Ningxiang vs. F₁ offspring, respectively. In Ningxiang vs. Berkshire pigs, the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs included CD163, MARCO, CXCL14, CCL19, and PPBP, which are associated with immunity. GO and KEGG analyses were also conducted comparing F₁ offspring and their parents. The DEGs, including BPIFB1, HAVCR2, CD163, DDX3X, CCR5, and ITGB3, were enriched in immune-related pathways. Protein–protein interaction (PPI) analysis indicated that the EGFR and ITGA2 genes were key hub genes. In conclusion, this study identifies significant immune DEGs in different pig breeds, providing data to support the exploration of breeding strategies for disease resistance in local and crossbred pig populations. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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13 pages, 4630 KiB

Open AccessArticle

Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population

by Lige Zhang, Songyuan Zhang, Meng Yuan, Fengting Zhan, Mingkun Song, Peng Shang, Feng Yang, Xiuling Li, Ruimin Qiao, Xuelei Han, Xinjian Li, Meiying Fang and Kejun Wang

Genes 2023, 14(12), 2133; https://doi.org/10.3390/genes14122133 - 27 Nov 2023

Cited by 1 | Viewed by 1111

Abstract

Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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11 pages, 1817 KiB

Open AccessArticle

Finding Predictors of Leg Defects in Pigs Using CNV-GWAS

by Lyubov Getmantseva, Maria Kolosova, Kseniia Fede, Anna Korobeinikova, Anatoly Kolosov, Elena Romanets, Faridun Bakoev, Timofey Romanets, Vladimir Yudin, Anton Keskinov and Siroj Bakoev

Genes 2023, 14(11), 2054; https://doi.org/10.3390/genes14112054 - 08 Nov 2023

Viewed by 794

Abstract

One of the most important areas of modern genome research is the search for meaningful relationships between genetic variants and phenotypes. In the livestock field, there has been research demonstrating the influence of copy number variants (CNVs) on phenotypic variation. Despite the wide range in the number and size of detected CNVs, a significant proportion differ between breeds and their functional effects are underestimated in the pig industry. In this work, we focused on the problem of leg defects in pigs (lumps/growths in the area of the hock joint on the hind legs) and focused on searching for molecular genetic predictors associated with this trait for the selection of breeding stock. The study was conducted on Large White pigs using three CNV calling tools (PennCNV, QuantiSNP and R-GADA) and the CNVRanger association analysis tool (CNV-GWAS). As a result, the analysis identified three candidate CNVRs associated with the formation of limb defects. Subsequent functional analysis suggested that all identified CNVs may act as potential predictors of the hock joint phenotype of pigs. It should be noted that the results obtained indicate that all significant regions are localized in genes (CTH, SRSF11, MAN1A1 and LPIN1) responsible for the metabolism of amino acids, fatty acids, glycerolipids and glycerophospholipids, thereby related to the immune response, liver functions, content intramuscular fat and animal fatness. These results are consistent with previously published studies, according to which a predisposition to the formation of leg defects can be realized through genetic variants associated with the functions of the liver, kidneys and hematological characteristics. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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18 pages, 6384 KiB

Open AccessArticle

Identifying Genetic Architecture of Carcass and Meat Quality Traits in a Ningxiang Indigenous Pig Population

by Shishu Yin, Gang Song, Ning Gao, Hu Gao, Qinghua Zeng, Peng Lu, Qin Zhang, Kang Xu and Jun He

Genes 2023, 14(7), 1308; https://doi.org/10.3390/genes14071308 - 21 Jun 2023

Cited by 1 | Viewed by 1248

Abstract

Ningxiang pig is a breed renowned for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 min and 24 h) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30~0.80) for carcass traits and from low to high (0.11~0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the GRM4 gene emerged as a pleiotropic gene that correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold the potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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19 pages, 6520 KiB

Open AccessArticle

Molecular Mechanism of MYL4 Regulation of Skeletal Muscle Development in Pigs

by Xueli Xu, Zonggang Yu, Nini Ai, Sui Liufu, Xiaolin Liu, Bohe Chen, Xintong Li, Jun Jiang, Yuebo Zhang, Haiming Ma and Yulong Yin

Genes 2023, 14(6), 1267; https://doi.org/10.3390/genes14061267 - 15 Jun 2023

Viewed by 1273

Abstract

The processes of muscle growth and development, including myoblast proliferation, migration, differentiation, and fusion, are modified by a variety of regulatory factors. MYL4 plays an important role in atrial development, atrial cardiomyopathy, muscle-fiber size, and muscle development. The structural variation (SV) of MYL4 was found via the de novo sequencing of Ningxiang pigs, and the existence of SV was verified in the experiments. The genotype distribution of Ningxiang pigs and Large White pigs was detected, and it was found that Ningxiang pigs were mainly of the BB genotype and that Large White pigs were mainly of the AB genotype. However, the molecular mechanisms behind the MYL4-mediated regulation of skeletal muscle development need to be deeply explored. Therefore, RT-qPCR, 3′RACE, CCK8, EdU, Western blot, immunofluorescence, flow cytometry, and bioinformation analysis were used to explore the function of MYL4 in myoblast development. The cDNA of MYL4 was successfully cloned from Ningxiang pigs, and its physicochemical properties were predicted. The expression profiles in six tissues and four stages of Ningxiang pigs and Large White pigs were found to be the highest in the lungs and 30 days after birth. The expression of MYL4 increased gradually with the extension of the myogenic differentiation time. The myoblast function test showed that the overexpression of MYL4 inhibited proliferation and promoted apoptosis and differentiation. The knockdown of MYL4 showed the opposite result. These results enhance our understanding of the molecular mechanisms of muscle development and provide a solid theoretical foundation for further exploring the role of the MYL4 gene in muscle development. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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13 pages, 2613 KiB

Open AccessArticle

Genomic Association Analysis of Growth and Backfat Traits in Large White Pigs

by Peng Zhou, Chang Yin, Yuwei Wang, Zongjun Yin and Yang Liu

Genes 2023, 14(6), 1258; https://doi.org/10.3390/genes14061258 - 13 Jun 2023

Cited by 1 | Viewed by 1414

Abstract

The pig industry is significantly influenced by complex traits such as growth rate and fat deposition, which have substantial implications for economic returns. Over the years, remarkable genetic advancements have been achieved through intense artificial selection to enhance these traits in pigs. In this study, we aimed to investigate the genetic factors that contribute to growth efficiency and lean meat percentages in Large White pigs. Specifically, we focused on analyzing two key traits: age at 100 kg live weight (AGE100) and backfat thickness at 100 kg (BF100), in three distinct Large White pig populations—500 Canadian, 295 Danish, and 1500 American Large White pigs. By employing population genomic techniques, we observed significant population stratification among these pig populations. Utilizing imputed whole-genome sequencing data, we conducted single population genome-wide association studies (GWAS) as well as a combined meta-analysis across the three populations to identify genetic markers associated with the aforementioned traits. Our analyses highlighted several candidate genes, such as CNTN1—which has been linked to weight loss in mice and is potentially influential for AGE100—and MC4R, which is associated with obesity and appetite and may impact both traits. Additionally, we identified other genes—namely, PDZRN4, LIPM, and ANKRD22—which play a partial role in fat growth. Our findings provide valuable insights into the genetic basis of these important traits in Large White pigs, which may inform breeding strategies for improved production efficiency and meat quality. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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14 pages, 4699 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs

by Sui Liufu, Qun Lan, Xiaolin Liu, Bohe Chen, Xueli Xu, Nini Ai, Xintong Li, Zonggang Yu and Haiming Ma

Genes 2023, 14(5), 1050; https://doi.org/10.3390/genes14051050 - 08 May 2023

Cited by 3 | Viewed by 1800

Abstract

The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality in pig breeding. The current study utilized transcriptome technology to explore the regulatory mechanisms of muscle growth and intramuscular fat (IMF) deposition in the Longissimus Dorsi muscle at three core developmental stages (natal stage on day 1, growing stage on day 60, and finishing stage on day 210) in Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) in common for day 1 vs. day 60 and day 60 vs. day 210, and GO (Gene Ontology) analysis showed that candidate genes RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, and HOMER1 may be closely related to muscle growth and development, while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, and CPT1B) involved the PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway and adipocytokine signaling pathway, which might play a pivotal role in the regulation of IMF deposition. PPI (Protein-Protein Interaction Networks) analysis found that the STAT1 gene was the top hub gene. Taken together, our results provide evidence for the molecular mechanisms of growth and development and IMF deposition in Longissimus Dorsi muscle to optimize carcass mass. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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13 pages, 4692 KiB

Open AccessArticle

Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

by Jingchun Sun, Jinhong Xiao, Yifan Jiang, Yaxin Wang, Minghao Cao, Jialin Wei, Taiyong Yu, Xiangdong Ding and Gongshe Yang

Genes 2023, 14(4), 861; https://doi.org/10.3390/genes14040861 - 02 Apr 2023

Cited by 3 | Viewed by 1782

Abstract

Reproductive traits have a key impact on production efficiency in the pig industry. It is necessary to identify the genetic structure of potential genes that influence reproductive traits. In this study, a genome-wide association study (GWAS) based on chip and imputed data of five reproductive traits, namely, total number born (TNB), number born alive (NBA), litter birth weight (LBW), gestation length (GL), and number of weaned (NW), was performed in Yorkshire pigs. In total, 272 of 2844 pigs with reproductive records were genotyped using KPS Porcine Breeding SNP Chips, and then chip data were imputed to sequencing data using two online software programs: the Pig Haplotype Reference Panel (PHARP v2) and Swine Imputation Server (SWIM 1.0). After quality control, we performed GWAS based on chip data and the two different imputation databases by using fixed and random model circulating probability unification (FarmCPU) models. We discovered 71 genome-wide significant SNPs and 25 potential candidate genes (e.g., SMAD4, RPS6KA2, CAMK2A, NDST1, and ADCY5). Functional enrichment analysis revealed that these genes are mainly enriched in the calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. In conclusion, our results help to clarify the genetic basis of porcine reproductive traits and provide molecular markers for genomic selection in pig breeding. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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15 pages, 1227 KiB

Open AccessArticle

Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs

by Qun Lan, Qiuchun Deng, Shijin Qi, Yuebo Zhang, Zhi Li, Shishu Yin, Yulian Li, Hong Tan, Maisheng Wu, Yulong Yin, Jun He and Mei Liu

Genes 2023, 14(2), 522; https://doi.org/10.3390/genes14020522 - 18 Feb 2023

Cited by 2 | Viewed by 1715

Abstract

With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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14 pages, 2995 KiB

Open AccessArticle

Novel Haplotype in the HHEX Gene Promoter Associated with Body Length in Pigs

by Yabiao Luo, Qiao Xu, Mingming Xue, Yubei Wang, Xiaoyang Yang, Shuheng Chan, Qiguo Tang, Feng Wang, Ruiping Sun, Zhe Chao and Meiying Fang

Genes 2023, 14(2), 511; https://doi.org/10.3390/genes14020511 - 17 Feb 2023

Cited by 1 | Viewed by 1333

Abstract

The screening of important candidate genes and the identification of genetic markers are important for molecular selection in the pig industry. The hematopoietically expressed homeobox (HHEX) gene plays an important role in embryonic development and organogenesis; however, the genetic variation and expression pattern of the porcine HHEX gene remains to be clarified. In this study, semiquantitative RT-PCR and immunohistochemistry results showed the specific expression of the HHEX gene in porcine cartilage tissues. A novel haplotype consisting of two SNPs rs80901185 (T > C) and rs80934526 (A > G) was detected in the promoter region of the HHEX gene. The expression of the HHEX gene was significantly higher in Yorkshire pigs (TA haplotype) than in Wuzhishan pigs (CG haplotype), and a population analysis showed that this haplotype was significantly associated with body length. An analysis subsequently revealed that the –586 to –1 bp region of the HHEX gene promoter showed the highest activity. Furthermore, we found that the activity of the TA haplotype was significantly higher than that of the CG haplotype by changing the potential binding of transcription factors YY1 and HDAC2. In summary, we conclude that the porcine HHEX gene may contribute to the breeding of pigs for body length traits. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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16 pages, 4258 KiB

Open AccessArticle

Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs

by Yaqing Dou, Kunlong Qi, Yingke Liu, Chenlei Li, Chenglei Song, Yilin Wei, Zhe Zhang, Xinjian Li, Kejun Wang, Xiuling Li, Ruimin Qiao, Feng Yang and Xuelei Han

Genes 2023, 14(1), 197; https://doi.org/10.3390/genes14010197 - 12 Jan 2023

Cited by 4 | Viewed by 2278

Abstract

Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)

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