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Lee J, Kim DH, Lee K. Myostatin gene role in regulating traits of poultry species for potential industrial applications. J Anim Sci Biotechnol 2024; 15:82. [PMID: 38825693 PMCID: PMC11145818 DOI: 10.1186/s40104-024-01040-5] [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: 01/17/2024] [Accepted: 04/22/2024] [Indexed: 06/04/2024] Open
Abstract
The myostatin (MSTN) gene is considered a potential genetic marker to improve economically important traits in livestock, since the discovery of its function using the MSTN knockout mice. The anti-myogenic function of the MSTN gene was further demonstrated in farm animal species with natural or induced mutations. In poultry species, myogenesis in cell culture was regulated by modulation of the MSTN gene. Also, different expression levels of the MSTN gene in poultry models with different muscle mass have been reported, indicating the conserved myogenic function of the MSTN gene between mammalian and avian species. Recent advances of CRISPR/Cas9-mediated genome editing techniques have led to development of genome-edited poultry species targeting the MSTN gene to clearly demonstrate its anti-myogenic function and further investigate other potential functions in poultry species. This review summarizes research conducted to understand the function of the MSTN gene in various poultry models from cells to whole organisms. Furthermore, the genome-edited poultry models targeting the MSTN gene are reviewed to integrate diverse effects of the MSTN gene on different traits of poultry species.
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Affiliation(s)
- Joonbum Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Dong-Hwan Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
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Wang J, Liu J, Lei Q, Liu Z, Han H, Zhang S, Qi C, Liu W, Li D, Li F, Cao D, Zhou Y. Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses. BMC Genomics 2024; 25:296. [PMID: 38509464 PMCID: PMC10956266 DOI: 10.1186/s12864-024-10185-6] [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: 08/10/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. METHODS We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. RESULTS We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. CONCLUSION Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens.
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Affiliation(s)
- Jie Wang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Jie Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Qiuxia Lei
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Zhihe Liu
- Sichuan agricultural university college of animal science and technology, Chengdu, 611130, China
| | - Haixia Han
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, Jinan, 250023, China
| | - Wei Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dapeng Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Fuwei Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Dingguo Cao
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China
| | - Yan Zhou
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250023, China.
- Jinan Key Laboratory of Poultry Germplasm Resources Innovation and Healthy Breeding, Jinan, Shandong, 250023, China.
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Zhang M, Wang S, Xu R, Liu Y, Zhang H, Sun M, Wang J, Liu Z, Wu K. Managing genomic diversity in conservation programs of Chinese domestic chickens. Genet Sel Evol 2023; 55:92. [PMID: 38097971 PMCID: PMC10722821 DOI: 10.1186/s12711-023-00866-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. RESULTS Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (FST), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation. CONCLUSIONS Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.
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Affiliation(s)
- Mengmeng Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd., No. 75 Bingjiaokou Hutong, Beijing, 100088, People's Republic of China
| | - Shiwei Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ran Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yijun Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
- College of Animal Science, Southwest University, Chongqing, 402460, People's Republic of China
| | - Han Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mengxia Sun
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junyan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhexi Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Keliang Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Guo Y, Tian J, Song C, Han W, Zhu C, Li H, Zhang S, Chen K, Li N, Carlborg Ö, Hu X. Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum. Mol Biol Evol 2023; 40:msad273. [PMID: 38069902 PMCID: PMC10735294 DOI: 10.1093/molbev/msad273] [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: 05/10/2023] [Revised: 10/21/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.
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Affiliation(s)
- Ying Guo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing CN-100193, China
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing CN-100193, China
- Yazhouwan National Laboratory, Sanya CN-572024, China
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-751 23, Sweden
| | - Jing Tian
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing CN-100193, China
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing CN-100193, China
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot CN-010031, China
| | - Chi Song
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Wei Han
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Chunhong Zhu
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Huifang Li
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Shuangjie Zhang
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Kuanwei Chen
- National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou CN-225125, Jiangsu, China
| | - Ning Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing CN-100193, China
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing CN-100193, China
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-751 23, Sweden
| | - Xiaoxiang Hu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing CN-100193, China
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing CN-100193, China
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Xu D, Zhu W, Wu Y, Wei S, Shu G, Tian Y, Du X, Tang J, Feng Y, Wu G, Han X, Zhao X. Whole-genome sequencing revealed genetic diversity, structure and patterns of selection in Guizhou indigenous chickens. BMC Genomics 2023; 24:570. [PMID: 37749517 PMCID: PMC10521574 DOI: 10.1186/s12864-023-09621-w] [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: 04/03/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The eight phenotypically distinguishable indigenous chicken breeds in Guizhou province of China are great resources for high-quality development of the poultry industry in China. However, their full value and potential have yet to be understood in depth. To illustrate the genetic diversity, the relationship and population structure, and the genetic variation patterns shaped by selection in Guizhou indigenous chickens, we performed a genome-wide analysis of 240 chickens from 8 phenotypically and geographically representative Guizhou chicken breeds and 60 chickens from 2 commercial chicken breeds (one broiler and one layer), together with 10 red jungle fowls (RJF) genomes available from previous studies. RESULTS The results obtained in this present study showed that Guizhou chicken breed populations harbored higher genetic diversity as compared to commercial chicken breeds, however unequal polymorphisms were present within Guizhou indigenous chicken breeds. The results from the population structure analysis markedly reflected the breeding history and the geographical distribution of Guizhou indigenous chickens, whereas, some breeds with complex genetic structure were ungrouped into one cluster. In addition, we confirmed mutual introgression within Guizhou indigenous chicken breeds and from commercial chicken breeds. Furthermore, selective sweep analysis revealed candidate genes which were associated with specific and common phenotypic characteristics evolved rapidly after domestication of Guizhou local chicken breeds and economic traits such as egg production performance, growth performance, and body size. CONCLUSION Taken together, the results obtained from the comprehensive analysis of the genetic diversity, genetic relationships and population structures in this study showed that Guizhou indigenous chicken breeds harbor great potential for commercial utilization, however effective conservation measures are currently needed. Additionally, the present study drew a genome-wide selection signature draft for eight Guizhou indigenous chicken breeds and two commercial breeds, as well as established a resource that can be exploited in chicken breeding programs to manipulate the genes associated with desired phenotypes. Therefore, this study will provide an essential genetic basis for further research, conservation, and breeding of Guizhou indigenous chickens.
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Affiliation(s)
- Dan Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Wei Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Youhao Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Shuo Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Gang Shu
- Department of Basic Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yaofu Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Xiaohui Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China
| | - Jigao Tang
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Yulong Feng
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Gemin Wu
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China
| | - Xue Han
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, China.
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, P. R. China.
- Key Laboratory of Livestock and Poultry Multi-Omics, MinistryofAgricultureandRuralAffairs, College of Animal Science and Technology(Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Ya'an, P. R. China.
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The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review. Poult Sci 2023; 102:102657. [PMID: 37054499 PMCID: PMC10123265 DOI: 10.1016/j.psj.2023.102657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (FST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.
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Noorai RE, Shankar V, Freese NH, Gregorski CM, Chapman SC. Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PLoS One 2019; 14:e0225834. [PMID: 31821332 PMCID: PMC6903725 DOI: 10.1371/journal.pone.0225834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Gallus gallus (chicken) is phenotypically diverse, with over 60 recognized breeds, among the myriad species within the Aves lineage. Domestic chickens have been under artificial selection by humans for thousands of years for agricultural purposes. The North American Araucana (NAA) breed arose as a cross between the Chilean “Collonocas” that laid blue eggs and was rumpless and the “Quetros” that had unusual tufts but with tail. NAAs were introduced from South America in the 1940s and have been kept as show birds by enthusiasts since then due to several distinctive traits: laying eggs with blue eggshells, characteristic ear-tufts, a pea comb, and rumplessness. The population has maintained variants for clean-faced and tufted, as well as tailed and rumplessness traits making it advantageous for genetic studies. Genome resequencing of six NAA chickens with a mixture of these traits was done to 71-fold coverage using Illumina HiSeq 2000 paired-end reads. Trimmed and concordant reads were mapped to the Gallus_gallus-5.0 reference genome (galGal5), generated from a female Red Junglefowl (UCD001). To identify candidate genes that are associated with traits of the NAA, their genome was compared with the Korean Araucana, Korean Domestic and White Leghorn breeds. Genomic regions with significantly reduced levels of heterogeneity were detected on five different chromosomes in NAA. The sequence data generated confirm the identity of variants responsible for the blue eggshells, pea comb, and rumplessness traits of NAA and propose one for ear-tufts.
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Affiliation(s)
- Rooksana E. Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, United States of America
- * E-mail:
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Nowlan H. Freese
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Christopher M. Gregorski
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Susan C. Chapman
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
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Wilson PB. Recent advances in avian egg science: A review. Poult Sci 2018; 96:3747-3754. [PMID: 28938769 PMCID: PMC5850298 DOI: 10.3382/ps/pex187] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/13/2017] [Indexed: 12/21/2022] Open
Abstract
Eggs and egg products form an integral part of the food chain. As such, research into egg structure, function, and production has made an important contribution to the field of poultry science. The past decade has seen significant advances in avian egg science research, with work supplementing our understanding of the nature of the avian egg, and its biological, chemical, and physical properties. Eggshell color, strength, and chemical composition, poultry nutrition, and genetics have all been intensively studied recently, with significant progress being made in a number of these areas. Indeed, with the prevalence of robust theoretical techniques, it is now commonplace to combine experimental investigations with theory, providing a balanced and interdisciplinary perspective.
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Affiliation(s)
- Philippe B Wilson
- Faculty of Health & Life Sciences, De Montfort University, The Gateway, Leicester, LE1 9BH, United Kingdom
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Genetic and phenotypic characterization of the novel mouse substrain C57BL/6N Korl with increased body weight. Sci Rep 2017; 7:14217. [PMID: 29079844 PMCID: PMC5660189 DOI: 10.1038/s41598-017-14196-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/03/2017] [Indexed: 01/10/2023] Open
Abstract
In inbred mouse lines, there is generally little genetic difference between individuals. This small genetic variability facilitates carrying out research on minute changes of various traits and the gene pool. Also, characterizing the diversity and detecting selective genetic and phenotypic signatures are crucial to understanding the genomic basis of a population and to identify specific patterns of evolutionary change. In this study, we investigated the underlying genetic profiles of a newly developed mouse strain, C57BL/6NKorl (Korl), established through sibling mating over 30 generations. To analyse the distinctive genomic features of Korl mice, we used whole-genome sequencing from six samples, which were compared to those of other C57BL/6N-based mouse strains. Korl strain-specific polymorphisms were identified and signatures of a selective sweep were detected. In particular, the candidate genes related to the increased body weight of the Korl strain were identified. Establishment of the genetic profile of Korl mice can provide insight into the inbreeding-induced changes to the gene pool, and help to establish this strain as a useful model for practical and targeted research purposes.
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Sujiwo J, Kim D, Yoon JY, Kim H, Kim JS, Lee SK, Jang A. Physicochemical and Functional Characterization of Blue-Shelled Eggs in Korea. Korean J Food Sci Anim Resour 2017; 37:181-190. [PMID: 28515642 PMCID: PMC5434205 DOI: 10.5851/kosfa.2017.37.2.181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to compare the quality and physicochemical characteristics of blue-shelled eggs (BE) and conventional eggs (CE). Proximate composition, quality, pH value, shell color, collagen content, fatty acid composition, total cholesterol, α-glucosidase inhibition activity, and antioxidation activity were determined. The proximate composition, general qualities, and pH values of CE and BE showed no significant differences, except in moisture composition, weight, and shell thickness. Moisture content and weight of BE were significantly lower than those of CE. However, shell thickness and weight of BE were higher than those of CE (p<0.05). Lightness of BE was significantly higher than that of CE (85.20 vs. 58.80), while redness (a*) and yellowness (b*) of BE were lower than those of CE (a*: −4.75 vs. 14.20; b*: 10.45 vs. 30.63). The fatty acid [C18:1n7 (cis-vaccenic acid) and C18:3n6 (gamma-linolenic acid)] contents of BE were significantly higher than those of CE. The total cholesterol contents of BE and CE were similar. DPPH radical scavenging activity of BE was significantly higher than that of CE (40.78 vs. 35.35). Interestingly, α-glucosidase inhibition activity of whole egg and egg yolk in BE (19.27 and 36.06) was significantly higher than that of whole egg and egg yolk in CE (13.95 and 32.46). This result indicated that BE could potentially be used as a functional food material. Further studies are required to evaluate the specific compounds that affect functional activity.
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Affiliation(s)
- Joko Sujiwo
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Dongwook Kim
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Ji-Yeol Yoon
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Hanna Kim
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jung-Soo Kim
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Sung-Ki Lee
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
| | - Aera Jang
- Department of Animal Products and Food Science, Kangwon National University, Chuncheon 24341, Korea
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