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Lin R, Li H, Lin W, Yang F, Bao X, Pan C, Lai L, Lin W. Whole-genome selection signature differences between Chaohu and Ji'an red ducks. BMC Genomics 2024; 25:522. [PMID: 38802792 PMCID: PMC11131323 DOI: 10.1186/s12864-024-10339-6] [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: 09/20/2023] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Huihuang Li
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weilong Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Fan Yang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xinguo Bao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Chengfu Pan
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Lianjie Lai
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Weimin Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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Sun GB, Lu YF, Duan XJ. Exploration of the genetic influence of MYOT and MB genes on the plumage coloration of Muscovy ducks. Open Life Sci 2024; 19:20220836. [PMID: 38585635 PMCID: PMC10998670 DOI: 10.1515/biol-2022-0836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 04/09/2024] Open
Abstract
Plumage color, a pivotal attribute delineating diverse Muscovy duck strains, assumes considerable significance within the field of Muscovy duck breeding research. This study extends the existing research by delving into the hereditary aspects of genes associated with plumage coloration in Muscovy ducks. The principal objective is to discern marker genes conducive to targeted breeding strategies based on plumage color, thereby furnishing indispensable technical foundations for the development of novel Muscovy duck varieties. Our investigation focused on scrutinizing the impact of MYOT and MB genes on the genetic expression of plumage color at both the RNA and protein levels in Muscovy ducks. The results elucidate that black Muscovy ducks manifest markedly elevated mRNA and protein expression levels of MYOT and MB genes in comparison to their white counterparts, indicating that both genes may play a constructive regulatory role in the context of plumage coloration in Muscovy ducks. The outcomes of this study delineate a discernible correlation between MYOT and MB genes and the plumage coloration in Muscovy ducks. Employing gene expression analysis, we successfully identified candidate genes that may be intricately linked to the determination of plumage color in these ducks.
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Affiliation(s)
- Guo-Bo Sun
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, No. 8 of Fenghuang East Road, Hailing District, Taizhou City, Jiangsu Province, 225300, China
| | - Yan-Feng Lu
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, No. 8 of Fenghuang East Road, Hailing District, Taizhou City, Jiangsu Province, 225300, China
| | - Xiu-Jun Duan
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, No. 8 of Fenghuang East Road, Hailing District, Taizhou City, Jiangsu Province, 225300, China
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Sun Y, Wu Q, Lin R, Chen H, Zhang M, Jiang B, Wang Y, Xue P, Gan Q, Shen Y, Chen F, Liu J, Zhou C, Lan S, Pan H, Deng F, Yue W, Lu L, Jiang X, Li Y. Genome-wide association study for the primary feather color trait in a native Chinese duck. Front Genet 2023; 14:1065033. [PMID: 36936414 PMCID: PMC10020179 DOI: 10.3389/fgene.2023.1065033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Background: To reveal candidate genes and the molecular genetic mechanism underlying primary feather color trait in ducks, a genome-wide association study (GWAS) for the primary feather color trait was performed based on the genotyping-by-sequencing (GBS) technology for a native Chinese female duck, Longyan Shan-ma ducks. Methods: Blood genomic DNA from 314 female Longyan Shan-ma duck were genotyped using GBS technology. A GWAS for the primary feather color trait with genome variations was performed using an univariate linear mixed model based on all SNPs in autosomes. Results: Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted p-value <8.03 × 10-7) within the introns of the genes STARD9, ZNF106, SLC7A5, and BANP genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted p-value <1.61 × 10-5) of 17 genes (besides ZNF106 and SLC7A5) were also identified. Seven SNPs were located at one 0.22 Mb region (38.65-38.87 Mb) on chromosome 5, and six SNPs were located at one 0.31 Mb region (19.53-19.84 Mb) on chromosome 11. The functions of STARD9, SLC7A5, BANP, LOC101798015, and IPMK were involved pigmentation and follicle development, especially, STARD9 upregulated expression in black feather (haplotype-CCCC) bulb tissue compared with in pockmarked feather (haplotype-TGTT) bulb tissue, implicating these genes as candidate genes for primary feather color trait. Conclusion: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.
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Affiliation(s)
- Yanfa Sun
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Qiong Wu
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Min Zhang
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
| | - Bingbing Jiang
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaru Wang
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Pengfei Xue
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Qiuyun Gan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Yue Shen
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Feifan Chen
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Jiantao Liu
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Chenxin Zhou
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Shishi Lan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Haozhe Pan
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Fan Deng
- College of Life Sciences, Longyan University, Longyan, Fujian, China
| | - Wen Yue
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, Fujian, China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian, China
- *Correspondence: Xiaobing Jiang, ; Yan Li,
| | - Yan Li
- College of Life Sciences, Longyan University, Longyan, Fujian, China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, China
- Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan, Fujian, China
- *Correspondence: Xiaobing Jiang, ; Yan Li,
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Lin R, Li J, Yang Y, Yang Y, Chen J, Zhao F, Xiao T. Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province. Animals (Basel) 2022; 12:ani12172302. [PMID: 36078022 PMCID: PMC9454422 DOI: 10.3390/ani12172302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary The aim of this study was to conduct a genome-wide comparative analysis of four indigenous Chinese duck breeds (Jinding, Liancheng white, Putian black, and Shanma ducks) from Fujian Province, to understand their genetic diversity and population structure. Population parameters showed that the four indigenous breeds were separated groups. Five genomic regions are presented as hotspots of autozygosity among these indigenous duck breeds, with candidate genes involved in muscle growth, pigmentation, and neuroregulation. Genomic information may play a vital role in the improvement of conservation strategies. Abstract The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.
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Shen Q, Zhou J, Li J, Zhao X, Zheng L, Bao H, Wu C. Genome-Wide Association Study Identifies Candidate Genes for Stripe Pattern Feather Color of Rhode Island Red Chicks. Genes (Basel) 2022; 13:genes13091511. [PMID: 36140679 PMCID: PMC9498448 DOI: 10.3390/genes13091511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
Feather colors of chickens are not only characteristics of breeds but also as phenotypic markers in chicken breeding. Pure-bred Rhode Island Red (RIR) chicks have a stripe pattern and a non-stripe pattern on the back. The stripe pattern of RIR is generally shown as four longitudinal black stripes on the back and is more likely to appear in females. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes controlling the stripe pattern of RIR chicks, and then, based on physical location and biological functions, quantitative RT-PCR analysis was used to validate the differential expression of candidate genes between stripe pattern and non-stripe pattern back skin tissue. The GWAS showed that a major signal contains 768 significant single nucleotide polymorphisms (SNPs) and 87 significant small insertions-deletions (INDELs) spanning 41.78 to 43.05 Mb (~1.27 Mb) on GGA1, corresponding to 16 genes associated with stripe pattern phenotype. Among these 16 genes, KITLG and TMTC3 could be considered candidate genes as they showed different expressions between back skin tissues of stripe pattern and non-stripe pattern chicks in value (p = 0.062) and the significant level (p < 0.05), respectively. This study provided novel insight into the mechanisms underlying feather pigmentation and stripe formation in RIR chicks.
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Affiliation(s)
- Qingmiao Shen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jieke Zhou
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Zhao
- Dawu Breeding Company, Baoding 072550, China
| | - Lijie Zheng
- Dawu Breeding Company, Baoding 072550, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Correspondence:
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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