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Zhang Y, Li X, Guo Q, Wang Z, Jiang Y, Yuan X, Chen G, Chang G, Bai H. Genome-wide association study reveals 2 copy number variations associated with the variation of plumage color in the white duck hybrid population. Poult Sci 2024; 103:104107. [PMID: 39094499 DOI: 10.1016/j.psj.2024.104107] [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: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Plumage color is an intuitive external poultry characteristic with rich manifestations and complex genetic mechanisms. In our previous study, we observed that there were more dark variations in plumage color in the F2 population derived from the hybridization of 2 white duck varieties. Therefore, based on the statistics of plumage color of 308 F2 populations, we further used the resequencing data of these individuals to detect copy number variations (CNVs) in the whole genome and conducted genome-wide association studies (GWAS) to determine the genetic basis related to plumage color traits. The CNV detection revealed 9,337 CNVs, with an average length of 15,950 bp and a total length of 142.02 MB, accounting for approximately 12.91% of the reference genome. The CNV distribution on the chromosomes was relatively uniform, and the number of CNVs on each chromosome positively correlated with the length of the chromosome. In the pure black plumage group, 2,101 CNVs were only identified, and 1,714 were specifically identified in the pure white plumage group. Ten CNVs were randomly selected for validation using quantitative real-time PCR, and 9 CNVs had the same CNV types as predicted, with an accuracy of 90%. Based on GWAS, we identified 2 CNVs potentially associated with plumage color variations, with the associated CNV regions covering 9 genes. Enrichment analysis of these 9 candidate genes showed significant enrichment of 3 pathways (ribosome biogenesis in eukaryotes, RNA transport, and protein export) and 17 gene ontology terms. Among these, VWA5A can downregulate MITF by binding to the regulatory factors SOX10. The occurrence of CNV may indirectly contribute to duck plumage color variation by affecting the regulatory factors of the switch gene MITF in the melanogenesis pathway. These findings have improved the understanding of the genetic basis of duck plumage color variation and have been beneficial for developing and using plumage color traits in subsequent poultry breeding.
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Affiliation(s)
- Yi Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaofan Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
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Wang Z, Guo Z, Mou Q, Liu H, Liu D, Tang H, Hou S, Schroyen M, Zhou Z. Unique feather color characteristics and transcriptome analysis of hair follicles in Liancheng White ducks. Poult Sci 2024; 103:103794. [PMID: 38718539 PMCID: PMC11097064 DOI: 10.1016/j.psj.2024.103794] [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: 03/03/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/19/2024] Open
Abstract
Avian feather color is a fascinating trait, and the genetic mechanism of duck plumage formation is still in the preliminary stage. In this study, feather color of Liancheng White ducks was analyzed by determination of melanin content and RNA-seq analysis. In this research, 9 ducks from Mallards (n = 3), Liancheng White (n = 3) and Pekin ducks (n = 3) were used by high performance liquid chromatography (HPLC) and Masson-Fontana staining to reveal the difference of feather melanin content. RNA-seq from 11 hair follicle tissues (1- and 8-wk-old) of Liancheng White ducks (n = 5) and Pekin ducks (n = 7) was used to analyze the candidate genes for the feather melanin synthesis, and Immunofluorescence experiment was used to show the protein expression in 6 black- and white-feathered ducks. Pectorale, skin, liver, fat, brain, heart, kidney, lung, spleen of an 8-wk-old black-feathered Mallard were collected for candidate gene expression. The results showed that the contents of feathers, beak, web melanin in Liancheng White ducks were higher than in Pekin ducks (p < 0.05). Melanin within hair follicles was located in the barb ridge and hair matrix of black feather duck, also we found that TYRP1, TYR, SOX10 genes were differentially expressed between Liancheng White and Pekin ducks (p < 0.05), and these genes were mainly expressed showed in duck skin tissues. This study revealed the unique feather color phenotype of Liancheng White duck shedding light on the transcriptome that underlies it.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium
| | - Zhanbao Guo
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qiming Mou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hongfei Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Dapeng Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hehe Tang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium
| | - Zhengkui Zhou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
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Sun GB, Lu YF, Duan XJ. Investigation into the association of FNDC1 and ADAMTS12 gene expression with plumage coloration in Muscovy ducks. Open Life Sci 2024; 19:20220877. [PMID: 38867923 PMCID: PMC11167702 DOI: 10.1515/biol-2022-0877] [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: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024] Open
Abstract
To elucidate the molecular genetic mechanisms underpinning feather color in Muscovy ducks. A cohort of 100 Muscovy ducks was meticulously selected for this research. Follicular tissues from ducks exhibiting black and white plumage served as the experimental samples. From these tissues, RNA and proteins were extracted for further analysis. The RNA underwent reverse transcription polymerase chain reaction amplification, followed by validation through western blot assays. The data revealed a significant upregulation in the expression of FN domain-containing protein 1 (FNDC1) and ADAMTS12 genes in Muscovy ducks with white plumage traits as opposed to those with black plumage traits. Specifically, individuals with pure white plumage demonstrated a markedly elevated expression of the FNDC1 gene in comparison to their pure black counterparts. Conversely, expression levels of the ADAMTS12 gene were found to be reduced in ducks with pure black plumage relative to those with pure white plumage. Notably, the expression patterns of FNDC1 and ADAMTS12 genes exhibited inconsistencies between mRNA and protein levels. This study offers significant insights into the molecular genetic mechanisms underlying feather color variation in Muscovy ducks. FNDC1 and ADAMTS12 could be considered potential targets for genetic manipulation or selective breeding strategies aimed at achieving specific feather color phenotypes in Muscovy ducks.
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Affiliation(s)
- Guo-Bo Sun
- Animal Science and Technology College, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, 225300, Jiangsu, China
| | - Yan-Feng Lu
- Animal Science and Technology College, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, 225300, Jiangsu, China
| | - Xiu-Jun Duan
- Animal Science and Technology College, Jiangsu Agri-animal Husbandry Vocational College, No. 8 of Fenghuang East Road, Hailing District, Taizhou, 225300, Jiangsu, China
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Zhang X, Yang L, Xie Z, Gan J, Zhu P, Song J, Kang H, Zhang Z, Liu L, Xiang H, Li H. Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity. BMC Genomics 2024; 25:577. [PMID: 38858651 PMCID: PMC11163754 DOI: 10.1186/s12864-024-10492-y] [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: 10/17/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.
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Affiliation(s)
- Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Liu Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Key Laboratory of National Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant, China Conservation and Research Centre for the Giant Panda, Panda National Park, Chengdu, 611830, China
| | - Zhuojun Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiankang Gan
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiani Song
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Zhengfen Zhang
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China.
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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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Liu Y, Li G, Guo Z, Zhang H, Wei B, He D. Transcriptome analysis of sexual dimorphism in dorsal down coloration in goslings. BMC Genomics 2024; 25:505. [PMID: 38778258 PMCID: PMC11110362 DOI: 10.1186/s12864-024-10394-z] [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: 11/10/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND In day-old Hungarian white goose goslings, there is a noticeable difference in dorsal down coloration between males and females, with females having darker dorsal plumage and males having lighter plumage. The ability to autosex day-old goslings based on their dorsal down coloration is important for managing them efficiently and planning their nutrition in the poultry industry. The aim of this study was to determine the biological and genetic factors underlying this difference in dorsal down colorationthrough histological analysis, biochemical assays, transcriptomic profiling, and q‒PCR analysis. RESULTS Tissue analysis and biochemical assays revealed that compared with males, 17-day-old embryos and day-old goslings of female geese exhibited a greater density of melanin-containing feather follicles and a greater melanin concentration in these follicles during development. Both female and male goslings had lower melanin concentrations in their dorsal skin compared to 17-day-old embryos. Transcriptome analysis identified a set of differentially expressed genes (DEGs) (MC1R, TYR, TYRP1, DCT and MITF) associated with melanogenesis pathways that were downregulated or silenced specifically in the dorsal skin of day-old goslings compared to 17-day-old embryos, affecting melanin synthesis in feather follicles. Additionally, two key genes (MC1R and MITF) associated with feather coloration showed differences between males and females, with females having higher expression levels correlated with increased melanin synthesis and darker plumage. CONCLUSION The expression of multiple melanogenesis genes determines melanin synthesis in goose feather follicles. The dorsal down coloration of day-old Hungarian white goose goslings shows sexual dimorphism, likely due to differences in the expression of the MC1R and MITF genes between males and females. These results could help us better understand why male and female goslings exhibit different plumage patterns.
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Affiliation(s)
- Yi Liu
- Shanghai Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Shanghai, China
| | - Guangquan Li
- Shanghai Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Shanghai, China
| | - Zhanbao Guo
- Chinese Academy of Agricultural Sciences, Institute of Animal Sciences, Beijing, China
| | - Huiling Zhang
- Shandong Rongda Agricultural Development Co., Ltd, Shandong, China
| | - Baozhi Wei
- Shandong Rongda Agricultural Development Co., Ltd, Shandong, China
| | - Daqian He
- Shanghai Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Shanghai, China.
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Guo P, Chen J, Luo L, Zhang X, Li X, Huang Y, Wu Z, Tian Y. Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese. Animals (Basel) 2024; 14:1508. [PMID: 38791725 PMCID: PMC11117251 DOI: 10.3390/ani14101508] [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: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.
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Affiliation(s)
- Pengyun Guo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Junpeng Chen
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou 515800, China;
| | - Lei Luo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xumeng Zhang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xiujin Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunmao Huang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Zhongping Wu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunbo Tian
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
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8
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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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Zhang R, Mu C, Chang L, Shen X, Bu Z, Yang M, Fu S, Tang Q, Liu P, Yang X. Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon. Animals (Basel) 2024; 14:1047. [PMID: 38612286 PMCID: PMC11011069 DOI: 10.3390/ani14071047] [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: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.
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Affiliation(s)
- Rui Zhang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Chunyu Mu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Lingling Chang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Xinyue Shen
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Zhu Bu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Mingjun Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Shengyong Fu
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Qingping Tang
- Institute of Poultry Science, Chinese Academy of Agricultural Sciences Poultry Institute, Yangzhou 225100, China; (R.Z.); (C.M.); (L.C.); (X.S.); (Z.B.); (S.F.)
| | - Peiyao Liu
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
| | - Xiaoming Yang
- Henan Tiancheng Pigeon Industry Co., Ltd., Pingdingshan 462513, China; (M.Y.); (P.L.); (X.Y.)
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10
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Twumasi G, Wang H, Xi Y, Qi J, Li L, Bai L, Liu H. Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks. Animals (Basel) 2023; 14:85. [PMID: 38200816 PMCID: PMC10778472 DOI: 10.3390/ani14010085] [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: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
In modern advanced genetics and breeding programs, the study of genes related to pigmentation in ducks is gaining much attention and popularity. Genes and DNA mutation cause variations in the plumage color traits of ducks. Therefore, discovering related genes responsible for different color traits and pigment patterns on each side of the single feathers in Chinese ducks is important for genetic studies. In this study, we collected feather images from 340 ducks and transported them into Image Pro Plus (IPP) 6.0 software to quantify the melanin content in the feathers. Thereafter, a genome-wide association study was conducted to reveal the genes responsible for variations in the feather color trait. The results from this study revealed that the pigmented region was larger in the male ducks as compared to the female ducks. In addition, the pigmented region was larger on the right side of the feather vane than on the left side in both dorsal and ventral feathers, and a positive correlation was observed among the feather color traits. Further, among the annotated genes, WNT3A, DOCK1, RAB1A, and ALDH1A3 were identified to play important roles in the variation in pigmented regions of the various feathers. This study also revealed that five candidate genes, including DPP8, HACD3, INTS14, SLC24A1, and DENND4A, were associated with the color pigment on the dorsal feathers of the ducks. Genes such as PRKG1, SETD6, RALYL, and ZNF704 reportedly play important roles in ventral feather color traits. This study revealed that genes such as WNT3A, DOCK1, RAB1A, and ALDH1A3 were associated with different pigmentation patterns, thereby providing new insights into the genetic mechanisms of single-feather pigmentation patterns in ducks.
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Affiliation(s)
- Grace Twumasi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Huazhen Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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11
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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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12
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Wang H, Yang C, Wang J, Xi Y, Qi J, Hu J, Bai L, Li L, Mustafa A, Liu H. Genome-wide association analysis of neck ring traits in NongHua ma male ducks. Br Poult Sci 2023; 64:670-677. [PMID: 37610317 DOI: 10.1080/00071668.2023.2249840] [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: 02/27/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
1. Male NongHua ma ducks have more colourful feathers than females, especially considering that the former have a distinctive neck ring that is different from that of females. This ring development might be influenced by sex selection, the environment, genetics and other elements.2. Genome-wide association analysis (GWAS) was used to locate candidate genes that affect the neck ring formation of male ducks to investigate the genetic basis of this phenomenon.3. In this study, the neck ring area and width of 180 male ducks were assessed at ages 80, 90, 100, 110 and 120 d. GWAS was used to identify associated genes. There were 0, 7, 14, 48 and 21 possible candidate genes annotated around the 0, 12, 25, 76 and 40 SNP loci n corresponding regions. A total of 13 candidate genes were identified around 21 SNP sites at the neck ring width of 120 d.4. These significant genes were annotated and GO and KEGG enrichment analyses were performed. All SNPs that exceeded the significance threshold were annotated and preliminarily screened as candidate genes affecting neck ring formation. From analysis of gene function and enriched KEGG pathways, genes such as THSD1, SLC6A4, DGAT2, PRKDC, B3GAT2, ROR1, GRK7, EXTL3, TXNDC12, COL4A2, PRKG1, ACTR3, were considered important candidate marker sites related to the neck ring. This provided a reference starting point for the genetic mechanism underlying duck feather colour.
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Affiliation(s)
- H Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - C Yang
- Sichuan Animal Science Academy, Sichuan Key Laboratory of Animal Genetics and Breeding, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Y Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Qi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - L Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - L Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - A Mustafa
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | - H Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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13
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Zhang X, Zhu T, Wang L, Lv X, Yang W, Qu C, Li H, Wang H, Ning Z, Qu L. Genome-Wide Association Study Reveals the Genetic Basis of Duck Plumage Colors. Genes (Basel) 2023; 14:genes14040856. [PMID: 37107611 PMCID: PMC10137861 DOI: 10.3390/genes14040856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Plumage color is an artificially and naturally selected trait in domestic ducks. Black, white, and spotty are the main feather colors in domestic ducks. Previous studies have shown that black plumage color is caused by MC1R, and white plumage color is caused by MITF. We performed a genome-wide association study (GWAS) to identify candidate genes associated with white, black, and spotty plumage in ducks. Two non-synonymous SNPs in MC1R (c.52G>A and c.376G>A) were significantly related to duck black plumage, and three SNPs in MITF (chr13:15411658A>G, chr13:15412570T>C and chr13:15412592C>G) were associated with white plumage. Additionally, we also identified the epistatic interactions between causing loci. Some ducks with white plumage carry the c.52G>A and c.376G>A in MC1R, which also compensated for black and spotty plumage color phenotypes, suggesting that MC1R and MITF have an epistatic effect. The MITF locus was supposed to be an upstream gene to MC1R underlying the white, black, and spotty colors. Although the specific mechanism remains to be further clarified, these findings support the importance of epistasis in plumage color variation in ducks.
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Affiliation(s)
- Xinye Zhang
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Tao Zhu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-Aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang 236037, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumchi 830052, China
| | - Huie Wang
- College of Animal Science, Tarim University, Alar 843300, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
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14
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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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15
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Li X, Gao R, Chen G, Price AL, Øksnebjerg DB, Hosner PA, Zhou Y, Zhang G, Feng S. Draft genome assemblies of four manakins. Sci Data 2022; 9:564. [PMID: 36100590 PMCID: PMC9470731 DOI: 10.1038/s41597-022-01680-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Manakins are a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family has served as a good model for the study of sexual selection. Here we present genome assemblies of four manakin species, including Cryptopipo holochlora, Dixiphia pipra (also known as Pseudopipra pipra), Machaeropterus deliciosus and Masius chrysopterus, generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 29 Mb and contig N50 of 169 Kb. On average, 12,055 protein-coding genes were annotated in the genomes, and 9.79% of the genomes were annotated as repetitive elements. We further identified 75 Mb of Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One notable finding from these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could have occurred in M. chrysopterus. These de novo genomes will contribute to a deeper understanding of evolutionary history and sexual selection in manakins. Measurement(s) | whole genome sequencing | Technology Type(s) | BGISEQ-500 Sequencing | Sample Characteristic - Organism | Pipridae |
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Affiliation(s)
- Xuemei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Rongsheng Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangji Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Alivia Lee Price
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Daniel Bilyeli Øksnebjerg
- GLOBE Institute, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Øster Farimagsgade 5, 1014, Copenhagen, Denmark
| | - Peter Andrew Hosner
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.,Villum Center for Global Mountain Biodiversity, Biodiversity Section, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China
| | - Shaohong Feng
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China. .,Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China.
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