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Alves AAC, Fernandes AFA, Lopes FB, Breen V, Hawken R, Rosa GJM. Genetic analysis of feed efficiency and novel feeding behavior traits measured in group-housed broilers using electronic feeders. Poult Sci 2024; 103:103737. [PMID: 38669821 PMCID: PMC11063640 DOI: 10.1016/j.psj.2024.103737] [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: 11/13/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for ten FB traits: daily feed intake (DFI), daily number of visits (NVIS), time spent at the feeders (TSF), number of visited feeders (NVF), visiting activity interval (VAI), feeding rate (FR), daily number of meals (NMEAL), average intake per meal (INTMEAL), number of visits per meal (VISMEAL) and interval between meals (MEALIVL). All FB traits were then considered as the average per bird across the feeding test period. Three growth traits (body weight at the start - SBW and at the end of the feeding test - FBW, and weight gain over the test period - BWG), and 2 feed efficiency (FE) traits (Feed Conversion Rate - FCR and Residual Feed Intake - RFI) were also recorded. The (co)variance components were estimated using multitrait animal mixed models. For growth and FE, the heritability (h2) estimates were moderate, ranging from 0.20 ± 0.01 (BWG) to 0.32 ± 0.02 (RFI). Overall, the h2 estimates for FB traits were higher than for productive traits, ranging from 0.31 ± 0.01 (DFI) to 0.56 ± 0.02 (TSF). DFI presented high genetic correlations (0.53-0.86) with all performance traits. Conversely, the remaining FB traits presented null to moderate genetic correlations with these traits, ranging from -0.38 to 0.42 for growth traits and between -0.14 and 0.25 for FE traits. Genetic selection for favorable feeding behavior is expected to exhibit a fast genetic response. The results suggest that it is possible to consider different feeding strategies without compromising the genetic progress of FE. Conversely, breeding strategies prioritizing a higher bird activity might result in lighter broiler lines in the long term, given the negative genetic correlations between visit-related traits (NV, NVF, and NMEAL) and growth traits (SBW and FBW).
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Affiliation(s)
- Anderson A C Alves
- Department of Animal and Dairy Sciences, University of Wisconsin, 53705, Madison, USA
| | | | | | | | | | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin, 53705, Madison, USA.
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2
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Chen Z, Wang G, Wang W, Wang X, Huang Y, Jia J, Gao Q, Xu H, He L, Xu Y, Liu Z, Sun J, Li C. Relationship between jejunum ATPase activity and antioxidant function on the growth performance, feed conversion efficiency, and jejunum microbiota in Hu sheep (Ovis aries). BMC Vet Res 2024; 20:242. [PMID: 38831422 PMCID: PMC11149274 DOI: 10.1186/s12917-024-04100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND ATPase activity and the antioxidant function of intestinal tissue can reflect intestinal cell metabolic activity and oxidative damage, which might be related to intestinal function. However, the specific influence of intestinal ATPase activity and antioxidant function on growth performance, feed conversion efficiency, and the intestinal microbiota in sheep remains unclear. RESULTS This study analyzed the correlation between ATPase activity and antioxidant function in the jejunum of 92 Hu sheep and their growth performance and feed conversion efficiency. Additionally, individuals with the highest (H group) and lowest (L group) jejunum MDA content and Na+ K+-ATPase activity were further screened, and the effects of jejunum ATPase activity and MDA content on the morphology and microbial community of sheep intestines were analyzed. There was a significant correlation between jejunum ATPase and SOD activity and the initial weight of Hu sheep (P < 0.01). The H-MDA group exhibited significantly higher average daily gain (ADG) from 0 to 80 days old and higher body weight (BW) after 80 days. ATPase and SOD activities, and MDA levels correlated significantly and positively with heart weight. The jejunum crypt depth and circular muscle thickness in the H-ATP group were significantly higher than in the L-ATP group, and the villus length, crypt depth, and longitudinal muscle thickness in the H-MDA group were significantly higher than in the L-MDA group (P < 0.01). High ATPase activity and MDA content significantly reduced the jejunum microbial diversity, as indicated by the Chao1 index and observed species, and affected the relative abundance of specific taxa. Among species, the relative abundance of Olsenella umbonata was significantly higher in the H-MDA group than in the L-MDA group (P < 0.05), while Methanobrevibacter ruminantium abundance was significantly lower than in the L-MDA group (P < 0.05). In vitro culture experiments confirmed that MDA promoted the proliferation of Olsenella umbonata. Thus, ATPase and SOD activities in the jejunum tissues of Hu sheep are predominantly influenced by congenital factors, and lambs with higher birth weights exhibit lower Na+ K+-ATPase, Ca2+ Mg2+-ATPase, and SOD activities. CONCLUSIONS The ATPase activity and antioxidant performance of intestinal tissue are closely related to growth performance, heart development, and intestinal tissue morphology. High ATPase activity and MDA content reduced the microbial diversity of intestinal tissue and affect the relative abundance of specific taxa, representing a potential interaction between the host and its intestinal microbiota.
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Affiliation(s)
- Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Guoxiu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Jiale Jia
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Qihao Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Haoyu Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yunfei Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Zhen Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Jinlin Sun
- Gansu Runmu Bio-Engineering Co.,LTD, Yongchang, Gansu, 737200, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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Zhao D, Liu R, Tan X, Kang H, Wang J, Ma Z, Zhao H, Xiang H, Zhang Z, Li H, Zhao G. Large-scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits. J Anim Sci Biotechnol 2024; 15:70. [PMID: 38730308 DOI: 10.1186/s40104-024-01026-3] [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: 10/14/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Carcass traits are crucial indicators of meat production efficiency. However, the molecular regulatory mechanisms associated with these traits remain unclear. RESULTS In this study, we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms. Based on association analyses with the elastic net (EN) model, we identified 12 candidate genes (AMY1A, AP3B2, CEBPG, EEF2, EIF4EBP1, FGFR1, FOXD3, GOLM1, LOC107052698, PABPC1, SERPINB6 and TBC1D16) for 4 carcass-related traits, namely live weight, dressed weight, eviscerated weight, and breast muscle weight. SERPINB6 was identified as the only overlapping gene by 3 analyses, EN model analysis, weighted gene co-expression network analysis and differential expression analysis. Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts. Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression. Furthermore, a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3'UTR of SERPINB6. CONCLUSIONS Collectively, our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation. Additionally, the downstream variant rs317934171 regulates SERPINB6 expression. These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.
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Affiliation(s)
- Di Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ranran Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaodong Tan
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jie Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Haiquan Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Zhengfen Zhang
- Guangdong Tinoo's Foods Group Co., Ltd., Qingyuan, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.
- Guangdong Tinoo's Foods Group Co., Ltd., Qingyuan, China.
| | - Guiping Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Ma X, Ying F, Li Z, Bai L, Wang M, Zhu D, Liu D, Wen J, Zhao G, Liu R. New insights into the genetic loci related to egg weight and age at first egg traits in broiler breeder. Poult Sci 2024; 103:103613. [PMID: 38492250 PMCID: PMC10959720 DOI: 10.1016/j.psj.2024.103613] [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: 12/19/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Egg weight (EW) and age at first egg (AFE) are economically important traits in breeder chicken production. The genetic basis of these traits, however, is far from understood, especially for broiler breeders. In this study, genetic parameter estimation, genome-wide association analysis, meta-analysis, and selective sweep analysis were carried out to identify genetic loci associated with EW and AFE in 6,842 broiler breeders. The study found that the heritability of EW ranged from 0.42 to 0.44, while the heritability of AFE was estimated at 0.33 in the maternal line. Meta-analysis and selective sweep analysis identified two colocalized regions on GGA4 that significantly influenced EW at 32 wk (EW32W) and at 43 wk (EW43W) with both paternal and maternal lines. The genes AR, YIPF6, and STARD8 were located within the significant region (GGA4: 366.86-575.50 kb), potentially affecting EW through the regulation of follicle development, cell proliferation, and lipid transfer etc. The promising genes LCORL and NCAPG were positioned within the significant region (GGA4:75.35-75.42 Mb), potentially influencing EW through pleiotropic effects on growth and development. Additionally, 3 significant regions were associated with AFE on chromosomes GGA7, GGA19, and GGA27. All of these factors affected the AFE by influencing ovarian development. In our study, the genomic information from both paternal and maternal lines was used to identify genetic regions associated with EW and AFE. Two genomic regions and eight genes were identified as the most likely candidates affecting EW and AFE. These findings contribute to a better understanding of the genetic basis of egg production traits in broiler breeders and provide new insights into future technology development.
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Affiliation(s)
- Xiaochun Ma
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fan Ying
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Zhengda Li
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lu Bai
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mengjie Wang
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dan Zhu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Dawei Liu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Jie Wen
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Chen Z, Wang G, Wang W, Wang X, Huang Y, Jia J, Gao Q, Xu H, Xu Y, Ma Z, He L, Cheng J, Li C. PDE9A polymorphism and association analysis with growth performance and gastrointestinal weight of Hu sheep. Gene 2024; 900:148137. [PMID: 38184018 DOI: 10.1016/j.gene.2024.148137] [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: 07/20/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Phosphodiesterase 9A (PDE9A) plays a crucial role in activating the cGMP-dependent signaling pathway and may have important effects on the growth and development of the gastrointestinal tract in Hu sheep. In this study, we analyzed the single nucleotide polymorphisms of PDE9A in 988 Hu sheep and their correlation with growth performance, feed efficiency, and gastrointestinal development. Additionally, we examined the expression level of different PDE9A genotypes in the gastrointestinal tract of Hu sheep by using fluorescence quantitative PCR. The results revealed a moderate level of polymorphism (0.25 < PIC < 0.50) at the g.286248617 T > C mutation site located in the first intron of PDE9A in Hu sheep, with three genotypes: CC, CT, and TT. The weights of the omasum, colon, and cecum were significantly greater in the CC genotype than in the TT genotype (P < 0.05), and the expression level of PDE9A in the tissues of the rumen, ileum, cecum, and colon was notably lower in the CC genotype individuals (P < 0.05). These findings suggest that the polymorphism of PDE9A affects the weight of the stomach, colon, and cecum in Hu sheep through expression regulation. Overall, the results of this study suggest that the g.286248617 T > C mutation site in the first intron of PDE9A can serve as a potential molecular marker for breeding practices related to the gastrointestinal weight of Hu sheep.
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Affiliation(s)
- Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Guoxiu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiale Jia
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qihao Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Haoyu Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yunfei Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Tan X, Liu R, Zhao D, He Z, Li W, Zheng M, Li Q, Wang Q, Liu D, Feng F, Zhu D, Zhao G, Wen J. Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens. J Adv Res 2024; 55:1-16. [PMID: 36871617 PMCID: PMC10770282 DOI: 10.1016/j.jare.2023.02.016] [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: 01/11/2023] [Revised: 02/16/2023] [Accepted: 02/26/2023] [Indexed: 03/07/2023] Open
Abstract
INTRODUCTION Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems. OBJECT Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood. METHOD We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping and the Mendelian randomization was applied. RESULT We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes. CONCLUSION Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory target (SOX6-MYH1s axis) for breast muscle yield and myopathy, which could aid in the development of genome-scale selective breeding aimed at high meat yield in broiler chickens.
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Affiliation(s)
- Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Di Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhengxiao He
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dawei Liu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Furong Feng
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Dan Zhu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Yang X, Wang W, Wang X, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Wang J, Xu D, Cheng J, Li W, Zhou B, Lin C, Zeng X, Zhai R, Ma Z, Liu J, Cui P, Zhang X. Polymorphism in ovine ADCY8 gene and its association with residual feed intake in Hu sheep. Anim Biotechnol 2023; 34:3355-3362. [PMID: 36384395 DOI: 10.1080/10495398.2022.2145294] [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: 11/18/2022]
Abstract
Feed efficiency makes up a large part of sheep production, which also has a crucial impact on the economic benefits of producers. This study explores the polymorphism of Adenylyl cyclase 8 gene associated with feed efficiency and detects the expression characteristics of ADCY8 in ten tissues of Hu sheep. The polymorphism of ADCY8 was recognized by using PCR amplification and Sanger sequencing, KASPar technology was used for genotyping subsequently, and the relationship between SNP and RFI is also studied. The results indicated that an intronic mutation g.24799148 C > T (rs 423395741) was identified in ADCY8, and association analysis showed that the SNP g.24799148 C > T (rs 423395741) was significantly associated with RFI at 100-120, 100-140, 100-160, and 100-180 days (p < 0.05). The quantitative real-time PCR (qRT-PCR) result showed that ADCY8 was expressed in ten tissues, and the expression of ADCY8 gene in rumen tissue was significantly higher than in the other tested tissues. Therefore, these results indicated that the ADCY8 mutation locus may be used as a candidate molecular marker for evaluating the feed efficiency of Hu sheep.
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Affiliation(s)
- Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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8
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He Z, Liu R, Wang M, Wang Q, Zheng J, Ding J, Wen J, Fahey AG, Zhao G. Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens. MICROBIOME 2023; 11:198. [PMID: 37653442 PMCID: PMC10472625 DOI: 10.1186/s40168-023-01627-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Improving feed efficiency is the most important goal for modern animal production. The regulatory mechanisms of controlling feed efficiency traits are extremely complex and include the functions related to host genetics and gut microbiota. Short-chain fatty acids (SCFAs), as significant metabolites of microbiota, could be used to refine the combined effect of host genetics and gut microbiota. However, the association of SCFAs with the gut microbiota and host genetics for regulating feed efficiency is far from understood. RESULTS In this study, 464 broilers were housed for RFI measuring and examining the host genome sequence. And 300 broilers were examined for cecal microbial data and SCFA concentration. Genome-wide association studies (GWAS) showed that four out of seven SCFAs had significant associations with genome variants. One locus (chr4: 29414391-29417189), located near or inside the genes MAML3, SETD7, and MGST2, was significantly associated with propionate and had a modest effect on feed efficiency traits and the microbiota. The genetic effect of the top SNP explained 8.43% variance of propionate. Individuals with genotype AA had significantly different propionate concentrations (0.074 vs. 0.131 μg/mg), feed efficiency (FCR: 1.658 vs. 1.685), and relative abundance of 14 taxa compared to those with the GG genotype. Christensenellaceae and Christensenellaceae_R-7_group were associated with feed efficiency, propionate concentration, the top SNP genotypes, and lipid metabolism. Individuals with a higher cecal abundance of these taxa showed better feed efficiency and lower concentrations of caecal SCFAs. CONCLUSION Our study provides strong evidence of the pathway that host genome variants affect the cecal SCFA by influencing caecal microbiota and then regulating feed efficiency. The cecal taxa Christensenellaceae and Christensenellaceae_R-7_group were identified as representative taxa contributing to the combined effect of host genetics and SCFAs on chicken feed efficiency. These findings provided strong evidence of the combined effect of host genetics and gut microbial SCFAs in regulating feed efficiency traits. Video Abstract.
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Affiliation(s)
- Zhengxiao He
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Mengjie Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Qiao Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jumei Zheng
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jiqiang Ding
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Alan G. Fahey
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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9
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Gao S, Zhang Q, Liu C, Shen H, Wang J. Effects of maggot antimicrobial peptides on growth performance, immune function, and cecal flora of yellow-feathered broilers. Front Vet Sci 2023; 10:1156964. [PMID: 37559887 PMCID: PMC10407657 DOI: 10.3389/fvets.2023.1156964] [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: 02/02/2023] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
INTRODUCTION This study investigated the effects of maggot antimicrobial peptides on growth performance, blood parameters, immune organ index, and cecum microbial diversity in yellow broilers. METHODS The addition of 100-300 mg/kg maggots antimicrobial peptides to the corn-soybean meal basal diet was evaluated. Two hundred and forty one-day-old yellow-feathered broilers were randomly divided into four groups (60 chickens in each group): basal diet group (BC group), basal diet group + 100, 200, 300 mg/kg maggots antimicrobial peptides (MDAL group, MDAM group, and MDAH group). RESULTS The result showed that the average daily feed intake (ADFI) of the BC group, MDAM group, and MDAH group was higher than that of the MDAL group (P > 0.05), the average daily gain of MDAM group and MDAH group was significantly higher than that of BC group and MDAL group (P < 0.05), but the feed-weight ratio (F/G) was significantly lower than that of BC group (P < 0.05). The total protein (TP) content in the MDAM group and MDAH group was significantly higher than that in the BC group (P < 0.05), and the albumin (ALB) content in the MDAH group was higher than that in the BC group (P > 0.05). The contents of IgA and IgG in the MDAH group were significantly higher than those in the BC group (P < 0.05). In contrast, the content of alanine aminotransferase (ALT) in the MDAH group was significantly lower than that in the BC group (P < 0.05). The thymus and spleen indexes of the MDAH group were significantly higher than those of the BC group (P < 0.05). 16S rDNA sequencing results showed that Bacteroidota and Bacteroides were the dominant phylum and genus of cecal microorganisms at the phylum and genus levels, respectively. Cecum microorganisms are mainly involved in biological processes such as energy production and conversion, amino acid transport and metabolism, and carbohydrate transport and metabolism. DISCUSSION It was concluded that adding different doses of maggot antimicrobial peptide to the basal diet could improve yellow-feathered broilers' growth and immune performance and change the cecum flora. The appropriate dose of antimicrobial peptide addition was 300 mg/kg.
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Affiliation(s)
- Shengjie Gao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | | | - Caixia Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Hong Shen
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jungang Wang
- College of Agriculture, Shihezi University, Shihezi, China
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10
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Zhao L, Wang W, Wang X, Zhang D, Li X, Zhao Y, Zhang Y, Xu D, Cheng J, Wang J, Li W, Lin C, Wu W, Zhang X, Zheng W. Identification of SNPs and expression patterns of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. Gene 2023; 853:147100. [PMID: 36470483 DOI: 10.1016/j.gene.2022.147100] [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: 07/20/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Growth traits are economically important traits in sheep breeding. This study was conducted to evaluate the polymorphisms of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. We measured and recorded the body weight (BW), body height (BH), body length (BL) and feed conversion ratio (FCR) of 1418 male Hu sheep raised in the same environment from 80 to 180 days of age. The total of four SNPs in the ALB, AHSG and GC genes were identified by direct sequencing technology. The results of association analysis showed that two loci (g.8699 A>T and g.13458 T>C) of ALB gene significantly affect average daily gain (ADG; P < 0.05). The genotypes of SNP g.2454 T>C in AHSG gene were significantly associated with ADG and FCR (P < 0.05). There were significant associations between GC g.19484 A>C and BW, BH and BL (P < 0.05). The results of qRT-PCR showed that ALB, AHSG, and GC genes were extremely significantly higher in H_BW sheep compared with those in the L_BW sheep (P < 0.01). These results revealed that ALB-1 g.8699 A>T, ALB-2 g.13458 T>C, AHSG g.2454 T>C and GC g.19484 A>C loci are potential molecular markers for Hu sheep breeding.
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Affiliation(s)
- Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang 830000, China.
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11
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Lin C, Wang W, Zhang D, Huang K, Li X, Zhang Y, Zhao Y, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhao L, Ma Z, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Sun L, Weng X, Wu W, Zhang X, Zheng W. Polymorphisms in SHISA3 and RFC3 genes and their association with feed conversion ratio in Hu sheep. Front Vet Sci 2023; 9:1010045. [PMID: 36686193 PMCID: PMC9850526 DOI: 10.3389/fvets.2022.1010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
In animal husbandry, feed efficiency is a crucial economic trait. In this study, the general linear model was used to perform association analysis for various genotypes and feed conversion ratio (FCR)-related traits. Reverse transcription-quantitative PCR (RT-qPCR) was used to detect the expression of SHISA3 and RFC3 mRNA levels in 10 tissues from 6 sheep. The results showed that SNPs in the NC_040257.1:c.625 T > C and NC_040261.1:g.9905 T > C were analyzed whether they were associated to feed efficiency parameters in Hu sheep (body weight, feed intake, average daily growth, and feed conversion ratio). NC_040257.1:c.625 T > C was shown to be significantly associated with body weight at 80, 100, and 120 days as well as feed conversion ratio (P < 0.05), whereas NC_040261.1:g.9905 T > C was found to be significantly associated with average daily weight gain from 80-140 days (ADG80-140) and FCR (P < 0.05). In Hu sheep, the CC genotypes of SHISA3 and RFC3 were the most common genotypes related to feed efficiency traits. Furthermore, the feed conversion ratio of the combined genotypes TT SHISA3-CC RFC3, TT SHISA3-CT RFC3, TT SHISA3-TT RFC3, CT SHISA3-CC RFC3 and CT SHISA3-CT RFC3 was significantly better than the FCR of CC SHISA3-TT RFC3. RT-qPCR results showed that the expression levels of SHISA3 were lower in the lung than in spleen, kidney, muscle and lymph (P < 0.05), and RFC3 was the lung had a highly significant higher expression level than the heart, liver, spleen, and muscle (P < 0.01). In conclusion, SHISA3 and RFC3 polymorphisms can be used as genetic markers for improving feed conversion efficiency in Hu sheep.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Landi Sun
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China,*Correspondence: Xiaoxue Zhang ✉
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China,Wenxin Zheng ✉
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12
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Jorge-Smeding E, Polakof S, Bonnet M, Durand S, Centeno D, Pétéra M, Taussat S, Cantalapiedra-Hijar G. Untargeted metabolomics confirms the association between plasma branched chain amino acids and residual feed intake in beef heifers. PLoS One 2022; 17:e0277458. [PMID: 36445891 PMCID: PMC9707789 DOI: 10.1371/journal.pone.0277458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/27/2022] [Indexed: 12/02/2022] Open
Abstract
This study explored plasma biomarkers and metabolic pathways underlying feed efficiency measured as residual feed intake (RFI) in Charolais heifers. A total of 48 RFI extreme individuals (High-RFI, n = 24; Low-RFI, n = 24) were selected from a population of 142 heifers for classical plasma metabolite and hormone quantification and plasma metabolomic profiling through untargeted LC-MS. Most efficient heifers (Low-RFI) had greater (P = 0.03) plasma concentrations of IGF-1 and tended to have (P = 0.06) a lower back fat depth compared to least efficient heifers. However, no changes were noted (P ≥ 0.10) for plasma concentrations of glucose, insulin, non-esterified fatty acids, β-hydroxybutyrate and urea. The plasma metabolomic dataset comprised 3,457 ions with none significantly differing between RFI classes after false discovery rate correction (FDR > 0.10). Among the 101 ions having a raw P < 0.05 for the RFI effect, 13 were putatively annotated by using internal databases and 6 compounds were further confirmed with standards. Metabolic pathway analysis from these 6 confirmed compounds revealed that the branched chain amino acid metabolism was significantly (FDR < 0.05) impacted by the RFI classes. Our results confirmed for the first time in beef heifers previous findings obtained in male beef cattle and pointing to changes in branched-chain amino acids metabolism along with that of body composition as biological mechanisms related to RFI. Further studies are warranted to ascertain whether there is a cause-and-effect relationship between these mechanisms and RFI.
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Affiliation(s)
- Ezequiel Jorge-Smeding
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genès-Champanelle, France
- Facultad de Agronomía, Departamento de Producción Animal y Pasturas, Universidad de la República, Montevideo, Uruguay
| | - Sergio Polakof
- INRAE, Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Muriel Bonnet
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genès-Champanelle, France
| | - Stephanie Durand
- INRAE, UNH, Plateforme d’Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Delphine Centeno
- INRAE, UNH, Plateforme d’Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mélanie Pétéra
- INRAE, UNH, Plateforme d’Exploration du Métabolisme, MetaboHUB Clermont, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sébastien Taussat
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- Eliance, Paris, France
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13
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Zou X, Liu T, Li Y, Chen P, Yan X, Ma J, Ji J, Qu H, Cai M, He Y, He J, Xu X, Lin C, Zhou G, Shu D, Luo C. Long-term divergent selection for residual feed intake in Chinese broiler chickens. Poult Sci 2022; 102:102298. [PMID: 36638759 PMCID: PMC9843260 DOI: 10.1016/j.psj.2022.102298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 01/12/2023] Open
Abstract
This study aimed to assess the effect of inbreeding on production traits using a long-term closed-line population recorded for residual feed intake (RFI). The study first used data from a previously reported population to determine the appropriate period of divergent selection for RFI. The results showed that RFI had similar moderate heritability estimates (0.28-0.34) during the fast-growing period (7-12 wk), and RFI at 7 to 10 wk had the highest heritability (0.34). Therefore, divergent selection was performed in a Chinese broiler population for RFI at 7 to 10 wk; the total sample size from generations zero (G0) to 13 was 9050. The divergence between the 2 lines increased steadily throughout generations, resulting in G13 with average RFI values of 304.55 in high RFI (HRFI) males, -160.31 in low RFI (LRFI) males, 296.30 in HRFI females and -157.55 in LRFI females. The feed intake (FI) and feed conversion ratio were almost higher in HRFI broilers than in LRFI broilers, and the magnitude of the difference in FI increased from approximately 4% for both sexes in G1 to approximately 33% in G13. Body weight gain was irregular from G1 to G13 and higher in LRFI broilers than in HRFI broilers after G10. Indeed, the HRFI broilers consumed more food, but they were lighter than LRFI broilers. In G13, LRFI males had heavier slaughter weight, longer cecum length, more white blood cells (WBC), red blood cells (RBC) and hemoglobin (HGB), but triglycerides, lower dressed percentage, percentage of half eviscerated yield, and eviscerated yield than HRFI males. LRFI females had a higher percentage of breast muscle and gizzard yield, longer cecum length, and more WBCs, RBCs and HGB but less abdominal fat and serum total cholesterol than HRFI females. This study was the first to verify that long-term divergent selection for RFI in Chinese broiler chickens is positive and beneficial.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Key Laboratory of Animal Breeding and Nutrition & Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Key Laboratory of Animal Breeding and Nutrition & Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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14
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Jiang Y, Song H, Gao H, Zhang Q, Ding X. Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals. Front Genet 2022; 13:963654. [PMID: 36092888 PMCID: PMC9459117 DOI: 10.3389/fgene.2022.963654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Genotype imputation from BeadChip to whole-genome sequencing (WGS) data is a cost-effective method of obtaining genotypes of WGS variants. Beagle, one of the most popular imputation software programs, has been widely used for genotype inference in humans and non-human species. A few studies have systematically and comprehensively compared the performance of beagle versions and parameter settings of farm animals. Here, we investigated the imputation performance of three representative versions of Beagle (Beagle 4.1, Beagle 5.0, and Beagle 5.4), and the effective population size (Ne) parameter setting for three species (cattle, pig, and chicken). Six scenarios were investigated to explore the impact of certain key factors on imputation performance. The results showed that the default Ne (1,000,000) is not suitable for livestock and poultry in small reference or low-density arrays of target panels, with 2.47%–10.45% drops in accuracy. Beagle 5 significantly reduced the computation time (4.66-fold–13.24-fold) without an accuracy loss. In addition, using a large combined-reference panel or high-density chip provides greater imputation accuracy, especially for low minor allele frequency (MAF) variants. Finally, a highly significant correlation in the measures of imputation accuracy can be obtained with an MAF equal to or greater than 0.05.
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Affiliation(s)
- Yifan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hailiang Song
- Beijing Key Laboratory of Fisheries Biotechnology, Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hongding Gao
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Xiangdong Ding,
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15
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Ramírez GA, Keshri J, Vahrson I, Garber AI, Berrang ME, Cox NA, González-Cerón F, Aggrey SE, Oakley BB. Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens. Front Vet Sci 2022; 9:904698. [PMID: 35799838 PMCID: PMC9255636 DOI: 10.3389/fvets.2022.904698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/19/2022] [Indexed: 11/24/2022] Open
Abstract
In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.
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Affiliation(s)
- Gustavo Antonio Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
- Leon H. Charney School of Marine Sciences, Haifa University, Haifa, Israel
| | - Jitendra Keshri
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Isabella Vahrson
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Arkadiy I. Garber
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Mark E. Berrang
- Poultry Microbiological Safety and Processing Research Unit, USDA Agricultural Research Service, Athens, GA, United States
| | - Nelson A. Cox
- Poultry Microbiological Safety and Processing Research Unit, USDA Agricultural Research Service, Athens, GA, United States
| | - Fernando González-Cerón
- Departamento de Zootecnia, Chapingo Autonomous University, Estado de Mexico, Mexico
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Samuel E. Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Brian B. Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
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He Z, Li S, Li W, Ding J, Zheng M, Li Q, Fahey AG, Wen J, Liu R, Zhao G. Comparison of genomic prediction methods for residual feed intake in broilers. Anim Genet 2022; 53:466-469. [PMID: 35292985 DOI: 10.1111/age.13186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
Residual feed intake (RFI) is a measure of the feed efficiency of animals. Previous studies have identified SNPs associated with RFI. The objective of this study was to compare the GBLUP model with the GA-BLUP model including previously identified associated SNPs. The nine associated SNPs were obtained from the genome-wide association study on a discovery population as preselection information. These models were analysed using ASREML software using a 5-fold cross-validation method on a validation population. With the genetic architecture (GA) matrix used, which was conducted with the nine RFI-associated SNPs, the prediction accuracy of RFI was improved compared with the original GBLUP model. The calculated optimal ω was 0.981 for RFI, which is in line with the optimal range from 0.9 to 1.0 in the gradient test. The prediction accuracy increased by 2% in the GA-BLUP model with ω being 0.981 compared with the GBLUP model. In conclusion, the GA-BLUP with the nine RFI-associated SNPs and an optimal ω can improve the prediction accuracy for a specific trait compared with GBLUP.
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Affiliation(s)
- Zhengxiao He
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sen Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiqiang Ding
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Alan G Fahey
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Tan X, Liu R, Li W, Zheng M, Zhu D, Liu D, Feng F, Li Q, Liu L, Wen J, Zhao G. Assessment the effect of genomic selection and detection of selective signature in broilers. Poult Sci 2022; 101:101856. [PMID: 35413593 PMCID: PMC9018145 DOI: 10.1016/j.psj.2022.101856] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (<0.1) was found between meat production and abdominal fat traits. Selection resulted in an increase of about 516 g in BW and 140 g in breast muscle weight. Percentage of breast muscle and whole thigh were increased 0.8 to 1.5%. No change was observed in abdominal fat percentage. The genomic estimated breeding value advances was positive for BW and meat production (except whole thigh percentage), while negative for abdominal fat percentage. By selective sweep analysis, 39 common chromosomal regions and 102 protein coding genes were found to be influenced, including MYH1A, MYH1B, and MYH1D of the MYH gene family. Tight junction pathway as well as myosin complex related terms were enriched. This study demonstrates the effective use of GS for improvements in BW and meat production in chicken line B. Further, genomic regions, responsive to intensive genetic selection, were identified to contain genes of the MYH family.
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Sun J, Tan X, Yang X, Bai L, Kong F, Zhao G, Wen J, Liu R. Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes. Genes (Basel) 2022; 13:genes13020307. [PMID: 35205354 PMCID: PMC8872516 DOI: 10.3390/genes13020307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (FST) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the FST and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially TBXAS1 (redness), GDPD5 (yellowness), SLC2A6 (lightness), and MMP27 (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color.
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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. BIOLOGY 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
Abstract
Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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20
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Yang X, Sun J, Zhao G, Li W, Tan X, Zheng M, Feng F, Liu D, Wen J, Liu R. Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers. Front Genet 2021; 12:645107. [PMID: 33859671 PMCID: PMC8042277 DOI: 10.3389/fgene.2021.645107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background Carcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study. Results The heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73–5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85–7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03–53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89–13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed. Conclusion We identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.
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Affiliation(s)
- Xinting Yang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahong Sun
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Furong Feng
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan, China
| | - Dawei Liu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan, China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhang D, Zhang X, Li F, Yuan L, Zhang Y, Li X, Zhao Y, Song Q, Li G, Wang W. Polymorphisms in ovine ME1 and CA1 genes and their association with feed efficiency in Hu sheep. J Anim Breed Genet 2021; 138:589-599. [PMID: 33586820 DOI: 10.1111/jbg.12541] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Improving feed efficiency would increase profitability for producers. The objective of this study was to detect the expression levels of ME1 and CA1 and the polymorphisms of ME1 and CA1 associated with the feed conversion ratio (FCR) and residual feed intake (RFI) of Hu sheep by using qRT-PCR, pooled DNA sequencing and KASPar assay. The qRT-PCR results indicated that the expression levels of ME1 and CA1 were significantly higher in the liver tissues of low-RFI sheep than in those of the high-RFI sheep (p <.01). Association analysis demonstrated that the polymorphism ME1 g.453 C > T was significantly associated with FCR and RFI (p <.05). The polymorphism CA1 g.199 C > T had a significantly associated with FCR (p <.05) and no association with RFI (p >.05). Significant differences were observed between the combined genotypes and FCR and RFI at different measurement periods (p <.05). Thus, we propose the use of these two polymorphisms as new candidate molecular markers for improving feed efficiency in sheep populations.
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Affiliation(s)
- Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Lvfeng Yuan
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Guoze Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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