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Tian J, Tan L, Wei S, Zhu W, Ji C, Yao Z, Xu Y, Nie Q. Using multiomics to explore the weight differences between genders in Muscovy ducks. Poult Sci 2024; 103:103787. [PMID: 38743967 PMCID: PMC11108995 DOI: 10.1016/j.psj.2024.103787] [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: 03/04/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024] Open
Abstract
Sexual dimorphism in poultry, especially in Muscovy ducks, is a proven phenomenon characterized by significant differences in body weight, growth patterns, and gene expression between male and female individuals. However, there is a dearth of research on the candidate genes and mechanisms underlying these weight differences. We selected 301 Muscovy ducks and recorded their weekly body weights from birth. We utilized 3 non-linear growth models (Logistic, Bertalanffy, and Gompertz) to fit the growth curve of Muscovy ducks, it was found that the logistic model was the most suitable model for describing the growth curve of Muscovy ducks. The results from the logistic model showed that the inflection point of male Muscovy ducks occurred at a later age, and they had a heavier mature body weight than female Muscovy ducks. At 10 wk of age, we collected Muscovy duck breast muscle tissues for transcriptome sequencing (RNA-seq). To exclude the impact of weight difference, 185 differentially expressed genes (DEGs), such as PPAR, FABP3, PLIN1, and FOXO1, were screened. These DEGs were predominantly enriched in terms related to mitochondria, lipids, and nucleic acids. In addition, the gut microbiota has the ability to influence host physiology through the regulation of multiple processes, including playing a crucial role in host muscle growth and development. We randomly selected male and female Muscovy ducks for 16S rRNA sequencing analysis of their cecal microbiota. The results showed that there were significant differences in the composition of cecal microbiota between male and female Muscovy ducks. At the genus level, the relative abundance of Enterenecus and CAG_269 were lower in males compared to females, while Lawsonibacter, Parabacteroides_B, Streptococcus, UBA2658, Caccousia, and Butyricimonas were higher in males than in females. In summary, this study provides a scientific theoretical basis for revealing the different growth patterns of male and female Muscovy ducks, and offers explanations from both the molecular level and microbiological perspectives.
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Affiliation(s)
- Jinghong Tian
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China
| | - Liangtian Tan
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China
| | - Shenghua Wei
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China
| | - Weijian Zhu
- Wens Foodstuff Group Co. Ltd., Yunfu, Guangdong 527400, China
| | - Congliang Ji
- Wens Foodstuff Group Co. Ltd., Yunfu, Guangdong 527400, China
| | - Zipei Yao
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China
| | - Yibin Xu
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of· Livestock· and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangzhou Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, Guangzhou 510642, China.
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2
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Hou G, Li R, Tian M, Ding J, Zhang X, Yang B, Chen C, Huang R, Yin Y. Improving Efficiency: Automatic Intelligent Weighing System as a Replacement for Manual Pig Weighing. Animals (Basel) 2024; 14:1614. [PMID: 38891661 PMCID: PMC11171250 DOI: 10.3390/ani14111614] [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: 04/30/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
To verify the accuracy of AIWS, we weighed 106 pen growing-finishing pigs' weights using both the manual and AIWS methods, respectively. Accuracy was evaluated based on the values of MAE, MAPE, and RMSE. In the growth experiment, manual weighing was conducted every two weeks and AIWS predicted weight data was recorded daily, followed by fitting the growth curves. The results showed that MAE, MAPE, and RMSE values for 60 to 120 kg pigs were 3.48 kg, 3.71%, and 4.43 kg, respectively. The correlation coefficient r between the AIWS and manual method was 0.9410, and R2 was 0.8854. The two were extremely significant correlations (p < 0.001). In growth curve fitting, the AIWS method has lower AIC and BIC values than the manual method. The Logistic model by AIWS was the best-fit model. The age and body weight at the inflection point of the best-fit model were 164.46 d and 93.45 kg, respectively. The maximum growth rate was 831.66 g/d. In summary, AIWS can accurately predict pigs' body weights in actual production and has a better fitting effect on the growth curves of growing-finishing pigs. This study suggested that it was feasible for AIWS to replace manual weighing to measure the weight of 50 to 120 kg live pigs in large-scale farming.
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Affiliation(s)
- Gaifeng Hou
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
| | - Rui Li
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
| | - Mingzhou Tian
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
| | - Jing Ding
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
| | - Xingfu Zhang
- College of Computer Science and Technology, Heilongjiang Institute of Technology, Harbin 150050, China;
- Beijing Focused Loong Technology Co., Ltd., Beijing 100086, China
| | - Bin Yang
- Key Laboratory of Visual Perception and Artificial Intelligence of Hunan Province, College of Electrical and Information Engineering, Hunan University, Changsha 410082, China;
| | - Chunyu Chen
- College of Information and Communication, Harbin Engineering University, Harbin 150001, China;
| | - Ruilin Huang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
| | - Yulong Yin
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Hunan Research Center of Livestock and Poultry Sciences, South Central Experimental Station of Animal Nutrition and Feed Science in the Ministry of Agriculture, National Engineering Laboratory for Poultry Breeding Pollution Control and Resource Technology, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.H.); (R.L.); (M.T.); (J.D.)
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Growth charts for small sample sizes using unsupervised clustering: Application to canine early growth. Vet Res Commun 2022; 47:693-706. [DOI: 10.1007/s11259-022-10029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
AbstractBreed-specific growth curves (GCs) are needed for neonatal puppies, but breed-specific data may be insufficient. We investigated an unsupervised clustering methodology for modeling GCs by augmenting breed-specific data with data from breeds having similar growth profiles. Puppy breeds were grouped by median growth profiles (bodyweights between birth and Day 20) using hierarchical clustering on principal components. Median bodyweights for breeds in a cluster were centered to that cluster’s median and used to model cluster GCs by Generalized Additive Models for Location, Shape and Scale. These were centered back to breed growth profiles to produce cluster-scale breed GCs. The accuracy of breed-scale GCs modeled with breed-specific data only and cluster-scale breed GCs were compared when modeled from diminishing sample sizes. A complete dataset of Labrador Retriever bodyweights (birth to Day 20) was split into training (410 puppies) and test (460 puppies) datasets. Cluster-scale breed and breed-scale GCs were modelled from defined sample sizes from the training dataset. Quality criteria were the percentages of observed data in the test dataset outside the target growth centiles of simulations. Accuracy of cluster-scale breed GCs remained consistently high down to sampling sizes of three. They slightly overestimated breed variability, but centile curves were smooth and consistent with breed-scale GCs modeled from the complete Labrador Retriever dataset. At sampling sizes ≤ 20, the quality of breed-scale GCs reduced notably. In conclusion, GCs for neonatal puppies generated using a breed-cluster hybrid methodology can be more satisfactory than GCs at purely the breed level when sample sizes are small.
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Contento J, Mass P, Cleveland V, Aslan S, Matsushita H, Hayashi H, Nguyen V, Kawaji K, Loke YH, Nelson K, Johnson J, Krieger A, Olivieri L, Hibino N. Location matters: Offset in tissue-engineered vascular graft implantation location affects wall shear stress in porcine models. JTCVS OPEN 2022; 12:355-363. [PMID: 36590712 PMCID: PMC9801286 DOI: 10.1016/j.xjon.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 01/04/2023]
Abstract
Objective Although surgical simulation using computational fluid dynamics has advanced, little is known about the accuracy of cardiac surgical procedures after patient-specific design. We evaluated the effects of discrepancies in location for patient-specific simulation and actual implantation on hemodynamic performance of patient-specific tissue-engineered vascular grafts (TEVGs) in porcine models. Methods Magnetic resonance angiography and 4-dimensional (4D) flow data were acquired in porcine models (n = 11) to create individualized TEVGs. Graft shapes were optimized and manufactured by electrospinning bioresorbable material onto a metal mandrel. TEVGs were implanted 1 or 3 months postimaging, and postoperative magnetic resonance angiography and 4D flow data were obtained and segmented. Displacement between intended and observed TEVG position was determined through center of mass analysis. Hemodynamic data were obtained from 4D flow analysis. Displacement and hemodynamic data were compared using linear regression. Results Patient-specific TEVGs were displaced between 1 and 8 mm during implantation compared with their surgically simulated, intended locations. Greater offset between intended and observed position correlated with greater wall shear stress (WSS) in postoperative vasculature (P < .01). Grafts that were implanted closer to their intended locations showed decreased WSS. Conclusions Patient-specific TEVGs are designed for precise locations to help optimize hemodynamic performance. However, if TEVGs were implanted far from their intended location, worse WSS was observed. This underscores the importance of not only patient-specific design but also precision-guided implantation to optimize hemodynamics in cardiac surgery and increase reproducibility of surgical simulation.
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Key Words
- 4D, four-dimensional
- AR, augmented reality
- CFD, computational fluid dynamics
- CHD, congenital heart disease
- LPA, left pulmonary artery
- MPA, main pulmonary artery
- MRA, magnetic resonance angiography
- MRI, magnetic resonance imaging
- PA, pulmonary artery
- RPA, right pulmonary artery
- SCA, subclavian artery
- STL, stereolithography
- TEVG, tissue-engineered vascular graft
- WSS, wall shear stress
- center of gravity
- computational fluid dynamics
- displacement
- hemodynamics
- surgical planning
- tissue-engineered vascular grafts
- wall shear stress
- αSMA, α-smooth muscle actin
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Affiliation(s)
| | - Paige Mass
- Department of Cardiology, Children's National Hospital, Washington, DC
| | - Vincent Cleveland
- Department of Cardiology, Children's National Hospital, Washington, DC
| | - Seda Aslan
- Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, Md
| | - Hiroshi Matsushita
- Division of Cardiac Surgery, Department of Surgery, University of Chicago, Chicago, Ill
| | - Hidenori Hayashi
- Division of Cardiac Surgery, Department of Surgery, University of Chicago, Chicago, Ill
| | - Vivian Nguyen
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, Ill
| | - Keigo Kawaji
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, Ill
| | - Yue-Hin Loke
- Department of Cardiology, Children's National Hospital, Washington, DC
| | | | | | - Axel Krieger
- Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, Md
| | - Laura Olivieri
- Department of Cardiology, Children's National Hospital, Washington, DC
| | - Narutoshi Hibino
- Division of Cardiac Surgery, Department of Surgery, University of Chicago, Chicago, Ill,Department of Cardiovascular Surgery, Advocate Children's Hospital, Oak Lawn, Ill,Address for reprints: Narutoshi Hibino, MD, PhD, Section of Cardiac Surgery, Department of Surgery, The University of Chicago, Advocate Children's Hospital, 5841 S Maryland Ave, Room E500B, MC5040, Chicago, IL 60637.
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Wang Q, Shi C, Liu D, Jiang G. Estimation of body weight in captive Amur tigers (Panthera tigris altaica). Integr Zool 2021; 17:1106-1120. [PMID: 34751498 DOI: 10.1111/1749-4877.12612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
So far, there has been no safe and convenient method to weigh the large fierce animals, like Amur tigers. To address this problem, we built models to predict the body weight of Amur tigers based on the fact that body weight is proportional to body measurements or age. Using the method of body measurements, we extracted the body measurements from four different kinds of the lateral body image of tigers, i.e., total lateral image, central lateral image, ellipse fitting image and rectangle fitting image, and then we respectively used artificial neural network (ANN) and power regression model to analyze the predictive relationships between body weight and body measurements. Our results demonstrated that, among all ANN models, the model built with rectangle fitting image had the smallest mean square error. Comparatively, we screened power regression models which had the smallest Akakai information criteria (AIC). In addition, using the method of age, we fitted nonlinear regression models for the relationship between body weight and age and found that, for male tigers, logistic model had the smallest AIC. For female tigers, Gompertz model had the smallest AIC. Consequently, this study could be applied to estimate body weight of captive, or even wild, Amur tigers safely and conveniently, helping to monitor individual health and growth of the Amur tiger populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qi Wang
- School of Mental Health, Wenzhou Medical University, Wenzhou, China.,Feline Research Center of NationalForestry and GrasslandAdministration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Chunmei Shi
- Feline Research Center of NationalForestry and GrasslandAdministration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,College of Science, Northeast Forestry University, Harbin, China
| | - Dan Liu
- Siberian Tiger Park, Harbin, China
| | - Guangshun Jiang
- Feline Research Center of NationalForestry and GrasslandAdministration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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Tan Y, Gan M, Shen L, Li L, Fan Y, Chen Y, Chen L, Niu L, Zhao Y, Jiang A, Jiang D, Zhang S, Zhu L. Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development. Int J Mol Sci 2021; 22:ijms22020503. [PMID: 33419093 PMCID: PMC7825455 DOI: 10.3390/ijms22020503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 11/16/2022] Open
Abstract
Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.
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Affiliation(s)
- Ya Tan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Yuan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ying Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Dongmei Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Shunhua Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
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7
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Luo J, Shen L, Gan M, Jiang A, Chen L, Ma J, Jin L, Liu Y, Tang G, Jiang Y, Li M, Li X, Zhang S, Zhu L. Profiling of skeletal muscle tissue for long non-coding RNAs related to muscle metabolism in the QingYu pig at the growth inflection point. Anim Biosci 2020; 34:1309-1320. [PMID: 33152219 PMCID: PMC8255898 DOI: 10.5713/ajas.20.0429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Investigation of muscle growth at different developmental stages is an appropriate strategy for studying the mechanisms underlying muscle development and differences in phenotypes. In particular, the muscle development mechanisms and the difference between the fastest and slowest growth rates. METHODS In this study, we used a growth curve model to fit the growth inflection point (IP) of QingYu pigs and compared differences in the long non-coding RNA (lncRNA) transcriptome of muscle both at the growth IP and plateau phase (PP). RESULTS The growth curve of the QingYu pig had a good fit (R2 = 0.974) relative to a typical S-curve and reached the IP at day 177.96. At the PP, marbling, intramuscular fat, and monounsaturated fatty acids had increased significantly and the percentage of lean muscle and polyunsaturated fatty acids had decreased. A total of 1,199 mRNAs and 62 lncRNAs were differentially expressed at the IP compared with the PP. Additional to gene ontology and Kyoto encyclopedia of genes and genomes pathway analyses, these differentially expressed protein coding genes were principally related to muscle growth and lipid metabolism. CONCLUSION Our results suggest that the identified differentially expressed lncRNAs, could play roles in muscle growth, fat deposition and regulation of fatty acid composition at the IP and PP.
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Affiliation(s)
- Jia Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Anan Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Yihui Liu
- Sichuan Province General Station of Animal Husbandry, Chengdu 610041, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan, Chengdu 611130, China
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8
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Liu B, Shen L, Guo Z, Gan M, Chen Y, Yang R, Niu L, Jiang D, Zhong Z, Li X, Zhang S, Zhu L. Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population. Anim Biosci 2020; 34:1105-1115. [PMID: 32777894 PMCID: PMC8255872 DOI: 10.5713/ajas.19.0884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/14/2020] [Indexed: 11/27/2022] Open
Abstract
Objective To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (PN) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.
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Affiliation(s)
- Bin Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhixian Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mailing Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ying Chen
- Sichuan Province General Station of Animal Husbandry, Chengdu 610066, China
| | - Runling Yang
- Agriculture and Rural Bureau of Mabian Yi Autonomous County, Mabian, 614600, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dongmei Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhijun Zhong
- Sichuan Academy of Animal Sciences, Chengdu 610066, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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9
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Gan M, Shen L, Chen L, Jiang D, Jiang Y, Li Q, Chen Y, Ge G, Liu Y, Xu X, Li X, Zhang S, Zhu L. Meat Quality, Amino Acid, and Fatty Acid Composition of Liangshan Pigs at Different Weights. Animals (Basel) 2020; 10:ani10050822. [PMID: 32397391 PMCID: PMC7278381 DOI: 10.3390/ani10050822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary The research on the quality of traditional pork can not only provide a reference for the thorough breeding and food development of pigs, but also make a reference for understanding the local history and social culture. The Liangshan pig is a traditional Chinese miniature pig breed. It is mainly raised in the Liangshan Yi area and is closely related to the dietary culture of the local people. The characteristics of, and changes in, the meat quality, amino acid composition and fatty acid composition of Liangshan pigs of different weights were revealed for the first time in this paper. It was found that as the weight of Liangshan pigs increased, the contents of marbling score, intramuscular fat, shear force, Met, Asp, Asn, C18: 0 and C20: 2 increased, and drip loss, Trp and C22: 6 decreased. Taken together, our findings serve as a reference for the development of the local Liangshan pig industry. Abstract Indigenous pig breeds are important biological resources and their diversity has been severely damaged. The Liangshan pig is a typical mountain-type local pig breed in southwest China. Here, the meat quality, amino acid, and fatty acid composition of Liangshan pigs were compared at seven stages within the weight range of 50–90 kg. A score for comprehensive factors of meat quality was maintained after rising and kept in a plateau within 74.9–91.5 kg of body weight. The total amount of amino acids in the longissimus dorsi muscle remained stable, and the total fatty acids showed an upward trend. Amino acid composition analysis revealed that as the body weight of Liangshan pigs increased, umami, basic, and acidic amino acid contents decreased, while the essential amino acids (EAA) content and the ratio of basic amino acids to acidic amino acids increased. Fatty acid composition analysis revealed that as body weight increased, the content of polyunsaturated fatty acids (PUFA) exhibited a downward trend, while the content of saturated fatty acids (SFA) exhibited an upward trend. This study is a primary step towards the development and utilization of Liangshan pigs and provides useful information for local pork processing and genetic improvement.
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Affiliation(s)
- Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Yaan 625014, China;
| | - Qiang Li
- Sichuan Province General Station of Animal Husbandry, Chengdu 611130, China; (Q.L.); (Y.C.); (G.G.); (Y.L.); (X.X.)
| | - Ying Chen
- Sichuan Province General Station of Animal Husbandry, Chengdu 611130, China; (Q.L.); (Y.C.); (G.G.); (Y.L.); (X.X.)
| | - Guihua Ge
- Sichuan Province General Station of Animal Husbandry, Chengdu 611130, China; (Q.L.); (Y.C.); (G.G.); (Y.L.); (X.X.)
| | - Yihui Liu
- Sichuan Province General Station of Animal Husbandry, Chengdu 611130, China; (Q.L.); (Y.C.); (G.G.); (Y.L.); (X.X.)
| | - Xu Xu
- Sichuan Province General Station of Animal Husbandry, Chengdu 611130, China; (Q.L.); (Y.C.); (G.G.); (Y.L.); (X.X.)
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (S.Z.); (L.Z.)
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.G.); (L.S.); (L.C.); (D.J.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (S.Z.); (L.Z.)
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The potential of Hoplias malabaricus (Characiformes: Erythrinidae), a Neotropical carnivore, for aquaculture. AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Lee W, Han KH, Kim HT, Choi H, Ham Y, Ban TW. Prediction of average daily gain of swine based on machine learning. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2019. [DOI: 10.3233/jifs-169869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Woongsup Lee
- Department of Information and Communication Engineering, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Kang-Hwi Han
- Department of Information and Communication Engineering, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Hyeon Tae Kim
- Department of Bio-Industrial Machinery Engineering, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Gyeongnam, Republic of Korea
| | - Heechul Choi
- Livestock environment division, National Institue of Animal Science, Kongjwipatjwi, lseo, Wanju, JeonBuk, Republic of Korea
| | - Younghwa Ham
- Agrirobotech Co., Ltd., Sina-ro, Bubal-eup, Icheon-si, Gyeonggi-do, Republic of Korea
| | - Tae-Won Ban
- Department of Information and Communication Engineering, Institute of Marine Industry, Gyeongsang National University, Tongyeong, Republic of Korea
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Using quantile regression methodology to evaluate changes in the shape of growth curves in pigs selected for increased feed efficiency based on residual feed intake. Animal 2018; 13:1009-1019. [PMID: 30306885 DOI: 10.1017/s1751731118002616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Growth rate is a major component of feed efficiency when estimating residual feed intake (RFI). Quantile regression (QR) methodology can be used to identify animals with different growth trajectories. The objective of this study was to evaluate the use of QR to identify phenotypic and genetic differences in pigs selected for low RFI. Using performance data on 750 Yorkshire pigs selected for low RFI, individual average daily gain (ADG), average daily feed intake (ADFI), RFI and Gompertz growth curve parameters (asymptotic weight (a), inflection point (b) and decay parameter (c)) were estimated for each pig. Using QR methodology, three Gompertz growth curves were estimated for the whole population for three quantiles (0.1, 0.5 and 0.9) of the BW data. Each animal was classified into one of the quantile regression groups (QRG) based on their overall Euclidian distance between each observed and estimated BW from the quantile growth curves. These three curves were also estimated using only part of the data (generations -1 to 3, and -1 to 4) in order to evaluate the agreement classification rate of animals from later generations into QRGs. We evaluated the effect of QRG on growth parameters and performance traits. Genetic parameters were estimated for these traits, as well as for QRG. In addition, genetic trends for each QRG were estimated. Three distinct growth curves were observed for animals classified into either quantiles 0.1 (QRG0.1), 0.5 (QRG0.5) or 0.9 (QRG0.9). When only part of the data was used to estimate quantile growth curves, all animals from QRG0.1 were correctly classified in their group. Animals in QRG0.1 had significantly lower ADFI, ADG and RFI, and greater a, b and c than animals in the other groups. Quantile regression groups analysed as a trait was highly heritable (0.41) and had high (0.8) and moderate (0.46) genetic correlations with ADG and RFI, respectively. Selection for reduced RFI increased the number of animals classified as QRG0.1 in the population. Overall, downward genetic trends were observed for all traits as a function of selection for reduced RFI. However, QRG0.1 was the only group that had a positive genetic trend for ADG. Altogether, these results indicate that selection for reduced RFI changes the shape of growth curves in Yorkshire in pigs, and that QR methodology was able to identify animals having different genetic potential for feed efficiency, bringing a new opportunity to improve selection for reduced RFI.
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Comparison reproductive, growth performance, carcass and meat quality of Liangshan pig crossbred with Duroc and Berkshire genotypes and heterosis prediction. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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