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Li H, Han L, Zhou F, Wu Z, Zhang L, Xie R, Jiang F, Tian Q, Huang X. Ningxiang Pig-Derived Microbiota Affects the Growth Performance, Gut Microbiota, and Serum Metabolome of Nursery Pigs. Animals (Basel) 2024; 14:2450. [PMID: 39272235 PMCID: PMC11394380 DOI: 10.3390/ani14172450] [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: 07/09/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
The gut microbiota is crucial for maintaining the host's intestinal homeostasis and metabolism. This study investigated the effects of fecal microbiota transplantation (FMT) from Ningxiang pigs on the growth performance, fecal microbiota, and serum metabolites of the same-old DLY pigs. The results indicated that the average daily gain of FMT pigs was significantly greater than that of the control (CON) group. Compared to the CON group, the FMT group significantly improved the apparent digestibility of crude fiber, crude ash, gross energy, and calcium of the pigs. The analysis of serum antioxidant status revealed that the activities of total superoxide dismutase and catalase in the serum of pigs in the FMT group were significantly elevated, whereas the level of malondialdehyde was significantly reduced. Furthermore, 16S rRNA sequencing analysis revealed that the Ningxiang pig-derived microbiota altered the fecal microbiota structure and modulated the diversity of the gut microbiota in the DLY pigs. Untargeted LC-MS metabolomics demonstrated that pigs in the FMT group exhibited distinct metabolomic profiles compared to those in the CON group. Significant changes were observed in key metabolites involved in amino acid, lipid, and carbohydrate metabolism. Additionally, a correlation analysis between serum differential metabolites and the gut microbiota revealed that the relative abundance of Lachnospiraceae_NK4A136_group and Corynebacterium was highly correlated with lipid compounds. In conclusion, Ningxiang pig-derived microbiota can alleviate oxidative stress and enhance growth performance in DLY pigs by modulating their gut microbiota and metabolic features.
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Affiliation(s)
- Hongkun Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Li Han
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Feng Zhou
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Zichen Wu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Longlin Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Renjie Xie
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Feng Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Qiyu Tian
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
| | - Xingguo Huang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Yuelushan Laboratory, Changsha 410128, China
- Hunan Agriculture Research System, Changsha 410128, China
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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [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: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Vinje H, Brustad HK, Heggli A, Sevillano CA, Van Son M, Gangsei LE. Classification of breed combinations for slaughter pigs based on genotypes-modeling DNA samples of crossbreeds as fuzzy sets from purebred founders. Front Genet 2023; 14:1289130. [PMID: 38116292 PMCID: PMC10729766 DOI: 10.3389/fgene.2023.1289130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
In pig production, the production animals are generally three- or four-way crossbreeds. Reliable information regarding the breed of origin of slaughtered pigs is useful, even a prerequisite, for a number of purposes, e.g., evaluating potential breed effects on carcass grading. Genetic data from slaughtered pigs can easily be extracted and used for crossbreed classification. In the current study, four classification methods, namely, random forest (RF), ADMIXTURE, partial least squares regression (PLSR), and partial least squares together with quadratic discriminant analysis (PLS-QDA) were evaluated on simulated (n = 7,500) genomic data of crossbreeds. The derivation of the theory behind PLS-QDA is a major part of the current study, whereas RF and ADMIXTURE are known and well-described in the literature. Classification success (CS) rate, square loss (SL), and Kullback-Leibler (KL) divergence loss for the simulated data were used to compare methods. Overall, PLS-QDA performed best with 99%/0.0018/0.002 (CS/SL/KL) vs. 97%/0.0084/0.051, 97%/0.0087/0.0623, and 17%/0.068/0.39 for PLSR, ADMIXTURE, and RF, respectively. PLS-QDA and ADMIXTURE, as the most relevant methods, were used on a real dataset (n = 1,013) from Norway where the two largest classes contained 532 and 192 (PLS-QDA), and 531 and 193 (ADMIXTURE) individuals, respectively. These two classes were expected to be dominating a priori. The Bayesian nature of PLS-QDA enables inclusion of desirable features such as a separate class "unknown breed combination" and informative priors for crossbreeds, making this a preferable method for the classification of breed combination in the industry.
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Affiliation(s)
- H. Vinje
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - H. K. Brustad
- Oslo Center of Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - A. Heggli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Animalia AS, Oslo, Norway
| | | | | | - L. E. Gangsei
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Animalia AS, Oslo, Norway
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