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Cai W, Hu J, Zhang Y, Guo Z, Zhou Z, Hou S. Cis-eQTLs in seven duck tissues identify novel candidate genes for growth and carcass traits. BMC Genomics 2024; 25:429. [PMID: 38689208 PMCID: PMC11061949 DOI: 10.1186/s12864-024-10338-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential candidate genes and causal DNA variants vital to complex traits in human and many farm animals. However, eQTL mapping has not been conducted in ducks. It is desirable to know whether eQTLs within GWAS signals contributed to duck economic traits. RESULTS In this study, we conducted an eQTL analysis using publicly available RNA sequencing data from 820 samples, focusing on liver, muscle, blood, adipose, ovary, spleen, and lung tissues. We identified 113,374 cis-eQTLs for 12,266 genes, a substantial fraction 39.1% of which were discovered in at least two tissues. The cis-eQTLs of blood were less conserved across tissues, while cis-eQTLs from any tissue exhibit a strong sharing pattern to liver tissue. Colocalization between cis-eQTLs and genome-wide association studies (GWAS) of 50 traits uncovered new associations between gene expression and potential loci influencing growth and carcass traits. SRSF4, GSS, and IGF2BP1 in liver, NDUFC2 in muscle, ELF3 in adipose, and RUNDC1 in blood could serve as the candidate genes for duck growth and carcass traits. CONCLUSIONS Our findings highlight substantial differences in genetic regulation of gene expression across duck primary tissues, shedding light on potential mechanisms through which candidate genes may impact growth and carcass traits. Furthermore, this availability of eQTL data offers a valuable resource for deciphering further genetic association signals that may arise from ongoing extensive endeavors aimed at enhancing duck production traits.
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Affiliation(s)
- Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Hu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunsheng Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhanbao Guo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuisheng Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Hu Z, Tian X, Lai R, Ji C, Li X. Airborne transmission of common swine viruses. Porcine Health Manag 2023; 9:50. [PMID: 37908005 PMCID: PMC10619269 DOI: 10.1186/s40813-023-00346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
The transmission of viral aerosols poses a vulnerable aspect in the biosecurity measures aimed at preventing and controlling swine virus in pig production. Consequently, comprehending and mitigating the spread of aerosols holds paramount significance for the overall well-being of pig populations. This paper offers a comprehensive review of transmission characteristics, influential factors and preventive strategies of common swine viral aerosols. Firstly, certain viruses such as foot-and-mouth disease virus (FMDV), porcine reproductive and respiratory syndrome virus (PRRSV), influenza A viruses (IAV), porcine epidemic diarrhea virus (PEDV) and pseudorabies virus (PRV) have the potential to be transmitted over long distances (exceeding 150 m) through aerosols, thereby posing a substantial risk primarily to inter-farm transmission. Additionally, other viruses like classical swine fever virus (CSFV) and African swine fever virus (ASFV) can be transmitted over short distances (ranging from 0 to 150 m) through aerosols, posing a threat primarily to intra-farm transmission. Secondly, various significant factors, including aerosol particle sizes, viral strains, the host sensitivity to viruses, weather conditions, geographical conditions, as well as environmental conditions, exert a considerable influence on the transmission of viral aerosols. Researches on these factors serve as a foundation for the development of strategies to combat viral aerosol transmission in pig farms. Finally, we propose several preventive and control strategies that can be implemented in pig farms, primarily encompassing the implementation of early warning models, viral aerosol detection, and air pretreatment. This comprehensive review aims to provide a valuable reference for the formulation of efficient measures targeted at mitigating the transmission of viral aerosols among swine populations.
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Affiliation(s)
- Zhiqiang Hu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
- China Agriculture Research System-Yangling Comprehensive Test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, People's Republic of China
| | - Xiaogang Tian
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Ranran Lai
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Chongxing Ji
- Key Laboratory of Feed and Livestock and Poultry Products Quality and Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd, 316 Jinshi Road, Chengdu, 610100, Sichuan, People's Republic of China
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China
| | - Xiaowen Li
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, People's Republic of China.
- Key Laboratory of Feed and Livestock and Poultry Products Quality and Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd, 316 Jinshi Road, Chengdu, 610100, Sichuan, People's Republic of China.
- Shandong New Hope Liuhe Co., Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, People's Republic of China.
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road, Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China.
- China Agriculture Research System-Yangling Comprehensive Test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, People's Republic of China.
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Hu Z, Liu Q, Tian X, Li L, Wu W, Gao W, Li X. Resumption of production operations during the silent disposal period of African swine fever outbreaks: a case study. Porcine Health Manag 2023; 9:43. [PMID: 37817220 PMCID: PMC10563274 DOI: 10.1186/s40813-023-00338-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Batch production, a widely implemented production model in large-scale pig farms, was characterized by its long-term duration, cost-effectiveness, and efficiency. Nevertheless, the recent occurrence of African swine fever (ASF) outbreaks in China has necessitated the implementation of discreet mating operations within this model, leading to disruptions in production cycles and substantial indirect losses. CASE PRESENTATION This study implemented a novel operational procedure, which involved the division of risk areas for zone management and allowed mating operations, in 12 farms experiencing ASF outbreaks. Another 12 farms were used as a control group, employing the old procedure. Subsequently, the prognoses of both the old and new procedures were calculated and analyzed. The findings indicate that the new method resulted in an enhanced retention rate and reduced non-productive days (NPD), without impacting the positive detection rate and disposal time. Consequently, this approach significantly mitigated economic losses (p < 0.05). CONCLUSION The efficacy of the novel procedure in mitigating the indirect economic losses stemming from ASF outbreaks, through the reduction of NPD while maintaining retention rates and disposition days, has been substantiated. This methodology has demonstrated feasibility in extensive pig farming operations and exhibits promise for broader application.
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Affiliation(s)
- Zhiqiang Hu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
- China Agriculture Research System-Yangling Comprehensive test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, P. R. China
| | - Qingyuan Liu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Xiaogang Tian
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Lulu Li
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
| | - Weisheng Wu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
| | - Wenchao Gao
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China
| | - Xiaowen Li
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Xiajin Economic Development Zone, Qingwo Venture Park, Dezhou, 253200, Shandong Province, P. R. China.
- Key Laboratory of Feed and Livestock and Poultry Products Quality & Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd, 316 Jinshi Road, Chengdu, 610100, Sichuan, P. R. China.
- Shandong New Hope Liuhe Co.,Ltd, No. 592-26 Jiushui East Road Laoshan District, Qingdao, 266100, Shandong, P. R. China.
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd (NHLH Academy of Swine Research), 6596 Dongfanghong East Road Yuanqiao Town, Dezhou, 253000, Shandong, People's Republic of China.
- China Agriculture Research System-Yangling Comprehensive test Station, Intersection of Changqing Road and Park Road 1, Yangling District, Xianyang, P. R. China.
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Zhang B, Qing J, Yan Z, Shi Y, Wang Z, Chen J, Li J, Li S, Wu W, Hu X, Li Y, Zhang X, Wu L, Zhu S, Yan Z, Wang Y, Guo X, Yu L, Li X. Investigation and analysis of porcine epidemic diarrhea cases and evaluation of different immunization strategies in the large-scale swine farming system. Porcine Health Manag 2023; 9:36. [PMID: 37537653 PMCID: PMC10401829 DOI: 10.1186/s40813-023-00331-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Porcine epidemic diarrhea (PED) is a contagious intestinal disease caused by porcine epidemic diarrhea virus (PEDV) characterized by vomiting, diarrhea, anorexia, and dehydration, which has caused huge economic losses around the world. However, it is very hard to find completely valid approaches to control the transmission of PEDV. At present, vaccine immunity remains the most effective method. To better control the spread of PED and evaluate the validity of different immunization strategies, 240 PED outbreak cases from 577 swine breeding farms were collected and analyzed. The objective of the present study was to analyze the epidemic regularity of PEDV and evaluate two kinds of different immunization strategies for controlling PED. RESULTS The results showed that the main reasons which led to the outbreak of PED were the movement of pig herds between different pig farms (41.7%) and delaying piglets from the normal production flow (15.8%). The prevalence of PEDV in the hot season (May to October) was obviously higher than that in the cold season (January to April, November to December). Results of different vaccine immunity cases showed that immunization with the highly virulent live vaccine (NH-TA2020 strain) and the commercial inactivated vaccine could significantly decrease the frequency of swine breeding farms (5.9%), the duration of PED epidemic (1.70 weeks), and the week batches of dead piglets (0.48 weeks weaned piglets), compared with immunization with commercial attenuated vaccines and inactivated vaccine of PED. Meanwhile, immunization with the highly virulent live vaccine and the commercial inactivated vaccine could bring us more cash flows of Y̶275,274 per year than immunization with commercial live attenuated vaccine and inactivated vaccine in one 3000 sow pig farm within one year. CONCLUSION Therefore, immunization with highly virulent live vaccine and inactivated vaccine of PED is more effective and economical in the prevention and control of PED in the large-scale swine farming system.
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Affiliation(s)
- Bingzhou Zhang
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Jie Qing
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Zhong Yan
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Yuntong Shi
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Zewei Wang
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Jing Chen
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Junxian Li
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Shuangxi Li
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Weisheng Wu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Xiaofang Hu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Yang Li
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Xiaoyang Zhang
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Lili Wu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Shouyue Zhu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Zheng Yan
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Yongquan Wang
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China
| | - Xiaoli Guo
- Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ligen Yu
- Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Xiaowen Li
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, 253034, China.
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd, Dezhou, 253200, China.
- China Agriculture Research System-Yangling Comprehensive test Station, Xianyang, 712100, China.
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Qingdao, China.
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Cai W, Hu J, Fan W, Xu Y, Tang J, Xie M, Zhang Y, Guo Z, Zhou Z, Hou S. Strategies to improve genomic predictions for 35 duck carcass traits in an F 2 population. J Anim Sci Biotechnol 2023; 14:74. [PMID: 37147656 PMCID: PMC10163724 DOI: 10.1186/s40104-023-00875-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/02/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Carcass traits are crucial for broiler ducks, but carcass traits can only be measured postmortem. Genomic selection (GS) is an effective approach in animal breeding to improve selection and reduce costs. However, the performance of genomic prediction in duck carcass traits remains largely unknown. RESULTS In this study, we estimated the genetic parameters, performed GS using different models and marker densities, and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F2 population of ducks. Most of the cut weight traits and intestine length traits were estimated to be high and moderate heritabilities, respectively, while the heritabilities of percentage slaughter traits were dynamic. The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method. The Permutation studies revealed that 50K markers had achieved ideal prediction reliability, while 3K markers still achieved 90.7% predictive capability would further reduce the cost for duck carcass traits. The genomic relationship matrix normalized by our true variance method instead of the widely used [Formula: see text] could achieve an increase in prediction reliability in most traits. We detected most of the bayesian models had a better performance, especially for BayesN. Compared to GBLUP, BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits. CONCLUSION This study demonstrates genomic selection for duck carcass traits is promising. The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models. Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.
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Affiliation(s)
- Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Hu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, 266108, China
| | - Wenlei Fan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yaxi Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Jing Tang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ming Xie
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunsheng Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhanbao Guo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuisheng Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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