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de Almeida AM, Latorre MA, Alvarez-Rodriguez J. Productive, Physiological, and Environmental Implications of Reducing Crude Protein Content in Swine Diets: A Review. Animals (Basel) 2024; 14:3081. [PMID: 39518804 PMCID: PMC11544889 DOI: 10.3390/ani14213081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 10/19/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024] Open
Abstract
Pig production is one of the most important providers of high-quality proteins and amino acids (AAs) to human nutrition. In this sector, feeding has an important economic and environmental impact. A strategy to reduce production costs and negative sustainability effects is reducing dietary crude protein (CP) contents with or without AA supplementation. This review addresses the different aspects related to this strategy, particularly the effects on growth performance and pork traits in piglets and growing and finishing pigs, as well as the physiological molecular mechanisms' underlying effects. Insight is also provided into the effects of dietary CP reduction on the productive performances of alternative pig production systems and breeding boars and sows. Finally, an overview is conducted on the effects of dietary CP reduction on ammonia, odor, and greenhouse gas emissions arising from pig production systems. Overall, CP reduction may lead to production losses, albeit they can be, to some extent, hindered by adequate AA supplementation. Losses are particularly relevant during the post-weaning phase, whereas in finishing pigs, it may bring additional benefits, such as high intramuscular fat contents in some markets or improved gut barrier function with benefits to the animals' health and welfare, as well as decreased ammonia emissions to the environment.
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Affiliation(s)
- André Martinho de Almeida
- LEAF—Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Maria Angeles Latorre
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-Universidad de Zaragoza, Calle Miguel Servet 177, 50013 Zaragoza, Spain;
| | - Javier Alvarez-Rodriguez
- Departamento de Ciencia Animal, Universidad de Lleida, Av. Rovira Roure 191, 25198 Lleida, Spain
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Qiu Z, Cai W, Liu Q, Liu K, Liu C, Yang H, Huang R, Li P, Zhao Q. Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs. J Anim Sci 2024; 102:skae036. [PMID: 38330300 PMCID: PMC10914368 DOI: 10.1093/jas/skae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.
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Affiliation(s)
- Zijian Qiu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Cai
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiyue Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenxi Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Huilong Yang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruihua Huang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Pinghua Li
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China
| | - Qingbo Zhao
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
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Wang D, Teng J, Ning C, Wang W, Liu S, Zhang Q, Tang H. Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens. Anim Biotechnol 2023; 34:3154-3161. [PMID: 36282276 DOI: 10.1080/10495398.2022.2137035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.
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Affiliation(s)
- Dan Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Jun Teng
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Chao Ning
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Wenwen Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Shuai Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Hui Tang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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Deng S, Qiu Y, Zhuang Z, Wu J, Li X, Ruan D, Xu C, Zheng E, Yang M, Cai G, Yang J, Wu Z, Huang S. Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population. Animals (Basel) 2023; 13:2414. [PMID: 37570223 PMCID: PMC10417164 DOI: 10.3390/ani13152414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023] Open
Abstract
Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.
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Affiliation(s)
- Shaoxiong Deng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Xuehua Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
| | - Enqing Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Sixiu Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (S.D.); (Y.Q.); (Z.Z.); (J.W.); (X.L.); (D.R.); (C.X.); (E.Z.); (G.C.); (J.Y.)
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Yang L, Li X, Zhuang Z, Zhou S, Wu J, Xu C, Ruan D, Qiu Y, Zhao H, Zheng E, Cai G, Wu Z, Yang J. Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs. Animals (Basel) 2023; 13:1880. [PMID: 37889833 PMCID: PMC10251818 DOI: 10.3390/ani13111880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/27/2023] [Accepted: 06/03/2023] [Indexed: 10/29/2023] Open
Abstract
The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.
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Affiliation(s)
- Lijuan Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Xuehua Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Hua Zhao
- National S&T Innovation Center for Modern Agricultural Industry, Guangzhou 510642, China;
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population. Genes (Basel) 2022; 13:genes13111990. [DOI: 10.3390/genes13111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/04/2022] Open
Abstract
Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.
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Du Z, D’Alessandro E, Asare E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes. Genes (Basel) 2022; 13:genes13081359. [PMID: 36011270 PMCID: PMC9407582 DOI: 10.3390/genes13081359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Via Palatucci snc, 98168 Messina, Italy;
| | - Emmanuel Asare
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
- Correspondence:
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8
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Wang X, D’Alessandro E, Chi C, Moawad AS, Zong W, Chen C, Song C. Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms. Animals (Basel) 2022; 12:ani12111345. [PMID: 35681812 PMCID: PMC9179424 DOI: 10.3390/ani12111345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary In a previous study, 30 SINE-RIPs were applied for population genetic analysis in 7 Chinese miniature pig populations and approved effectively in the genetic distances and breed-relationships between these populations. There are abundant indigenous pigs famous across the world for their prolificacy in the Jiangsu Province of eastern China, such as Meishan, Erhualian. Since pork production relies on limited commercial breeds such as Landrace, Large White, and Duroc pigs, characterized by maximizing productivity in intensive production systems, these indigenous pigs are nowadays decrease sharply. The genetic characterizations of these resources are essential requirements for the development of conservation, selection, and sustainable utilizations. Therefore, SINE-RIPs were selected to evaluate the genetic variation and population structure of Jiangsu pig populations and the results may assist with the conservation and utilization of these native pig populations. Abstract Short interspersed nuclear elements (SINEs), one type of retrotransposon, are considered to be ideal molecular markers due to their wide distribution in the genome, high copy number, and high polymorphism. Preliminary studies have identified more than 35,000 SINE-retrotransposon insertion polymorphisms (RIPs) in the pig genome. In this study, 18 SINE-RIPs were used to evaluate the genetic variation and population structure of seven native pig populations and two crossbreeds in the Jiangsu Province of China. Two commercial pig breeds (Duroc and Large White) and one Italian native breed (Sicilian Black pig) were selected as the control. The results showed that all 18 SINE-RIPs were polymorphic among these pigs. The Jiangsu native pig populations (Erhualian, Fengjing, Middle Meishan, Mi, Shawutou, Small Meishan, and Huai) were shown to be more polymorphic than the crossbreeds (Sushan and Sujiang) and external breeds (Sicilian Black pig, Large White, and Duroc) based on the expected heterozygosity and polymorphic information content values. Some native pigs, including Small Meishan, Mi, Middle Meishan, and Erhualian, had a higher degree of inbreeding according to the FIS values. Based on the neighbor-joining tree, all of the Jiangsu native pig populations formed one branch, while the three external pig breeds formed the other branches, with the two crossbreeds containing more than 50% external pig ancestry. The Huai pigs were independent of the other Jiangsu native pigs but shared a common ancestor with Sujiang and Mi. The results provide a new perspective on the population structure of these native pig breeds and will assist with the conservation and utilization of Chinese native pigs.
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Affiliation(s)
- Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Enrico D’Alessandro
- Unit of Animal Production, Department of Veterinary Science, University of Messina, 98168 Messina, Italy;
| | - Chenglin Chi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Ali Shoaib Moawad
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
- Correspondence: ; Tel./Fax: +86-514-87979034
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Liu Z, Li H, Zhong Z, Jiang S. A Whole Genome Sequencing-Based Genome-Wide Association Study Reveals the Potential Associations of Teat Number in Qingping Pigs. Animals (Basel) 2022; 12:1057. [PMID: 35565484 PMCID: PMC9100799 DOI: 10.3390/ani12091057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Teat number plays an important role in the reproductive performance of sows and the growth of piglets. However, the quantitative trait loci (QTLs) and candidate genes for the teat number-related traits in Qingping pigs remain unknown. In this study, we performed GWAS based on whole-genome single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) for the total number of teats and five other related traits in 100 Qingping pigs. SNPs and Indels of all 100 pigs were genotyped using 10× whole genome resequencing. GWAS using General Linear Models (GLM) detected a total of 28 SNPs and 45 Indels as peak markers for these six traits. We also performed GWAS for the absolute difference between left and right teat number (ADIFF) using Fixed and random model Circulating Probability Unification (FarmCPU). The most strongly associated SNP and Indel with a distance of 562,788 bp were significantly associated with ADIFF in both GLM and FarmCPU models. In the 1-Mb regions of the most strongly associated SNP and Indel, there were five annotated genes, including TRIML1, TRIML2, ZFP42, FAT1 and MTNR1A. We also highlighted TBX3 as an interesting candidate gene for SSC14. Enrichment analysis of candidate genes suggested the Wnt signaling pathway may contribute to teat number-related traits. This study expanded significant marker-trait associations for teat number and provided useful molecular markers and candidate genes for teat number improvement in the breeding of sows.
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Affiliation(s)
- Zezhang Liu
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China;
| | - Zhuxia Zhong
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
| | - Siwen Jiang
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; (Z.L.); (Z.Z.)
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10
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Du Z, D’Alessandro E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes. Animals (Basel) 2022; 12:ani12080969. [PMID: 35454216 PMCID: PMC9031378 DOI: 10.3390/ani12080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 12/17/2022] Open
Abstract
The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, Italy;
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
- Correspondence:
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11
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Zhao Y, Pu Y, Liang B, Bai T, Liu Y, Jiang L, Ma Y. A study using single-locus and multi-locus genome-wide association study to identify genes associated with teat number in Hu sheep. Anim Genet 2022; 53:203-211. [PMID: 35040155 PMCID: PMC9303709 DOI: 10.1111/age.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/08/2021] [Accepted: 12/24/2021] [Indexed: 01/19/2023]
Abstract
The multiple teats trait is common in many species of mammals and is considered related to lactation ability in swine. However, in Hu sheep, related gene research is still relatively limited. In this study, a genome‐wide association study was used to identify genetic markers and genes related to the number of teats in the Hu sheep population, a native Chinese sheep breed. A single marker method and several multi‐locus methods were utilized. A total of 61 SNPs were found to be related to the number of teats. Among these, 11 SNPs and one SNP were consistently detected by two and three multi‐locus models respectively. Four SNPs were concordantly identified between the single marker and multi‐locus methods. We also performed quantitative real‐time PCR testing of these identified candidate genes, identifying three genes with significantly different expression. Our study suggested that the LHFP, DPYSL2, and TDP‐43 genes may be related to the number of teats in sheep. The combination of single and multi‐locus GWAS detected additional SNPs not found with only one model. Our results provide new and important insights into the genetic mechanisms of the mammalian multiparous teat phenotype. These findings may be useful for future breeding and understanding the genetics of sheep and other livestock.
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Affiliation(s)
- Yuhetian Zhao
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Yabin Pu
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Benmeng Liang
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Tianyou Bai
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Yue Liu
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Lin Jiang
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
| | - Yuehui Ma
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Haidian, Beijing, China
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12
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Hong Y, Ye J, Dong L, Li Y, Yan L, Cai G, Liu D, Tan C, Wu Z. Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs. Front Genet 2021; 12:650370. [PMID: 34408768 PMCID: PMC8366400 DOI: 10.3389/fgene.2021.650370] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/15/2021] [Indexed: 01/08/2023] Open
Abstract
Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.
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Affiliation(s)
- Yifeng Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Jian Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Linsong Dong
- National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Yalan Li
- National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Limin Yan
- National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Dewu Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Cheng Tan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, China
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A Moderate Reduction of Dietary Crude Protein Provide Comparable Growth Performance and Improve Metabolism via Changing Intestinal Microbiota in Sushan Nursery Pigs. Animals (Basel) 2021; 11:ani11041166. [PMID: 33921586 PMCID: PMC8073206 DOI: 10.3390/ani11041166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
In this paper, we investigated the effects of a diet with a moderate reduction of dietary crude protein (CP) level, supplemented with five crystalline amino acids (Lys, Met, Thr, Try, and Val), on the growth, metabolism, and fecal microbiota of Sushan nursery pigs. Seventy Sushan nursery pigs with an average body weight of 19.56 ± 0.24 kg were randomly allocated to two experimental dietary treatments: 18% CP (high protein; group HP), and 15% CP (low protein; group LP). We found that the differences in the two diets had no significant effect on the growth performance of Sushan nursery pigs. Nursery pigs on the 15% CP diet showed significantly improved protein, amino acid, and energy utilization. Furthermore, the LP diet cloud optimized the gut microflora composition to some extent. The functional structure of bacterial communities implied improved metabolic capabilities in group LP. Additionally, correlation analysis between fecal microbiota and metabolic profiles confirmed that the increase of beneficial bacterial in the feces was beneficial to the health and metabolism of the nursery pigs. In conclusion, a moderate reduction in the dietary protein level can improve growth and metabolism due to the improvement of intestinal microbiota in Sushan nursery pigs. This finding could provide useful reference data for the application of a different nutrition strategy in indigenous pig production.
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