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Bai H, Zhao N, Li X, Ding Y, Guo Q, Chen G, Chang G. Whole-genome resequencing identifies candidate genes associated with heat adaptation in chickens. Poult Sci 2024; 103:104139. [PMID: 39127007 DOI: 10.1016/j.psj.2024.104139] [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: 03/17/2024] [Revised: 06/17/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.
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Affiliation(s)
- Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Ning Zhao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xing Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yifan Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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Nawaz AH, Setthaya P, Feng C. Exploring Evolutionary Adaptations and Genomic Advancements to Improve Heat Tolerance in Chickens. Animals (Basel) 2024; 14:2215. [PMID: 39123741 PMCID: PMC11311085 DOI: 10.3390/ani14152215] [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: 05/31/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Climate change poses a significant threat to the poultry industry, especially in hot climates that adversely affect chicken growth, development, and productivity through heat stress. This literature review evaluates the evolutionary background of chickens with the specific genetic characteristics that can help chickens to cope with hot conditions. Both natural selection and human interventions have influenced the genetic characteristics of the breeds used in the current poultry production system. The domestication of chickens from the Red junglefowl (Gallus gallus) has resulted in the development of various breeds with distinct genetic differences. Over the past few years, deliberate breeding for desirable traits (such as meat production and egg quality) in chickens has resulted in the emergence of various economically valuable breeds. However, this selective breeding has also caused a decrease in the genetic diversity of chickens, making them more susceptible to environmental stressors like heat stress. Consequently, the chicken breeds currently in use may possess a limited ability to adapt to challenging conditions, such as extreme heat. This review focuses on evaluating potential genes and pathways responsible for heat tolerance, including heat shock response, antioxidant defense systems, immune function, and cellular homeostasis. This article will also discuss the physiological and behavioral responses of chicken varieties that exhibit genetic resistance to heat, such as the naked neck and dwarf traits in different indigenous chickens. This article intends to review the current genomic findings related to heat tolerance in chickens that used methods such as the genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping, offering valuable insights for the sustainability of poultry in the face of global warming.
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Affiliation(s)
- Ali Hassan Nawaz
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Phatthawin Setthaya
- Multidisciplinary Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
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3
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Zhao J, Mu Y, Gong P, Liu B, Zhang F, Zhu L, Shi C, Lv X, Luo J. Whole-genome resequencing of native and imported dairy goat identifies genes associated with productivity and immunity. Front Vet Sci 2024; 11:1409282. [PMID: 39040818 PMCID: PMC11260678 DOI: 10.3389/fvets.2024.1409282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 07/24/2024] Open
Abstract
Understanding the differences in genetic variation between local Chinese dairy goat breeds and imported breeds can help germplasm innovation and molecular breeding. However, the research is limited in this area. In this study, whole-genome resequencing data from 134 individuals of both local and imported dairy goat breeds were analyzed, and their differences in genomic genetic variation, genetic diversity, and population structure were subsequently identified. We also screened candidate genes associated with important traits of dairy goats such as milk production (STK3, GHR, PRELID3B), reproduction (ATP5E), growth and development (CTSZ, GHR), and immune function (CTSZ, NELFCD). Furthermore, we examined allele frequency distributions for the genes of interest and found significant differences between the two populations. This study provides valuable resources for the study of genetic diversity in dairy goats and lays the foundation for the selective breeding of dairy goats in the future.
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Affiliation(s)
- Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yuanpan Mu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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Mao H, Chen J, Zhang J, Zhang X, Xu S, Zhang L. High-energy and high-amino acid diet enhances production performance and antioxidant capacity in yellow-feathered broilers under heat stress. Poult Sci 2024; 103:103790. [PMID: 38713989 PMCID: PMC11091689 DOI: 10.1016/j.psj.2024.103790] [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: 02/25/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024] Open
Abstract
This study investigated the ameliorating effects of high-energy and high-amino acid (HEHA) diets on heat stress (HS) in yellow-feathered broilers. Broilers aged 35 d were randomly assigned to 3 groups: control and HS groups fed the basic normal diet, and the HEHA group fed the HEHA diet (basal diet + 100 kcal/kg AME + 15 % DAAs). The HS and HEHA groups were exposed to cyclic HS (30 ± 1 to 34 ± 1 ℃) for 2 wk, while the control group was maintained at 26 ± 1 ℃. The results indicated that the HEHA diet significantly alleviated HS-induced feed intake and body weight loss. HEHA feeding mitigated the increase in body temperature during HS. Compared with observations in the HS group, the HEHA diet reduced the levels of ALT, Alb, and corticosterone in the serum and downregulated the gene expression of HSP27 and HSP60 in the liver. Moreover, the HEHA group showed higher GSH-px activity in the serum and SOD and GSH-Px activity in the jejunal mucosa than that of the HS group. HEHA supplementation also reduced MDA levels in the liver. In conclusion, the HEHA diet improved the production performance of broilers under HS by increasing their antioxidant capacities. These findings suggest an effective strategy to combat HS in poultry production.
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Affiliation(s)
- Huihua Mao
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing, Jiang Su, China
| | - Jinglong Chen
- Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China
| | - Jinbi Zhang
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing, Jiang Su, China
| | - Xu Zhang
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing, Jiang Su, China
| | - Shiyong Xu
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing, Jiang Su, China
| | - Ling Zhang
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiang Su, China.
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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024:1-13. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [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: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, China
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6
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Zhang L, Li H, Zhao X, Wu Y, Li J, Yao Y, Yao Y, Wang L. Whole genome resequencing reveals the adaptability of native chickens to drought, tropical and frigid environments in Xinjiang. Poult Sci 2024; 103:103947. [PMID: 38986358 PMCID: PMC11295967 DOI: 10.1016/j.psj.2024.103947] [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: 02/27/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Chickens exhibit extensive genetic diversity and are distributed worldwide. Different chicken breeds have evolved to thrive in diverse environmental conditions. However, research on the genetic mechanisms underlying chicken adaptation to extreme environments, such as tropical, frigid and drought-prone regions, remains limited. In this study, we conducted whole-genome sequencing of 240 individuals from six native chicken breeds in Xinjiang, China, as well as 4 publicly available chicken breeds inhabiting regions with varying annual precipitations, temperatures, and altitudes. Our analysis revealed several genetic variants among the examined breeds. Furthermore, we investigated the genetic diversity and population structure of breeds residing in extreme drought and temperature environments by comparing them. Notably, native chicken breeds exhibited different genetic diversity and population structures. Moreover, we identified candidate genes associated with chicken adaptability to the environment, such as CORO2A, CTNNA3, AGMO, GRID2, BBOX1, COL3A1, INSR, SOX5, MAP2 and PLPPR1. Additionally, pathways such as lysosome, cysteine and methionine metabolism, glycosaminoglycan degradation, and Wnt signaling may be play crucial roles in regulating chicken adaptation to drought environments. Overall, these findings contribute to our understanding of the genetic mechanisms governing chicken adaptation to extreme environments, and also offer insights for enhancing the resilience of chicken breeds to different climatic conditions.
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Affiliation(s)
- Lihua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
| | - Xiaoyu Zhao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yingping Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jiahui Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yingying Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yang Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Lin Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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7
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Hou Q, Li G, Pan X, Zhong X, Geng X, Yang X, Yang X, Zhang B. Long-term supplementation of genistein improves immune homeostasis in the aged gut and extends the laying cycle of aged laying hens. Poult Sci 2024; 103:103670. [PMID: 38598909 PMCID: PMC11017059 DOI: 10.1016/j.psj.2024.103670] [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: 01/12/2024] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Aging is associated with alterations in gut function, including intestinal inflammation, leaky gut, and impaired epithelial regeneration. Rejuvenating the aged gut is imperative to extend the laying cycle of aged laying hens. Genistein is known to have beneficial effects on age-related diseases, but its precise role in homeostasis of the aged gut of laying hens remains to be elucidated. In this study, 160 45-wk-old Hyline Brown laying hens were continuously fed a basal diet or a diet supplemented with 40 mg/kg genistein until they reached 100 wk of age. The results revealed that long-term genistein supplementation led to an improvement in the egg production rate and feed conversion ratio, as well as an increase in egg quality. Moreover, the expression levels of senescence markers, such as β-galactosidase, P16, and P21, were decreased in the gut of genistein-treated aged laying hens. Furthermore, genistein ameliorated gut dysfunctions, such as intestinal inflammation, leaky gut, and impaired epithelial regeneration. Treg cell-derived IL-10 plays a crucial role in the genistein-induced regulation of age-related intestinal inflammation. This study demonstrates that long-term consumption of genistein improves homeostasis in the aged gut and extends the laying cycle of aged laying hens. Moreover, the link between genistein and Treg cells provides a rationale for dietary intervention against age-associated gut dysfunction.
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Affiliation(s)
- Qihang Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Guang Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science & Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Xianjie Pan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science & Technology, China Agricultural University, Haidian District, Beijing 100193, China
| | - Xiang Zhong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangfei Geng
- Beijing Lab Anim Sci Tech Develp Co., LTD, Beijing 100193, China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Bingkun Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science & Technology, China Agricultural University, Haidian District, Beijing 100193, China.
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8
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An ZX, Shi LG, Hou GY, Zhou HL, Xun WJ. Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data. Animal 2024; 18:101147. [PMID: 38843669 DOI: 10.1016/j.animal.2024.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 06/22/2024] Open
Abstract
Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.
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Affiliation(s)
- Z X An
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - L G Shi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - G Y Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - H L Zhou
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - W J Xun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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Kong S, Cai B, Li X, Zhou Z, Fang X, Yang X, Cai D, Luo X, Guo S, Nie Q. Assessment of selective breeding effects and selection signatures in Qingyuan partridge chicken and its strains. Poult Sci 2024; 103:103626. [PMID: 38513549 PMCID: PMC10966089 DOI: 10.1016/j.psj.2024.103626] [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: 12/22/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/23/2024] Open
Abstract
Qingyuan partridge chicken (QYM) is a highly regarded native breed in China, highly esteemed for its exceptional breeding characteristics. However, the investigation into the selection signatures and its strains remains largely unexplored. In this study, blood sampling, DNA extracting, and high-depth resequencing were performed in 27 QYMs. Integrating the genomic data of 14 chicken (70 individuals) breeds from other researches, to analyze the genetic structure, selection signatures, and effects of selective breeding within QYM and its 3 strains (QYMA, QYMB, and QYMC). Population structure analysis revealed an independent QYM cluster, which exhibited distinct from other breeds, with each of its 3 strains displaying distinct clustering patterns. Linkage disequilibrium analysis highlighted QYMB's notably slower decay rate, potentially influenced by selection pressure from various production indicators. Examination of selection signatures uncovered genes and genetic mechanisms associated with genomic changes resulting from extensive selective breeding within the QYM and its strains. Intriguingly, diacylglycerol kinase beta (DGKB) and catenin alpha 2 (CTNNA2) were identified as commonly selected genes across the 3 QYM strains, linked to energy metabolism, muscle development, and fat metabolism. Our research validates the substantial impact of selective breeding on QYM and its strains, concurrently identifying genomic regions and signaling pathways associated with their distinctive characters. This research also establishes a fundamental framework for advancing yellow-feathered broiler breeding strategies.
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Affiliation(s)
- Shaofen Kong
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiaojing Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhen Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiang Fang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danfeng Cai
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xuehui Luo
- Qingyuan Chicken Research Institute, Qingcheng District, Qingyuan City, China
| | - Suyin Guo
- Animal Epidemic Prevention Center, Qingcheng District, Qingyuan City, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory of Swine and Poultry Breeding Industry, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China.
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10
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Jin M, Wang H, Liu G, Lu J, Yuan Z, Li T, Liu E, Lu Z, Du L, Wei C. Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation. Genet Sel Evol 2024; 56:26. [PMID: 38565986 PMCID: PMC10988870 DOI: 10.1186/s12711-024-00880-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations. RESULTS Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability. CONCLUSIONS Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gang Liu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Jian Lu
- National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Engming Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lan-Zhou, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Zhao X, Wen J, Zhang X, Zhang J, Zhu T, Wang H, Yang W, Cao G, Xiong W, Liu Y, Qu C, Ning Z, Qu L. Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 2024; 15:45. [PMID: 38556896 PMCID: PMC10983685 DOI: 10.1186/s40104-024-01006-7] [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: 11/06/2023] [Accepted: 01/31/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens. RESULTS We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens. CONCLUSIONS In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.
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Affiliation(s)
- Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junhui Wen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinxin Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huie Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Yong Liu
- Beijing Agricultural Effect Poultry Industry Co., Ltd., Beijing, 101100, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Gu LH, Wu RR, Zheng XL, Fu A, Xing ZY, Chen YY, He ZC, Lu LZ, Qi YT, Chen AH, Zhang YP, Xu TS, Peng MS, Ma C. Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens. Poult Sci 2024; 103:103376. [PMID: 38228059 PMCID: PMC10823079 DOI: 10.1016/j.psj.2023.103376] [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: 09/27/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.
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Affiliation(s)
- Li-Hong Gu
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ran-Ran Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li Zheng
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An Fu
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China
| | - Zeng-Yang Xing
- Wenchang Long-quan Wenchang Chicken Industrial Co., Ltd., Wenchang 571346, China
| | - Yi-Yong Chen
- Hainan Chuang Wen Wenchang Chicken Industry Co., Ltd., Wenchang 571321, China
| | - Zhong-Chun He
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Li-Zhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan-Tao Qi
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An-Hong Chen
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie-Shan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min-Sheng Peng
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Ma
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China.
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13
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Miao J, Wei X, Cao C, Sun J, Xu Y, Zhang Z, Wang Q, Pan Y, Wang Z. Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 2024; 15:32. [PMID: 38389084 PMCID: PMC10882747 DOI: 10.1186/s40104-023-00984-4] [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: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. RESULTS In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. CONCLUSIONS Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.
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Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China.
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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14
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Tan X, Zhang J, Dong J, Huang M, Li Q, Wang H, Bai L, Cui M, Zhou Z, Yang S, Wang D. Whole-genome variants dataset of 209 local chickens from China. Sci Data 2024; 11:169. [PMID: 38316816 PMCID: PMC10844214 DOI: 10.1038/s41597-024-02995-w] [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: 03/24/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
Compared to commercial chickens, local breeds exhibit better in meat quality and flavour, but the productivity (e.g., growth rate, body weight) of local chicken breeds is rather low. Genetic analysis based on whole-genome sequencing contributes to elucidating the genetic markers or putative candidate genes related to some economic traits, facilitating the improvement of production performance, the acceleration of breeding progress, and the conservation of genetic resources. Here, a total of 209 local chickens from 13 breeds were investigated, and the observation of approximately 91.4% high-quality sequences (Q30 > 90%) and a mapping rate over 99% for each individual indicated good results of this study, as confirmed by a genome coverage of 97.6%. Over 19 million single nucleotide polymorphisms (SNPs) and 1.98 million insertion-deletions (InDels) were identified using the reference genome (GRCg7b), further contributing to the public database. This dataset provides valuable resources for studying genetic diversity and adaptation and for the cultivation of new chicken breeds/lines.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shuyuan Yang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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15
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Pan R, Qi L, Xu Z, Zhang D, Nie Q, Zhang X, Luo W. Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population. Poult Sci 2024; 103:103341. [PMID: 38134459 PMCID: PMC10776626 DOI: 10.1016/j.psj.2023.103341] [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: 09/17/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Carcass traits in broiler chickens are complex traits that are influenced by multiple genes. To gain deeper insights into the genetic mechanisms underlying carcass traits, here we conducted a weighted single-step genome-wide association study (wssGWAS) in a population of Chinese yellow-feathered chicken. The objective was to identify genomic regions and candidate genes associated with carcass weight (CW), eviscerated weight with giblets (EWG), eviscerated weight (EW), breast muscle weight (BMW), drumstick weight (DW), abdominal fat weight (AFW), abdominal fat percentage (AFP), gizzard weight (GW), and intestine length (IL). A total of 1,338 broiler chickens with phenotypic and pedigree information were included in this study. Of these, 435 chickens were genotyped using a 600K single nucleotide polymorphism chip for association analysis. The results indicate that the most significant regions for 9 traits explained 2.38% to 5.09% of the phenotypic variation, from which the region of 194.53 to 194.63Mb on chromosome 1 with the gene RELT and FAM168A identified on it was significantly associated with CW, EWG, EW, BMW, and DW. Meanwhile, the 5 traits have a strong genetic correlation, indicating that the region and the genes can be used for further research. In addition, some candidate genes associated with skeletal muscle development, fat deposition regulation, intestinal repair, and protection were identified. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that the genes are involved in processes such as vascular development (CD34, FGF7, FGFR3, ITGB1BP1, SEMA5A, LOXL2), bone formation (FGFR3, MATN1, MEF2D, DHRS3, SKI, STC1, HOXB1, HOXB3, TIPARP), and anatomical size regulation (ADD2, AKT1, CFTR, EDN3, FLII, HCLS1, ITGB1BP1, SEMA5A, SHC1, ULK1, DSTN, GSK3B, BORCS8, GRIP2). In conclusion, the integration of phenotype, genotype, and pedigree information without creating pseudo-phenotype will facilitate the genetic improvement of carcass traits in chickens, providing valuable insights into the genetic architecture and potential candidate genes underlying carcass traits, enriching our understanding and contributing to the breeding of high-quality broiler chickens.
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Affiliation(s)
- Rongyang Pan
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Xugang Yellow Poultry Seed Industry Group Co., Ltd, Jiangmen City, Guangdong Province, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Lin Qi
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhenqiang Xu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Dexiang Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong 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, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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16
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Rachman MP, Bamidele O, Dessie T, Smith J, Hanotte O, Gheyas AA. Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress. Sci Rep 2024; 14:2209. [PMID: 38278850 PMCID: PMC10817956 DOI: 10.1038/s41598-024-52569-4] [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: 09/25/2023] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.
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Affiliation(s)
- Mifta P Rachman
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
| | - Oladeji Bamidele
- African Chicken Genetic Gains (ACGG), Department of Animal Sciences, Obafemi Awolowo University, Ile Ife, 220282, Nigeria
| | - Tadelle Dessie
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Jacqueline Smith
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Almas A Gheyas
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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17
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Sun H, Zheng X, Yang B, Yan M, Wang H, Yang S, Shi D, Guo S, Liu C. Effect of Wu Zhi San supplementation in LPS-induced intestinal inflammation and barrier damage in broilers. Front Vet Sci 2023; 10:1234769. [PMID: 38111733 PMCID: PMC10725941 DOI: 10.3389/fvets.2023.1234769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023] Open
Abstract
Intestinal inflammation and barrier damage can inhibit the absorption and transportation of nutrients in the small intestine, and lead to various chronic diseases. Wu Zhi San (WZS) is a traditional Chinese formula composed of Schisandrae, Anemarrhenae, Lonicerae, and Glycyrrhizae that was made to cure intestinal inflammation and barrier damage in broilers. To evaluate the protective effect of WZS on intestinal inflammation and barrier damage of broilers under lipopolysaccharide (LPS) stress, a total of 200 one-day-old broilers were randomly divided into five groups, namely, the CON group, LPS group, and three WZS groups (WZS-H, WZS-M, and WZS-L). The groups were designed for stress phase I (days 15, 17, 19, and 21) and stress phase II (days 29, 31, 33, and 35). The protective effect of WZS on the intestinal tract was evaluated by measuring the levels of serum myeloperoxidase (MPO), diamine oxidase (DAO), super oxide dismutase (SOD), and serum D-lactate (D-LA) and the expression of inflammatory factors in jejunum. The results showed that the diet supplemented with WZS could significantly reduce serum MPO, DAO, and D-LA levels and jejunal CD in broilers (p < 0.05), increase serum SOD levels and jejunal VH (p < 0.05), significantly downregulate the expression of NF-κB, TLR4, MyD88, and inflammatory cytokines (TNF-α, IL-1β, IL-6, and IL-10), and upregulate Claudin-1, Occludin-1, and ZO-1 in broiler jejunum mucosa (p < 0.05). On the other hand, WZS could significantly reduce the protein expression of NF-κB (p65) in broiler jejunum (p < 0.05). These results indicate that supplementing WZS in the diet can reduce intestinal inflammation and alleviate intestinal barrier damage, and by inhibiting the NF-κB/TLR4/MyD88 signaling pathway, supplementation with WZS intervenes in LPS-induced stress injury in broilers.
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Affiliation(s)
- Han Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xirui Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bowen Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingen Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Huiting Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shijing Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dayou Shi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Nature Medicine, Guangzhou, China
- International Institute of Traditional Chinese Veterinary Medicine, Guangzhou, China
| | - Shining Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Nature Medicine, Guangzhou, China
- International Institute of Traditional Chinese Veterinary Medicine, Guangzhou, China
| | - Cui Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Nature Medicine, Guangzhou, China
- International Institute of Traditional Chinese Veterinary Medicine, Guangzhou, China
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18
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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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19
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Li Q, Ouyang J, Deng C, Zhou H, You J, Li G. Effects of dietary tryptophan supplementation on rectal temperature, humoral immunity, and cecal microflora composition of heat-stressed broilers. Front Vet Sci 2023; 10:1247260. [PMID: 37841460 PMCID: PMC10572358 DOI: 10.3389/fvets.2023.1247260] [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: 06/25/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
This trial aimed to determine the effects of tryptophan (Trp) on the rectal temperature, hormone, humoral immunity, and cecal microflora composition in broiler chickens under heat stress (HS). One hundred and eighty 18 days-old female Arbor Acres broilers were randomly divided into three treatment groups, with six replicates of ten birds in each replicate. The broilers were either raised under thermoneutral conditions (TN, 23 ± 1°C) or subjected to heat stress (34 ± 1°C for 8 h daily). The TN group received a basal diet, and another two heat-stressed groups were fed the basal diet (HS) or the basal diet supplemented with 0.18% Trp (HS + 0.18% Trp) for 21 consecutive days. The basal diet contained 0.18% Trp. Results revealed that HS increased the rectal temperature, serum epinephrine (EPI), and corticotropin-releasing hormone (CRH) concentrations (p < 0.05), reduced the bursal index, the levels of serum immunoglobulin A (IgA), IgG, IgM, and serotonin (5-HT) as well as the relative abundance of Actinobacteria in cecum (p < 0.05) compared with the TN group. Dietary supplementation of Trp decreased the rectal temperature, serum dopamine (DA), EPI, and the levels of CRH and L-kynurenine (p < 0.05), increased the bursal index, the levels of serum IgA, IgM, and 5-HT as well as the relative abundance of Ruminococcus torques group in cecum of heat-stressed broilers (p < 0.05) compared to HS group. In conclusion, dietary Trp supplementation decreased rectal temperature, improved cecal microbiota community and Trp metabolism, and enhanced humoral immunity of heat-stressed broilers.
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Affiliation(s)
- Qiufen Li
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
- Institute of Veterinary Drug, Jiangxi Agricultural University, Nanchang, China
| | - Jingxin Ouyang
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
| | - Chenxi Deng
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
| | - Hua Zhou
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
| | - Jinming You
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
| | - Guanhong Li
- Jiangxi Province Key Laboratory of Animal Nutrition, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Innovation Center of Integration in Production and Education for High-quality and Safe Livestock and Poultry, Nanchang, China
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20
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Juiputta J, Chankitisakul V, Boonkum W. Appropriate Genetic Approaches for Heat Tolerance and Maintaining Good Productivity in Tropical Poultry Production: A Review. Vet Sci 2023; 10:591. [PMID: 37888543 PMCID: PMC10611393 DOI: 10.3390/vetsci10100591] [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: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Heat stress is a major environmental threat to poultry production systems, especially in tropical areas. The effects of heat stress have been discovered in several areas, including reduced growth rate, reduced egg production, low feed efficiency, impaired immunological responses, changes in intestinal microflora, metabolic changes, and deterioration of meat quality. Although several methods have been used to address the heat stress problem, it persists. The answer to this problem can be remedied sustainably if genetic improvement approaches are available. Therefore, the purpose of this review article was to present the application of different approaches to genetic improvement in poultry in the hope that users will find suitable solutions for their poultry population and be able to plan future poultry breeding programs.
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Affiliation(s)
- Jiraporn Juiputta
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
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21
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Li S, Zhang X, Dong X, Guo R, Nan J, Yuan J, Schlebusch CM, Sheng Z. Genetic structure and characteristics of Tibetan chickens. Poult Sci 2023; 102:102767. [PMID: 37321029 PMCID: PMC10404676 DOI: 10.1016/j.psj.2023.102767] [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: 12/06/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.
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Affiliation(s)
- Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Dong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiyang Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiuhong Nan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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22
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Liu L, Wu P, Guo A, Yang Y, Chen F, Zhang Q. Research progress on the regulation of production traits by gastrointestinal microbiota in dairy cows. Front Vet Sci 2023; 10:1206346. [PMID: 37592942 PMCID: PMC10427726 DOI: 10.3389/fvets.2023.1206346] [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: 04/15/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The composition and abundance of microorganisms in the gastrointestinal tract of cows are complex and extensive, and they play a crucial role in regulating nutrient digestion, absorption, maintaining digestive tract stability, and promoting the production and health of the host. The fermentation carried out by these microorganisms in the gastrointestinal tract is fundamental to the health and productivity of cows. Rumen microorganisms produce the majority of enzymes required to break down feed substrates, such as cellulose, protein, lipids, and other plant materials, through fermentation. This process provides energy metabolism substrates that satisfy approximately 70% of the host's energy requirements for physiological activities. Gut microorganisms primarily decompose cellulose that is difficult to digest in the rumen, thereby providing heat and energy to the hosts. Additionally, they have an impact on host health and productivity through their role in immune function. Understanding the composition and function of the cow gut microbiota can help regulate dairy cattle breeding traits and improve their health status. As a result, it has become a popular research topic in dairy cattle breeding. This article provides a review of the composition, structure, physiological characteristics, and physiological effects of the cow gut microbiota, serving as a theoretical foundation for future studies that aim to utilize the gut microbiota for dairy cattle breeding or improving production traits. It may also serve as a reference for research on gut microbiota of other ruminants.
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Affiliation(s)
- Lily Liu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Peifu Wu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Aiwei Guo
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Yajin Yang
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Fenfen Chen
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Qin Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
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23
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Deng Y, Cheng H, Li J, Han H, Qi M, Wang N, Tan B, Li J, Wang J. Effects of glutamine, glutamate, and aspartate on intestinal barrier integrity and amino acid pool of the small intestine in piglets with normal or low energy diet. Front Vet Sci 2023; 10:1202369. [PMID: 37576837 PMCID: PMC10414990 DOI: 10.3389/fvets.2023.1202369] [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: 04/08/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
Aspartate (asp), glutamate (glu), and glutamine (gln) are the major energy fuels for the small intestine, and it had been indicated in our previous study that the mix of these three amino acid supplementations could maintain intestinal energy homeostasis. This study aimed to further investigate whether the treatment of gln, glu, and asp in low energy diet affects the intestinal barrier integrity and amino acid pool in weaning piglets. A total of 198 weaned piglets were assigned to 3 treatments: control (basal diet + 1.59% L-Ala); T1 (basal diet + 1% L-Gln + 0.5% L-Glu + 0.1% L-Asp); and T2 (low energy diet + 1% L-Gln + 0.5% L-Glu + 0.1% L-Asp). The blood, jejunum, and ileum were obtained on day 5 or on day 21 post-weaning, respectively. Our results showed that T1 and T2 treatments increased the abundances of occludin, claudin-1, and claudin-3 in the small intestine while decreasing the serum diamine oxidase (DAO) and D-lactate levels in weaning piglets. Meanwhile, T1 and T2 treatments significantly increased the positive rate of proliferating cell nuclear antigen (PCNA) of the small intestine, promoting intestinal cell proliferation. We also found that supplementation with glu, gln, and asp improved the serum amino acid pool and promoted ileal amino acid transporter gene expression of slc3a2, slc6a14, and slc7a11 in weaned piglets. Additionally, on day 21 post-weaning, T1 and T2 treatments stimulated the phosphorylation of the mTOR-S6K1-4EBP1 signaling pathway in the small intestine, which may implicate the enhanced protein synthesis rate. In summary, dietary supplementation of gln, glu, and asp was beneficial to the intestinal barrier function and amino acid pool regulation, while the benefits of gln, glu, and asp treatment might be diminished by the low-energy diet. The results demonstrated that the supplementation of gln, glu, and asp under low energy levels was preferentially supplied as the energy fuel to restore the gut barrier function in piglets on day 5 post-weaning. With the increase in age and intestinal maturation (on day 21 post-weaning), gln, glu, and asp supplementation could also show an effect on the regulation of the amino acid pool and protein synthesis.
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Affiliation(s)
- Yuankun Deng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Hao Cheng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Junyao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Hui Han
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Ming Qi
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Nan Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Bi'e Tan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jianjun Li
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Jing Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
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24
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Ren Y, Zhao T, Zhang K, Zhu Z, Li L, Li Y, Jiang S, Jiao N, Yang W. Effect of replacing dicalcium phosphate with mono-dicalcium phosphate to supplement phosphorus on laying performance, phosphorus-calcium metabolism and bone metabolism of aged laying hens. Front Vet Sci 2023; 10:1196334. [PMID: 37332735 PMCID: PMC10275408 DOI: 10.3389/fvets.2023.1196334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
The objective of this study was to evaluate the effect of replacing dicalcium phosphate (DCP) with mono-dicalcium phosphate (MDCP) to formulate low-phosphorus (P) diets on laying performance, egg quality, phosphorus-calcium metabolism, and bone metabolism of 69-78-week-old aged laying hens. Hy-Line Brown laying hens (n = 1,350, 69 weeks old) were randomly assigned to six treatments, each with five replicates of 45 hens. A corn-soybean meal-based diet was formulated to contain 0.12% non-phytate phosphorus (NPP), 3.81% calcium (Ca), and 1,470 FTU/kg phytase. The control group (CON) was supplemented with DCP inorganic phosphorus (Pi) at the NPP level of 0.20% (dietary NPP levels of 0.32%). Test groups (T1-T5) were supplemented with MDCP Pi at NPP levels of 0.07%, 0.11%, 0.15%, 0.18, and 0.20% (dietary NPP levels of 0.19, 0.23, 0.27, 0.30, and 0.32%, respectively). Calcium carbonate levels were adjusted to ensure all experimental diets contained the same Ca levels (3.81%). The feeding trial lasted 10 weeks, with hens increasing in age from 69 to 78 weeks. When supplemented with 1,470 FTU/kg phytase, extra DCP Pi or MDCP Pi did not affect (p > 0.05) laying performance (day laying rate, average egg weight, feed intake, feed-to-egg mass ratio, broken egg rate), egg quality (eggshell strength, albumen height, haugh units), or serum P, Ca, copper (Cu), iron (Fe), zinc (Zn), and manganese (Mn) levels. However, when laying hens were fed MDCP Pi (NPP levels of 0.07 to 0.20%), yolk color improved (p = 0.0148). The tibia breaking strength was significantly higher (p < 0.05) in the 0.18 and 0.20% NPP MDCP Pi groups than in the 0.20% NPP DCP Pi group. The breaking strength, Ca content, and P content of tibia in 0.11% and 0.15% NPP MDCP Pi hens were not significantly (p > 0.05) different from those in 0.20% NPP DCP Pi hens. Hens fed 0.07% NPP MDCP Pi had higher (p < 0.01) serum levels of osteoprotegerin (OPG), type-I collagen c-telopeptide (CTX-I), and tartrate-resistant acid phosphatase 5b (TRACP-5b) than those in all other groups. Serum levels of TRACP-5b and CTX-I in the 0.11% and 0.15% NPP MDCP Pi group were significantly lower than those in 0.18 and 0.20% NPP MDCP Pi groups and the 0.20% NPP DCP Pi group (p < 0.0001). Hens fed 0.07% and 0.11% NPP MDCP Pi had higher (p < 0.05) serum levels of parathyroid hormone (PTH) than those in all other groups. No differences were detected in serum calcitonin (CT), 1,25-dihydroxy-vitamin D3 (1,25-(OH)2D3), bone alkaline phosphatase (BAP), osteocalcin(OCN), and osteopontin (OPN) among all groups (p > 0.05). The expression of P transporters type IIa Na/Pi cotransporter (NaPi-IIa) in 0.11% and 0.15% NPP MDCP Pi hens were higher than those in 0.20% NPP MDCP Pi group and 0.20% NPP DCP Pi group (p < 0.05). The results indicated that both renal P reabsorption and bone resorption were involved in adapting to a low-P diet. In summary, when MDCP was used instead of DCP to supplement P, NPP levels could be reduced to 0.11% (dietary NPP level of 0.23%) without negative effects on laying performance and skeletal health of aged hens. In addition, MDCP was more beneficial than DCP for tibia quality. The results of the current study would provide references for the application of MDCP in low-P diets of aged laying hens.
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Affiliation(s)
- Yuechang Ren
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Tianyu Zhao
- College of Food Science and Engineering, Shandong Agricultural University, Tai’an, China
| | - Kaiying Zhang
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Zhengqi Zhu
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Linkui Li
- Laiyang Animal Husbandry and Veterinary Bureau, Yantai, China
| | - Yang Li
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Shuzhen Jiang
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Ning Jiao
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
| | - Weiren Yang
- Department of Animal Sciences and Technology, Shandong Agricultural University, Tai’an, China
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25
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Xiong X, Liu J, Rao Y. Whole Genome Resequencing Helps Study Important Traits in Chickens. Genes (Basel) 2023; 14:1198. [PMID: 37372379 DOI: 10.3390/genes14061198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The emergence of high-throughput sequencing technology promotes life science development, provides technical support to analyze many life mechanisms, and presents new solutions to previously unsolved problems in genomic research. Resequencing technology has been widely used for genome selection and research on chicken population structure, genetic diversity, evolutionary mechanisms, and important economic traits caused by genome sequence differences since the release of chicken genome sequence information. This article elaborates on the factors influencing whole genome resequencing and the differences between these factors and whole genome sequencing. It reviews the important research progress in chicken qualitative traits (e.g., frizzle feather and comb), quantitative traits (e.g., meat quality and growth traits), adaptability, and disease resistance, and provides a theoretical basis to study whole genome resequencing in chickens.
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Affiliation(s)
- Xinwei Xiong
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
| | - Jianxiang Liu
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
| | - Yousheng Rao
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
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26
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Wang J, Wang L, Zhang H, Mei X, Qiu L, Liu J, Zhou Y. Development of a time-resolved immunochromatographic strip for rapid and quantitative determination of deoxynivalenol. Front Vet Sci 2023; 10:1142820. [PMID: 37008353 PMCID: PMC10060663 DOI: 10.3389/fvets.2023.1142820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Deoxynivalenol (DON) contamination of food crops and feeds is almost impossible to avoid completely; however, through best management practices, this risk can be effectively managed and maximumly mitigated. Accurate and rapid detection of DON contamination as early in the entire value chain as possible is critical. To achieve this goal, we developed a DON test strip based on time-resolved fluorescence immunoassay (TRFIA) and a specific DON monoclonal antibody for the rapid quantification of DON in food crops and feeds. The strip displayed a good linearity (R2 = 0.9926), with a limit of quantification of 28.16 μg/kg, a wide linear range of 50 ~ 10,000 μg/kg. The intra-batch coefficient of variation (CV) and the inter-batch CV was <5.00 and 6.60%, respectively. This TRFIA-DON test strip was applied to detect DON in real samples, and the accuracy and reliability were confirmed by liquid chromatography-mass spectrometry (LC-MS/MS). Results showed that the relative standard deviation between the DON strips and LC-MS/MS was <9%. The recovery rates in corn samples ranged from 92 to 104%. The established TRFIA-DON test strip had the characteristics of high sensitivity, high accuracy, and a wide linear range which was suitable for rapid and quantitative determination of DON in food crops and feeds at both on-site and laboratory.
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Affiliation(s)
- Jingneng Wang
- Shanghai Xiongtu Biotechnology Co., Ltd., Shanghai, China
| | - Lihua Wang
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, China
| | - Hui Zhang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xinglin Mei
- Shanghai Xiongtu Biotechnology Co., Ltd., Shanghai, China
| | - Liangzhu Qiu
- Shanghai Xiongtu Biotechnology Co., Ltd., Shanghai, China
| | - Jing Liu
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, China
- *Correspondence: Jing Liu
| | - Yongsong Zhou
- Shanghai Xiongtu Biotechnology Co., Ltd., Shanghai, China
- Yongsong Zhou
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Lin X, Ju L, Cheng Q, Jiang Y, Hou Q, Hu Z, Wang Y, Wang Z. Comparison of growth performance and rumen metabolic pathways in sheep and goats under the same feeding pattern. Front Vet Sci 2023; 10:1013252. [PMID: 36846256 PMCID: PMC9948245 DOI: 10.3389/fvets.2023.1013252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Diet and species are important factors affecting the rumen microbiota, with roughage stimulating rumen development and concentrate feeds being broken down by the decomposition of Ruminal flora to provide the organism with a large amount of energy. This study aimed to explore the effects of host and dietary factors on rumen flora composition and diversity, as well as on host metabolism. The study reports the research conducted on 5-month-old male Small-tail Han sheep and 5-month-old male Boer goat, each with an average weight of 33.87 ± 1.70 kg. Five animals of each species were divided into two groups, namely, the S group (Small-tail Han sheep) and the B group (Boer goat). The experiment was carried out in two various periods, namely, X and Y for groups S and B, respectively. The rations were fed with concentrate-to-roughage ratios of 3:7 and 5:5, respectively. Growth performance was measured by the weight increase index. The results showed that, under the same raising conditions, the ratio between body weight increases and the amount of feed was lower in the S group than in the B group, but the differences were not significant. According to the analysis of the apparent digestibility ratio of nutrition ingredients, the XS group had a significantly higher apparent digestibility ratio for acid detergent fiber than the XB group (p < 0.05). Even though the analysis of rumen fermentation parameters showed that the rumen pH has no significant differences between the XS and XB groups, it was significantly lower in the YS group than in the YB group. The XS group contained a significantly lower content of total volatile fatty acids than the XB group (p < 0.05). Analysis of the 16S rDNA sequencing results revealed that, compared to the B group, the S group was highly enriched with the following bacteria: Proteobacteria, γ-proteobacteria, Aeromonadales, and Succinivibrionaceae. Thus, the host species affected the abundance and diversity of rumen bacteria. Feed utilization efficiency of Small-tail Han sheep was higher than Boer goats, which might be specifically associated with Succinivibrionaceae. The results from this study show that animals belonging to the same family but different genera and species can differ in metabolic pathways even when they are provided with the same animal feed.
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Affiliation(s)
| | | | - Qianjin Cheng
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yue Jiang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Qiuling Hou
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Zhiyong Hu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yun Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
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Li D, Dang DX, Xu H, Zhou H, Lou Y, Liu X, Cui Y. Growth performance, jejunal morphology, disaccharidase activities, and sugar transporter gene expression in Langde geese as affected by the in ovo injection of maltose plus sucrose. Front Vet Sci 2023; 10:1061998. [PMID: 36777674 PMCID: PMC9909528 DOI: 10.3389/fvets.2023.1061998] [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: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The vigorous metabolic activity of an embryo increases the risk of low energy supply during incubation. The lack of energy during this critical period will lead to the death of an embryo. To avoid this risk, the in ovo injection technique in ovo allows for the injection of energy substances into an embryo. Methods This study investigated the effects of in ovo injection of maltose and sucrose (MS) in ovo on post-hatching growth performance, jejunal morphology and disaccharidase activities, and sugar transporter gene expression in Langde geese. A total of 300 fertilized eggs (115.75 ± 1.25 g) obtained from 3-year-old Langde geese were used in this study. The eggs were randomly assigned to two groups, and the difference between the two groups was whether 25g/L maltose and 25g/L sucrose (MS) dissolved in 7.5g/L NaCl were injected into the amnion on embryonic day 24. Each group had six replicates, which each replicate containing 25 eggs. The goslings were raised till day 28. Results and discussion The results showed that the in ovo injection of MS increased final body weight, average daily gain (ADG), and feed efficiency. Additionally, MS injection improved post-hatching jejunal morphology, disaccharidase activities, and sugar transporter gene expression at an early stage. Therefore, we considered that the in ovo injection of MS had positive effects on the nutrient absorption capacity of goslings, thus contributing to the improvement in their growth performance.
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Affiliation(s)
- Desheng Li
- College of Animal Science and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - De Xin Dang
- College of Animal Science and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China,Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Han Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Haizhu Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Yujie Lou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiao Liu
- College of Animal Science and Technology, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yan Cui
- College of Animal Science and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China,*Correspondence: Yan Cui ✉
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Dynamic Changes in the Gut Microbiota and Metabolites during the Growth of Hainan Wenchang Chickens. Animals (Basel) 2023; 13:ani13030348. [PMID: 36766238 PMCID: PMC9913245 DOI: 10.3390/ani13030348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Gut microbiota and their metabolites play important roles in animal growth by influencing the host's intake, storage, absorption, and utilization of nutrients. In addition to environmental factors, mainly diet, chicken breed and growth stage also affect changes in the gut microbiota. However, little research has been conducted on the development of gut microbiota and its metabolites in local chickens. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With aging, the structure of gut microbiota tended to be more stable. The relative proportions of dominant bacteria phyla Firmicutes, Bacteroidetes, and Proteobacteria showed stage changes with the development. With aging, gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. Several microbial and metabolic biomarkers with statistical differences were detected in different development stages. The bacteria that form networks with their significant related metabolites were different in various growth stages, including uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, Faecalibacterium, uncultured_bacterium_o_Bacteroidales, and uncultured_bacterium_f_Lachnospiraceae. Partially differential bacteria were significantly correlated with short-chain fatty acids such as butyric acid. These findings may provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breeds, as well as resources for microbial and metabolic biomarker identification to improve growth efficiency.
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Li C, Li X, Li P, Wei B, Zhang C, Zhu X, Zhang J. Sodium humate alters the intestinal microbiome, short-chain fatty acids, eggshell ultrastructure, and egg performance of old laying hens. Front Vet Sci 2022; 9:986562. [PMID: 36311664 PMCID: PMC9597201 DOI: 10.3389/fvets.2022.986562] [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: 07/10/2022] [Accepted: 08/11/2022] [Indexed: 11/04/2022] Open
Abstract
This study investigated the effect of sodium humate supplementation on changes in the intestinal microbiome, intestinal short-chain fatty acids production, and trace element absorption in older laying hens, with consequent effects on egg performance and shell quality. We used the same hens as their own control; a total of 720 laying hens aged 422 days were randomly divided into three replicates, with the CON group fed a commercial diet at 422–441 days of age and the HANa group fed a commercial diet supplemented with 0.05% sodium humate at 442–461 days of age. Compared with the CON group, in the HANa group, Bacteroidetes and Actinobacteria were significantly increased, whereas, Firmicutes was significantly decreased. Further, Veillonella, Enterococcus, Lactobacillus, and Turricibacter significantly decreased, and Peptoniphilus, Helcococcus, GW-34, Psychrobacter, Anaerococcus, Corynebacterium, Facklamia, Trichococcus, Gallicola, Clostridium, and Oscillospira were significantly increased. The results showed that sodium humate significantly altered the alpha and beta diversity and changed the structure of the intestinal microbiome. Acetic acid, isovaleric acid, and isobutyric acid, among short-chain fatty acids were significantly increased in the HANa group, whereas trace elements such as Mn, Zn, and Fe were significantly reduced. The eggshell strength and ultrastructure were significantly altered. In this study, sodium humate was found to alter the intestinal microbiome structure of aged hens, change the production of short-chain fatty acids, and promote the absorption of trace elements to keep aged hens from experiencing a decrease in egg production performance.
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Affiliation(s)
- Chenqinyao Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xue Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Bin Wei
- Shandong Asia-Pacific Haihua Biotechnology Co., Ltd., Jinan, China
| | - Cong Zhang
- Shandong Asia-Pacific Haihua Biotechnology Co., Ltd., Jinan, China
| | - Xiaoling Zhu
- Shandong Academy of Agricultural Sciences, Jinan, China,Xiaoling Zhu
| | - Jie Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China,*Correspondence: Jie Zhang
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Lin M, Jiang M, Yang T, Zhao G, Zhan K. Overexpression of GPR41 attenuated glucose production in propionate-induced bovine hepatocytes. Front Vet Sci 2022; 9:981640. [PMID: 36118357 PMCID: PMC9478460 DOI: 10.3389/fvets.2022.981640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine liver mainly utilizes the propionate as a gluconeogenic substrate to synthesize the glucose. However, the mechanism underlying the regulatory effects of propionate on the glucose production in bovine hepatocytes remains less known. Previous studies have demonstrated G protein-coupled receptor 41 (GPR41) as receptors for propionate. We hypothesized that propionate may regulate the glucose production by GPR41 in bovine hepatocytes. Therefore, the aim of the study was to investigate the regulatory effects of propionate and GPR41 on glucose production in bovine hepatocytes. Hepatocytes with GPR41 overexpression were incubated in the presence of either 0 or 3 mM propionate for 24 h. These results showed that the expression of phosphoenolpyruvate carboxykinase 2 (PCK2) and pyruvate carboxylase (PC) genes involved in gluconeogenesis was enhanced (P < 0.01) with propionate treatment. Remarkably, the addition of propionate promotes the glucose production in bovine hepatocytes. Expression of GPR41 was increased by the addition of propionate in bovine hepatocytes overexpressed GPR41 by overexpression plasmid AAV1 compared with the absence of propionate. Interestingly, expression of PCK2 was markedly attenuated in GPR41 overexpressed-hepatocytes with propionate. Importantly, overexpression of GPR41 attenuated glucose output in propionate-induced bovine hepatocytes. These findings revealed that GPR41 negatively regulates glucose production by downregulating the expression of PCK2 in propionate-induced bovine hepatocytes.
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Affiliation(s)
- Miao Lin
- Institute of Animal Culture Collection and Application, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Maocheng Jiang
- Institute of Animal Culture Collection and Application, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianyu Yang
- Institute of Animal Culture Collection and Application, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guoqi Zhao
- Institute of Animal Culture Collection and Application, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kang Zhan
- Institute of Animal Culture Collection and Application, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- *Correspondence: Kang Zhan
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Li JY, Tang YH, Tang L, Chen LY. Adsorption of thiotepa anticancer drugs on the C 3N nanotube as promising nanocarriers for drug delivery. J Mol Model 2022; 28:249. [PMID: 35933501 DOI: 10.1007/s00894-022-05248-y] [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: 06/22/2022] [Accepted: 07/25/2022] [Indexed: 10/15/2022]
Abstract
This paper focused on the efficiency of carbon nitride nanotubes functionalized with alanine amino acid (f-C3NNTs) in thiotepa (TPA) anti-cancerous drug delivery via density functional theory (DFT). Pristine C3NNTs were incorporated for comparison. TPA was found to spontaneously undergo exothermic adsorption onto the nanostructures. The f-C3NNT/TPA complexes showed the highest interaction strength. The adsorption distance of TPA was found to be smaller, with a greater adsorption capacity and solubility on the f-C3NNT surface than on the pristine C3NNT surface. As they were polar, all the complexes were concluded to be insoluble within an aqueous phase. The quantum molecular descriptors revealed the f-C3NNT nanocarriers to be more reactive than the C3NNT carrier. The drug was found to spontaneously and exothermically interact with f-C3NNT. As a result, f-C3NNT would be promising for TPA adsorption in drug delivery applications.
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Affiliation(s)
- Jia Yu Li
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Songjiang, Shanghai, 201620, China
| | - Yu Han Tang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Songjiang, Shanghai, 201620, China
| | - Li Tang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Songjiang, Shanghai, 201620, China
| | - Ling Yan Chen
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Songjiang, Shanghai, 201620, China.
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