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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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Mazocco CC, de Castro Júnior SL, Silveira RMF, Poletto R, da Silva IJO. Laying Hens: Why Smothering and Not Surviving?-A Literature Review. Animals (Basel) 2024; 14:1518. [PMID: 38891565 PMCID: PMC11171085 DOI: 10.3390/ani14111518] [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: 02/14/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 06/21/2024] Open
Abstract
The proliferation of rearing systems providing opportunities for birds to engage in natural behaviors can trigger behavioral repertoires that when not manageable compromise animal welfare and the economic viability of the flock. Smothering in laying hens has long been perceived as "natural" or the result of hysteria among birds in the flock. However, the current literature has recognized smothering as an abnormal outcome with the potential to result in significant losses in cage-free poultry systems. Recent studies have specifically aimed to categorize the organization of smothering behavior and highlight its potential causes and consequences. In this study, literature review and bibliographic mapping, drawing on published articles and engagement with poultry farmers through extension and rural technical assistance, were employed. The findings indicate that smothering is a behavior triggered by factors related to the environment in which the laying hens are kept. This study concludes that there is a critical need for more rigorous and detailed research to elucidate the nuances of avian behavioral physiology and assess the impact of production systems on animal welfare and the economic impacts on the flock. This research contributes to a deeper understanding of bird behavior in high-production environments and provides practical insights for the poultry industry.
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Affiliation(s)
- Caroline Citta Mazocco
- Núcleo de Pesquisa em Ambiência (NUPEA), Escola Superior de Agricultura ‘‘Luiz de Queiroz’’ (ESALQ), Universidade de São Paulo (USP), Piracicaba 13418-900, SP, Brazil; (S.L.d.C.J.); (R.M.F.S.); (I.J.O.d.S.)
| | - Sérgio Luís de Castro Júnior
- Núcleo de Pesquisa em Ambiência (NUPEA), Escola Superior de Agricultura ‘‘Luiz de Queiroz’’ (ESALQ), Universidade de São Paulo (USP), Piracicaba 13418-900, SP, Brazil; (S.L.d.C.J.); (R.M.F.S.); (I.J.O.d.S.)
| | - Robson Mateus Freitas Silveira
- Núcleo de Pesquisa em Ambiência (NUPEA), Escola Superior de Agricultura ‘‘Luiz de Queiroz’’ (ESALQ), Universidade de São Paulo (USP), Piracicaba 13418-900, SP, Brazil; (S.L.d.C.J.); (R.M.F.S.); (I.J.O.d.S.)
| | - Rosangela Poletto
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul (IFRS)-Campus Sertão, Sertão 99170-000, RS, Brazil;
| | - Iran José Oliveira da Silva
- Núcleo de Pesquisa em Ambiência (NUPEA), Escola Superior de Agricultura ‘‘Luiz de Queiroz’’ (ESALQ), Universidade de São Paulo (USP), Piracicaba 13418-900, SP, Brazil; (S.L.d.C.J.); (R.M.F.S.); (I.J.O.d.S.)
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Velasco VV, Ochiai T, Tsudzuki M, Goto N, Ishikawa A. Quantitative trait loci mapping of innate fear behavior in day-old F2 chickens of Japanese Oh-Shamo and White Leghorn breeds using restriction site-associated DNA sequencing. Poult Sci 2024; 103:103228. [PMID: 37989001 PMCID: PMC10667749 DOI: 10.1016/j.psj.2023.103228] [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: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
Understanding the genetic mechanisms that underlie innate fear behavior is essential for improving the management and performance of the poultry industry. This study aimed to map QTL associated with innate fear responses in open field (OF) and tonic immobility (TI) tests, using an F2 chicken intercross population between 2 behaviorally distinct breeds: the aggressive Japanese Oh-Shamo (OSM) and the docile White Leghorn T-line (WL-T). Genome-wide QTL analysis for the OF and TI traits was conducted using 2,109 single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RAD-seq). While several suggestive QTL were identified for TI and OF traits at genome-wide 20% significance threshold levels, the analysis revealed 2 significant QTL for 2 OF traits (total distance and maximum speed) at genome-wide 5% significance threshold levels. These significant QTL were located between 12.34 and 30.49 megabase (Mb) on chromosome 1 and between 40.02 and 63.38 Mb on chromosome 2, explaining 6.75 to 7.40% of the total variances. These findings provide valuable insights for the poultry industry, particularly in refining chicken management strategies and informing targeted breeding efforts.
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Affiliation(s)
| | - Takayuki Ochiai
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Naoki Goto
- Hendrix Genetics BU Layers, Boxmeer 5831 CK, The Netherlands
| | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Ishikawa A, Takanuma T, Hashimoto N, Goto T, Tsudzuki M. New Behavioral Handling Test Reveals Temperament Differences in Native Japanese Chickens. Animals (Basel) 2023; 13:3556. [PMID: 38003175 PMCID: PMC10668715 DOI: 10.3390/ani13223556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
It is well known in the poultry industry that fear and stress experienced during the handling of day-old chicks in commercial hatcheries can have long-lasting effects on their behavior later in life. These hatchery-related stresses are more intense and complex than those encountered in traditional behavioral tests. Consequently, a single behavioral test may not be sufficient to measure hatchery stresses and chicken temperament. In this study, we developed a new behavioral handling test for day-old chickens, which incorporated concepts from established behavioral tests used with both young and adult birds. The new test assessed 10 behavioral traits, including vocalization frequency and responses to human interaction. It was conducted on 96 two-day-old chicks from seven breeds of native Japanese and Western chickens. The results of the principal component analysis classified chicken temperaments into three distinct categories: bustle, aggression, and timidity. Using these categories, the seven breeds were classified into five groups, each with distinct temperaments. This study highlights the reliability and value of the new handling test in characterizing the temperaments of various chicken breeds and provides insights into the complex behaviors of chickens.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoka Takanuma
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Norikazu Hashimoto
- Laboratory of Poultry, Livestock Experiment Station, Wakayama Prefecture, Hidaka-Gun, Wakayama 644-1111, Japan;
| | - Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan;
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8525, Japan;
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Tiemann I, Becker S, Fournier J, Damiran D, Büscher W, Hillemacher S. Differences among domestic chicken breeds in tonic immobility responses as a measure of fearfulness. PeerJ 2023; 11:e14703. [PMID: 37033722 PMCID: PMC10081456 DOI: 10.7717/peerj.14703] [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: 02/15/2021] [Accepted: 12/15/2022] [Indexed: 04/07/2023] Open
Abstract
Background One priority for animal welfare is for animals to experience less fear, especially during human contact. For domestic animals, breeds that are less fearful may provide genetic resources to develop strains with improved welfare due to lower susceptibility to fear. Genetic predispositions inherited in these breeds might reflect the large diversity of chicken breeds. The goal of the present study was to systematically test a diverse group of chicken breeds to search for breeds that experience less fear. Methods Nineteen chicken breeds from commercial hybrid lines, native layer-type, meat-type and dual-purpose breeds, ornamental breeds as well as bantam breeds were tested in a standardized tonic immobility (TI) test. Chickens were manually restrained on their back, and the time to first head movement and first leg movement, the duration of TI, as well as the number of attempts needed to induce TI were measured. Results The TI response differed among chicken breeds (p ≤ 0.001) for naïve, mature hens. The median number of attempts required to induce TI ranged from 1 to 2 and did not differ significantly among breeds. Median durations were much more variable, with Lohmann Brown showing shortest durations (6 s, 12 s, 58 s for time to first head movement, first leg movement and total duration of TI, respectively). In contrast, medians reached the maximum of 600 s for all three measures in German Creepers. Repeated tests on the same individuals did not affect attempts needed to induce TI nor TI durations. Breeds clustered into two main groups, with layer-type native breeds and ornamental breeds having longer TI durations, and bantam, dual-purpose and meat-type native breeds having shorter TI durations. Conclusions Our findings provide evidence for substantial variation of fearfulness among breeds. This variation could be linked to the intended use during the breed's specific history. Knowledge and quantitative measurement of these behavioural responses provide the opportunity to improve welfare through selection and future breeding.
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Affiliation(s)
- Inga Tiemann
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Senta Becker
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Jocelyn Fournier
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Daalkhaijav Damiran
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Wolfgang Büscher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Sonja Hillemacher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
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Ochiai T, Sakaguchi M, Kawakami SI, Ishikawa A. Identification of candidate genes responsible for innate fear behavior in the chicken. G3 (BETHESDA, MD.) 2022; 13:6861905. [PMID: 36454218 PMCID: PMC9911055 DOI: 10.1093/g3journal/jkac316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/05/2022]
Abstract
Identifying the genes responsible for quantitative traits remains a major challenge. We previously found a major QTL on chromosome 4 affecting several innate fear behavioral traits obtained by an open-field test in an F2 population between White Leghorn and Nagoya breeds of chickens (Gallus gallus). Here, an integrated approach of transcriptome, haplotype frequency, and association analyses was used to identify candidate genes for the QTL in phenotypically extreme individuals selected from the same segregating F2 population as that used in the initial QTL analysis. QTL mapping for the first principal component, which summarizes the variances of all affected behavioral traits in the F2 population, revealed the behavioral QTL located at 14-35 Mb on chromosome 4 with 333 genes. After RNA-seq analysis using two pooled RNAs from extreme F2 individuals, real-time qPCR analysis in the two parental breeds and their F1 individuals greatly reduced the number of candidate genes in the QTL interval from 333 to 16 genes. Haplotype frequency analysis in the two extreme F2 groups further reduced the number of candidate genes from 16 to 11. After comparing gene expression in the two extreme groups, a conditional correlation analysis of diplotypes between gene expression and phenotype of extreme individuals revealed that NPY5R and LOC101749214 genes were strong candidate genes for innate fear behavior. This study illustrates how the integrated approach can identify candidate genes more rapidly than fine mapping of the initial QTL interval and provides new information for studying the genetic basis of innate fear behavior in chickens.
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Affiliation(s)
- Takayuki Ochiai
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Marina Sakaguchi
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shin-Ichi Kawakami
- Laboratory of Animal Behavior and Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Akira Ishikawa
- Corresponding author: Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan.
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Tiemann I, Becker S, Büscher W, Meuser V. Exploring animal genetic resources of the domestic chicken and their behavior in the open field. J APPL POULTRY RES 2022. [DOI: 10.1016/j.japr.2022.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Mol Genet Genomics 2021; 296:1147-1159. [PMID: 34251529 DOI: 10.1007/s00438-021-01806-w] [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: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.
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