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Tu TC, Lin CJ, Liu MC, Hsu ZT, Chen CF. Comparison of genomic prediction accuracy using different models for egg production traits in Taiwan country chicken. Poult Sci 2024; 103:104063. [PMID: 39098301 DOI: 10.1016/j.psj.2024.104063] [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: 12/15/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024] Open
Abstract
In local chickens targeted for niche markets, genotyping costs are relatively high due to the small population size and diverse breeding goals. The single-step genomic best linear unbiased prediction (ssGBLUP) model, which combines pedigree and genomic information, has been introduced to increase the accuracy of genomic estimated breeding value (GEBV). Therefore, this model may be more beneficial than the genomic BLUP (GBLUP) model for genomic selection in local chickens. Additionally, the single-step genome-wide association study (ssGWAS) can be used to extend the ssGBLUP model results to animals with available phenotypic information but without genotypic data. In this study, we compared the accuracy of (G)EBVs using the pedigree-based BLUP (PBLUP), GBLUP, and ssGBLUP models. Moreover, we conducted single-SNP GWAS (SNP-GWAS), GBLUP-GWAS, and ssGWAS methods to identify genes associated with egg production traits in the NCHU-G101 chicken to understand the feasibility of using genomic selection in a small population. The average prediction accuracy of (G)EBV for egg production traits using the PBLUP, GBLUP, and ssGBLUP models is 0.536, 0.531, and 0.555, respectively. In total, 22 suggestive- and 5% Bonferroni genome-wide significant-level SNPs for total egg number (EN), average laying rate (LR), average clutch length, and total clutch number are detected using 3 GWAS methods. These SNPs are mapped onto Gallus gallus chromosomes (GGA) 4, 6, 10, 18, and 25 in NCHU-G101 chicken. Furthermore, through SNP-GWAS and ssGWAS methods, we identify 2 genes on GGA4 associated with EN and LR: ENSGALG00000023172 and PPARGC1A. In conclusion, the ssGBLUP model demonstrates superior prediction accuracy, performing on average 3.41% than the PBLUP model. The implications of our gene results may guide future selection strategies for Taiwan Country chickens. Our results highlight the applicability of the ssGBLUP model for egg production traits selection in a small population, specifically NCHU-G101 chicken in Taiwan.
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Affiliation(s)
- Tsung-Che Tu
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan; Ray Hsing Agricultural Biotechnology Co. Ltd., Yunlin 633, Taiwan
| | - Chen-Jyuan Lin
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Ming-Che Liu
- Ray Hsing Agricultural Biotechnology Co. Ltd., Yunlin 633, Taiwan
| | - Zhi-Ting Hsu
- Ray Hsing Agricultural Biotechnology Co. Ltd., Yunlin 633, Taiwan
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.
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2
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Sun Y, Li Y, Jiang X, Wu Q, Lin R, Chen H, Zhang M, Zeng T, Tian Y, Xu E, Zhang Y, Lu L. Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck. Poult Sci 2024; 103:104032. [PMID: 39003796 PMCID: PMC11298941 DOI: 10.1016/j.psj.2024.104032] [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: 04/23/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yan Li
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, P.R. China
| | - Qiong Wu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Min Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Tao Zeng
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Yong Tian
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Enrong Xu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yeqiong Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China..
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3
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Wadood AA, Zhang X. The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review. Curr Issues Mol Biol 2024; 46:6248-6266. [PMID: 38921044 PMCID: PMC11202932 DOI: 10.3390/cimb46060373] [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: 05/16/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.
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Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, 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
| | - Xiquan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, 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
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4
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Lei Q, Zhang S, Wang J, Qi C, Liu J, Cao D, Li F, Han H, Liu W, Li D, Tang C, Zhou Y. Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken. Poult Sci 2024; 103:103705. [PMID: 38598913 DOI: 10.1016/j.psj.2024.103705] [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: 01/17/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.
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Affiliation(s)
- Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Wang
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dapeng Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Cunwei Tang
- Fujian Sunnzer Biological Technology Development Co. Ltd., 354100, Guang'ze, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China..
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Chen A, Wang Q, Zhao X, Wang G, Zhang X, Ren X, Zhang Y, Cheng X, Yu X, Mei X, Wang H, Guo M, Jiang X, Wei G, Wang X, Jiang R, Guo X, Ning Z, Qu L. Molecular genetic foundation of a sex-linked tailless trait in Hongshan chicken by whole genome data analysis. Poult Sci 2024; 103:103685. [PMID: 38603937 PMCID: PMC11017342 DOI: 10.1016/j.psj.2024.103685] [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: 01/18/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
As a Chinese local chicken breed, Hongshan chickens have 2 kinds of tail feather phenotypes, normal and taillessness. Our previous studies showed that taillessness was a sex-linked dominant trait. Abnormal development of the tail vertebrae could be explained this phenomenon in some chicken breeds. However, the number of caudal vertebrae in rumpless Hongshan chickens was normal, so rumplessness in Hongshan chicken was not related to the development of the caudal vertebrae. Afterwards, we found that rumplessness in Hongshan was due to abnormal development of tail feather rather than abnormal development of caudal vertebrae. In order to understand the genetic foundation of the rumplessness of Hongshan chickens, we compared and reanalyzed 2 sets of data in normal and rumpless Hongshan chickens from our previous studies. By joint analysis of genome-wide selection signature analysis and genome-wide association approach, we found that 1 overlapping gene (EDIL3) and 16 peak genes (ENSGALG00000051843, ENSGALG00000053498, ENSGALG00000054800, KIF27, PTPRD, ENSGALG00000047579, ENSGALG00000041052, ARHGEF28, CAMK4, SERINC5, ENSGALG00000050776, ERCC8, MCC, ADAMTS19, ENSGALG00000053322, CHRNA8) located on the Z chromosome was associated with the rumpless trait. The results of this study furtherly revealed the molecular mechanism of the rumpless trait in Hongshan chickens, and identified the candidate genes associated with this trait. Our results will help to improve the shape of chicken tail feathers and to rise individual economic value in some specific market in China.
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Affiliation(s)
- Anqi Chen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiong Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- 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
| | - Xufang Ren
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Cheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaofan Yu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaohan Mei
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huie Wang
- Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Menghan Guo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Jiang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guozhen Wei
- Qingliu Animal Husbandry, Veterinary and Aquatic Products Center, Sanming, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Beijing, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, 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; Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
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6
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Li X, Chen X, Wang Q, Yang N, Sun C. Integrating Bioinformatics and Machine Learning for Genomic Prediction in Chickens. Genes (Basel) 2024; 15:690. [PMID: 38927626 PMCID: PMC11202573 DOI: 10.3390/genes15060690] [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: 04/09/2024] [Revised: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel approaches are necessary for future genomic prediction. In this study, we used an illumina 50K SNP chip to genotype 4190 egg-type female Rhode Island Red chickens. Machine learning (ML) and classical bioinformatics methods were integrated to fit genotypes with 10 economic traits in chickens. We evaluated the effectiveness of ML methods using Pearson correlation coefficients and the RMSE between predicted and actual phenotypic values and compared them with rrBLUP and BayesA. Our results indicated that ML algorithms exhibit significantly superior performance to rrBLUP and BayesA in predicting body weight and eggshell strength traits. Conversely, rrBLUP and BayesA demonstrated 2-58% higher predictive accuracy in predicting egg numbers. Additionally, the incorporation of suggestively significant SNPs obtained through the GWAS into the ML models resulted in an increase in the predictive accuracy of 0.1-27% across nearly all traits. These findings suggest the potential of combining classical bioinformatics methods with ML techniques to improve genomic prediction in the future.
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Affiliation(s)
| | | | | | | | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China; (X.L.); (X.C.); (Q.W.); (N.Y.)
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7
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Wu S, Dou T, Wang K, Yuan S, Yan S, Xu Z, Liu Y, Jian Z, Zhao J, Zhao R, Wu H, Gu D, Liu L, Li Q, Wu DD, Ge C, Su Z, Jia J. Artificial selection footprints in indigenous and commercial chicken genomes. BMC Genomics 2024; 25:428. [PMID: 38689225 PMCID: PMC11061962 DOI: 10.1186/s12864-024-10291-5] [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] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. RESULTS We found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds. CONCLUSION We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.
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Affiliation(s)
- Siwen Wu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sisi Yuan
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rouhan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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Yu C, Lin Z, Song X, Hu C, Qiu M, Yang L, Zhang Z, Pen H, Chen J, Xiong X, Xia B, Jiang X, Du H, Li Q, Zhu S, Liu S, Yang C, Liu Y. Whole transcriptome analysis reveals the key genes and noncoding RNAs related to follicular atresia in broilers. Anim Biotechnol 2023; 34:3144-3153. [PMID: 36306258 DOI: 10.1080/10495398.2022.2136680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Broodiness, a maternal behavior, is accompanied by the atresia of follicles and the serious degradation of poultry reproductive performance. The comparison of follicles between brooding and laying hens is usually an ideal model for exploring the regulation mechanism of follicle atresia. In this study, we selected three brooding hens and three laying hens to collect their follicles for whole transcriptome sequencing. The results demonstrated different expression patterns between the follicles of brooding hens and laying hens. In the top 10 differentially expressed genes with the highest expression, MMP10 was relatively low expressed in the follicles of brooding hens, but other nine genes were relatively highly expressed, including LRR1, RACK1, SPECC1L, ABHD2, COL6A3, RPS17, ATRN, BIRC6, PGAM1 and SPECC1L. While miR-21-3p, miR-146a-5p, miR-142-5p and miR-1b-3p were highly expressed in the follicles of brooding hen, miR-106-5p, miR-451, miR-183, miR-7, miR-2188-5p and miR-182-5p were lowly expressed in brooding hen. In addition, we identified 124 lncRNAs specifically expressed in the follicles of brooding hens and 147 lncRNAs specifically expressed in the follicles of laying hens. Our results may provide a theoretical basis for further exploration of the molecular mechanism of broodiness in broilers.
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Affiliation(s)
- Chunlin Yu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyan Song
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chenming Hu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Mohan Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Li Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zengrong Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Han Pen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jialei Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xia Xiong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Bo Xia
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Huarui Du
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Qingyun Li
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Shiliang Zhu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Siyang Liu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Fu M, Wu Y, Shen J, Pan A, Zhang H, Sun J, Liang Z, Huang T, Du J, Pi J. Genome-Wide Association Study of Egg Production Traits in Shuanglian Chickens Using Whole Genome Sequencing. Genes (Basel) 2023; 14:2129. [PMID: 38136951 PMCID: PMC10742582 DOI: 10.3390/genes14122129] [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: 10/28/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Egg production is the most important economic trait in laying hens. To identify molecular markers and candidate genes associated with egg production traits, such as age at first egg (AFE), weight at first egg (WFE), egg weight (EW), egg number (EN), and maximum consecutive egg laying days (MCD), a genome-wide analysis by whole genome sequencing was performed in Shuanglian chickens. Through whole genome sequencing and quality control, a total of 11,006,178 SNPs were obtained for further analysis. Heritability estimates ranged from moderate to high for EW (0.897) and MCD (0.632), and from low to moderate (0.193~0.379) for AFE, WFE, and EN. The GWAS results showed 11 genome-wide significant SNPs and 23 suggestive significant SNPs were identified to be associated with EN, MCD, WFE, and EW. Linkage disequilibrium analysis revealed twenty-seven SNPs associated with EN were located in a 0.57 Mb region on GGA10, and clustered into five blocks. Through functional annotation, three candidate genes NEO1, ADPGK, and CYP11A1, were identified to be associated with EN, while the S1PR4, LDB2, and GRM8 genes was linked to MCD, WFE, and EW, respectively. These findings may help us to better understand the molecular mechanisms underlying egg production traits in chickens and contribute to genetic improvement of these traits.
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Affiliation(s)
- Ming Fu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Yan Wu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Hao Zhang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Jing Sun
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Tao Huang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China; (M.F.); (J.S.); (A.P.); (H.Z.); (J.S.); (Z.L.); (T.H.); (J.D.); (J.P.)
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan 430064, China
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Wang J, Liu Z, Cao D, Liu J, Li F, Han H, Han H, Lei Q, Liu W, Li D, Wang J, Zhou Y. Elucidation of the genetic determination of clutch traits in Chinese local chickens of the Laiwu Black breed. BMC Genomics 2023; 24:686. [PMID: 37968610 PMCID: PMC10652520 DOI: 10.1186/s12864-023-09798-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/08/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Egg laying rate (LR) is associated with a clutch, which is defined as consecutive days of oviposition. The clutch trait can be used as a selection indicator to improve egg production in poultry breeding. However, little is known about the genetic basis of clutch traits. In this study, our aim was to estimate genetic parameters and identify quantitative trait single nucleotide polymorphisms for clutch traits in 399 purebred Laiwu Black chickens (a native Chinese breed) using a genome-wide association study (GWAS). METHODS In this work, after estimating the genetic parameters of age at first egg, body weight at first egg, LR, longest clutch until 52 week of age, first week when the longest clutch starts, last week when the longest clutch ends, number of clutches, and longest number of days without egg-laying until 52 week of age, we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chickens. The restricted maximum likelihood method was used to estimate genetic parameters of clutch pattern in 399 Laiwu Black hens, using the GCTA software. RESULTS The results showed that SNP-based heritability estimates of clutch traits ranged from 0.06 to 0.59. Genotyping data were obtained from whole genome re-sequencing data. After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS revealed that 421 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, NELL2, SMYD9, SPTLC2, SMYD3 and PLCL1 were the most promising candidates for clutch traits in Laiwu Black chickens. CONCLUSION The findings of this research provide critical insight into the genetic basis of clutch traits. These results contribute to the identification of candidate genes and variants. Genes and SNPs potentially provide new avenues for further research and would help to establish a framework for new methods of genomic prediction, and increase the accuracy of estimated genetic merit for egg production and clutch traits.
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Affiliation(s)
- Jie Wang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Zhansheng Liu
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Dingguo Cao
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Jie Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Fuwei Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Heguo Han
- Lijin County Center for Animal Disease Control, Lijin, 257400, China
| | - Haixia Han
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Qiuxia Lei
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Wei Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Dapeng Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China
| | - Jianxia Wang
- Administrative Examination and Approval Service Bureau of Lijin County, Lijin, 257400, China
| | - Yan Zhou
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, Shandong, China.
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11
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Tian J, Zhu X, Wu H, Wang Y, Hu X. Serum metabolic profile and metabolome genome-wide association study in chicken. J Anim Sci Biotechnol 2023; 14:69. [PMID: 37138301 PMCID: PMC10158329 DOI: 10.1186/s40104-023-00868-7] [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: 12/12/2022] [Accepted: 03/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. RESULTS Here, comprehensive metabolome detection was performed using non-targeted LC-MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. CONCLUSIONS We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing, 100193, China.
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12
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Bouba I, van den Brand H, Kemp B, Rodenburg TB, Visser B. Genetics of rearing success in four pure laying hen lines during the first 17 weeks of age. Poult Sci 2023; 102:102576. [PMID: 36913755 PMCID: PMC10023977 DOI: 10.1016/j.psj.2023.102576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
This study aimed to investigate the genetics of rearing success (RS) in laying hens. Four rearing traits: clutch size (CS), first week mortality (FWM), rearing abnormalities (RA), and natural death (ND), were included as factors determining RS. Pedigree, genotypic, and phenotypic records of 4 purebred genetic lines of White Leghorn layers were available for 23,000 rearing batches obtained between 2010 and 2020. FWM and ND showed little or no variation amongst the 4 genetic lines over the years 2010-2020, whereas an increase was observed for CS and a decrease for RA. To determine whether these traits were heritable, genetic parameters for each trait were estimated, using a Linear Mixed Model. Heritabilities within lines were low (0.05-0.19 for CS, 0.01-0.04 for FWM, 0.02-0.06 for RA, 0.02-0.04 for ND, and 0.01-0.07 for RS). Additionally, genome wide association study was done to scan the genomes of the breeders to reveal single nucleotide polymorphisms (SNPs) associated with these traits. Manhattan plots indicated the existence of 12 different SNPs having a significant effect on RS. Thus, the identified SNPs will increase the understanding of the genetics of RS in laying hens.
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Affiliation(s)
- I Bouba
- Hendrix Genetics Research, Technology & Services B.V., 5831 CK Boxmeer, The Netherlands; Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
| | - H van den Brand
- Department of Animal Sciences, Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - B Kemp
- Department of Animal Sciences, Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - T Bas Rodenburg
- Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands; Department of Animal Sciences, Adaptation Physiology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - B Visser
- Hendrix Genetics Research, Technology & Services B.V., 5831 CK Boxmeer, The Netherlands
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13
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Zhao J, Pan H, Liu Y, He Y, Shi H, Ge C. Interacting Networks of the Hypothalamic-Pituitary-Ovarian Axis Regulate Layer Hens Performance. Genes (Basel) 2023; 14:141. [PMID: 36672882 PMCID: PMC9859134 DOI: 10.3390/genes14010141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Egg production is a vital biological and economic trait for poultry breeding. The 'hypothalamic-pituitary-ovarian (HPO) axis' determines the egg production, which affects the layer hens industry income. At the organism level, the HPO axis is influenced by the factors related to metabolic and nutritional status, environment, and genetics, whereas at the cellular and molecular levels, the HPO axis is influenced by the factors related to endocrine and metabolic regulation, cytokines, key genes, signaling pathways, post-transcriptional processing, and epigenetic modifications. MiRNAs and lncRNAs play a critical role in follicle selection and development, atresia, and ovulation in layer hens; in particular, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells. The current review elaborates on the regulation of the HPO axis and its role in the laying performance of hens at the organism, cellular, and molecular levels. In addition, this review provides an overview of the interactive network regulation mechanism of the HPO axis in layer hens, as well as comprehensive knowledge for successfully utilizing their genetic resources.
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Affiliation(s)
- Jinbo Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161005, China
| | - Hongbin Pan
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Yang He
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Hongmei Shi
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
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14
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A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken. J Anim Sci Biotechnol 2022; 13:96. [PMID: 35941697 PMCID: PMC9361671 DOI: 10.1186/s40104-022-00744-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Egg production is economically important in the meat-type chicken industry. To better understand the molecular genetic mechanism of egg production in meat-type chicken, genetic parameter estimation, genome-wide association analyses combined with meta-analyses, Bayesian analyses, and selective sweep analyses were performed to screen single nucleotide polymorphisms (SNPs) and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines. RESULTS Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age, with heritability ranging from 0.034-0.258. Based on meta-analyses and selective sweep analyses, one region (10.81-13.05 Mb) on chromosome Z was associated with egg number in all lines. Further analyses using the W2 line was also associated with the same region, and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers. The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2. There are 36 genes in the region, with glial cell derived neurotrophic factor, DAB adaptor protein 2, protein kinase AMP-activated catalytic subunit alpha 1, NAD kinase 2, mitochondrial, WD repeat domain 70, leukemia inhibitory factor receptor alpha, complement C6, and complement C7 identified as being potentially affecting to egg number. In addition, three SNPs (rs318154184, rs13769886, and rs313325646) associated with egg number were located on or near the prolactin receptor gene. CONCLUSION Our study used genomic information from different chicken lines and populations to identify a genomic region (spanning 2.24 Mb) associated with egg number. Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production. These results contribute to the identification of candidate genes and variants for egg traits in poultry.
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Khalkhali-Evrigh R, Hedayat N, Ming L, Jirimutu. Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data. Sci Rep 2022; 12:9653. [PMID: 35688969 PMCID: PMC9187634 DOI: 10.1038/s41598-022-14376-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
The Old World camels play an important role as one of the main food sources in large parts of Asia and Africa. Natural selection combined with artificial selection by human has affected parts of the domestic animal genome for adapting them to their habitats and meeting human needs. Here, we used whole genome sequencing data of 34 camels (including 14 dromedaries and 20 Bactrian camels) to identify the genomic signature of selection in the Iranian dromedary (ID) and Bactrian camels (IB). To detect the mentioned regions, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. Based on gene ontology analysis on the candidate genes identified for IB camels, we found GO terms associated with lung development, nervous system development, immune system and behavior. Also, we identified several genes related to body thermoregulation (ZNF516), meat quality (ANK1 and HSPA13), and high-altitude adaptation (OPA1) for IB camels. In the list of detected candidate genes under selection in ID camels, the genes related to energy metabolism (BDH1), reproduction (DLG1, IMMP2L and FRASI), long-term memory (GRIA1), kidney (SLC12A1), lung development (EMILIN2 and FBN1) and immunity (SOCS2, JAK1, NRROS and SENP1) were found. Our findings, along with further studies in this field, will strengthen our knowledge about the effect of selection on the camelid genome under different geographical, climatic and even cultural conditions.
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Affiliation(s)
- Reza Khalkhali-Evrigh
- Department of Animal Science, Faculty of Agriculture and Natural Recourses, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Nemat Hedayat
- Department of Animal Science, Faculty of Agriculture and Natural Recourses, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Liang Ming
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Jirimutu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
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Zhang Z, Sui Z, Zhang J, Li Q, Zhang Y, Xing F. Transcriptome Sequencing-Based Mining of Genes Associated With Pubertal Initiation in Dolang Sheep. Front Genet 2022; 13:818810. [PMID: 35309120 PMCID: PMC8928774 DOI: 10.3389/fgene.2022.818810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022] Open
Abstract
Improving the fertility of sheep is an important goal in sheep breeding as it greatly increases the productivity. Dolang sheep is a typical representative breed of lamb in Xinjiang and is the main local sheep breed and meat source in the region. To explore the genes associated with the initiation of puberty in Dolang sheep, the hypothalamic tissues of Dolang sheep prepubertal, pubertal, and postpubertal periods were collected for RNA-seq analysis on the Illumina platform, generating 64.08 Gb clean reads. A total of 575, 166, and 648 differentially expressed genes (DEGs) were detected in prepuberty_vs._puberty, postpuberty_vs._prepuberty, and postpuberty_vs._puberty analyses, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, the related genes involved in the initiation of puberty in Dolang sheep were mined. Ten genes that have direct or indirect functions in the initiation of puberty in Dolang sheep were screened using the GO and KEGG results. Additionally, quantitative real-time PCR was used to verify the reliability of the RNA-Seq data. This study provided a new approach for revealing the mechanism of puberty initiation in sheep and provided a theoretical basis and candidate genes for the breeding of early-pubertal sheep by molecular techniques, and at the same time, it is also beneficial for the protection, development, and utilization of the fine genetic resources of Xinjiang local sheep.
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