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Huang R, Zhu C, Zhen Y. Genetic diversity, demographic history, and selective signatures of Silkie chicken. BMC Genomics 2024; 25:754. [PMID: 39095706 PMCID: PMC11295612 DOI: 10.1186/s12864-024-10671-x] [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: 02/09/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl. RESULTS In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie. CONCLUSIONS Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.
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Affiliation(s)
- Ruoshi Huang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences and Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Chengqi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences and Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Ying Zhen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences and Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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Chan YF, Lu CW, Kuo HC, Hung CM. A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3 (BETHESDA, MD.) 2024; 14:jkae077. [PMID: 38607414 DOI: 10.1093/g3journal/jkae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/04/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.
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Affiliation(s)
- Yuan-Fu Chan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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Recuerda M, Campagna L. How structural variants shape avian phenotypes: Lessons from model systems. Mol Ecol 2024; 33:e17364. [PMID: 38651830 DOI: 10.1111/mec.17364] [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: 11/06/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.
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Affiliation(s)
- María Recuerda
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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4
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Nyirimana P, Kondoh D, Tomiyasu J, Watanabe M, Okada Y, Nishida Y, Goto T. Morphological variation of tail bone among two chicken breeds and their F 1 progeny. J Morphol 2024; 285:e21704. [PMID: 38702980 DOI: 10.1002/jmor.21704] [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: 02/16/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Fancy breeds of Japanese indigenous chicken display extensive morphological diversity, particularly in tail feathers. Although marked differences in tail and bone traits have been reported between Tosa-jidori (wild type) and Minohikichabo (rich type) breeds, little is known about the pattern of genetic inheritance in cross experiments. Therefore, this study aimed to investigate the strain and sex effects, and inheritance patterns, in the morphometric variation of pygostyle bones among Tosa-jidori, Minohikichabo, and their F1 hybrids. Five morphological traits, angle of the apex of the pygostyle, pygostyle length, margo cranialis length, tail feather number, and body weight, were evaluated at the adult stage. A significant strain difference was detected in all traits, whereas significant sex differences were observed in only three traits, but not in the angle of the apex of the pygostyle and tail feather number. In F1 hybrids, the angle of the apex of the pygostyle was significantly different to that of Tosa-jidori but not that of Minohikichabo, whereas the pygostyle length and tail number of F1 hybrids were significantly different from those of Minohikichabo but not those of Tosa-jidori. A significant heterosis effect was found in the margo cranialis length and body weight. All five traits showed nonadditive inheritance patterns but varied in each trait between partial dominance (angle of the apex of pygostyle), full dominance (pygostyle length and tail feather number), and over-dominance (margo cranialis length and body weight). Interestingly, different patterns of genetic inheritance in the F1 hybrid were observed at different locations, even within the same pygostyle bone. Using the Japanese indigenous chicken model, these results provide a substantial step toward understanding the genetic architecture of morphology in chickens.
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Affiliation(s)
- Prudence Nyirimana
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Daisuke Kondoh
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Jumpei Tomiyasu
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Momoka Watanabe
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yume Okada
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yuma Nishida
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Tatsuhiko Goto
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
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Wu S, Dou T, Wang K, Yuan S, Yan S, Xu Z, Liu Y, Jian Z, Zhao J, Zhao R, Wu H, Gu D, Liu L, Li Q, Wu DD, Ge C, Su Z, Jia J. Artificial selection footprints in indigenous and commercial chicken genomes. BMC Genomics 2024; 25:428. [PMID: 38689225 PMCID: PMC11061962 DOI: 10.1186/s12864-024-10291-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. RESULTS We found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds. CONCLUSION We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.
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Affiliation(s)
- Siwen Wu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sisi Yuan
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Rouhan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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6
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Mañes-García J, Marco-Ferreres R, Beccari L. Shaping gene expression and its evolution by chromatin architecture and enhancer activity. Curr Top Dev Biol 2024; 159:406-437. [PMID: 38729683 DOI: 10.1016/bs.ctdb.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Transcriptional regulation plays a pivotal role in orchestrating the intricate genetic programs governing embryonic development. The expression of developmental genes relies on the combined activity of several cis-regulatory elements (CREs), such as enhancers and silencers, which can be located at long linear distances from the genes that they regulate and that interact with them through establishment of chromatin loops. Mutations affecting their activity or interaction with their target genes can lead to developmental disorders and are thought to have importantly contributed to the evolution of the animal body plan. The income of next-generation-sequencing approaches has allowed identifying over a million of sequences with putative regulatory potential in the human genome. Characterizing their function and establishing gene-CREs maps is essential to decode the logic governing developmental gene expression and is one of the major challenges of the post-genomic era. Chromatin 3D organization plays an essential role in determining how CREs specifically contact their target genes while avoiding deleterious off-target interactions. Our understanding of these aspects has greatly advanced with the income of chromatin conformation capture techniques and fluorescence microscopy approaches to visualize the organization of DNA elements in the nucleus. Here we will summarize relevant aspects of how the interplay between CRE activity and chromatin 3D organization regulates developmental gene expression and how it relates to pathological conditions and the evolution of animal body plan.
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Affiliation(s)
| | | | - Leonardo Beccari
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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7
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Wang K, Hua G, Li J, Yang Y, Zhang C, Yang L, Hu X, Scheben A, Wu Y, Gong P, Zhang S, Fan Y, Zeng T, Lu L, Gong Y, Jiang R, Sun G, Tian Y, Kang X, Hu H, Li W. Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. IMETA 2024; 3:e154. [PMID: 38868520 PMCID: PMC10989122 DOI: 10.1002/imt2.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/07/2023] [Indexed: 06/14/2024]
Abstract
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
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Affiliation(s)
- Kejun Wang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yu Yang
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Chenxi Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Lan Yang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiaoyu Hu
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Armin Scheben
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Yanan Wu
- Department of preventive veterinary medicine, College of Veterinary MedicineHenan Agricultural UniversityZhengzhouChina
- International Joint Research Center for National Animal ImmunologyZhengzhouHenanChina
| | - Ping Gong
- Wuhan Academy of Agricultural ScienceWuhanChina
| | - Shuangjie Zhang
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Yanfeng Fan
- Quality Safety and Processing LaboratoryJiangsu Institute of Poultry SciencesYangzhouChina
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Animal Husbandry and Veterinary ScienceZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Intelligent Husbandry Department, College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ruirui Jiang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guirong Sun
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Yadong Tian
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Xiangtao Kang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding and Guangdong Rice Engineering LaboratoryGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Wenting Li
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Department of Animal Genetic and Breeding, College of Animal Science and TechnologyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
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Yang K, Zhang J, Zhao Y, Shao Y, Zhai M, Liu H, Zhang L. Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers. BIOLOGY 2023; 12:1397. [PMID: 37997996 PMCID: PMC10669838 DOI: 10.3390/biology12111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
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Affiliation(s)
- Kai Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
| | - Yonggang Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Manjun Zhai
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.S.); (M.Z.)
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (H.L.)
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.Y.); (Y.Z.)
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9
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Zheng X, Zhang Y, Zhang Y, Chen J, Nie R, Li J, Zhang H, Wu C. HOXB8 overexpression induces morphological changes in chicken mandibular skin: an RNA-seq analysis. Poult Sci 2023; 102:102971. [PMID: 37562126 PMCID: PMC10432836 DOI: 10.1016/j.psj.2023.102971] [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: 05/07/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023] Open
Abstract
The Huiyang beard chicken is a well-known Chinese local breed known for its elongated feathers gathered from both sides of the face (muffs) and below the beak (beard), as well as short wattles (SW). The muff and beard (Mb) mutation is caused by ectopic upregulation of the homeobox B8 (HOXB8) gene in the mandibular skin; and the chi-square test showed a significant correlation between SW and Mb genotypes. However, the underlying molecular mechanisms that regulate Mb and SW variations remain unclear. In this study, we investigated the transcriptomes of the mandibular skin and wattles of chickens with and without the Mb genotype to elucidate the molecular basis of these traits. Our results show that HOXB8 is expressed at significantly higher levels in both the mandibular skin and wattles of Mb chickens than in those of wild-type chickens, indicating that HOXB8 regulates both the Mb and SW phenotypes. Key genes for keratin synthesis were highly expressed in the mandibular skin of Mb chickens, suggesting that HOXB8 may play a role in feather development. In wattles, changes in the expression of extracellular matrix synthesis genes may contribute to SW traits. DNA-binding motif analyses revealed that differentially expressed genes were likely to be directly regulated by HOXB8 binding, indicating that HOXB8 may directly or indirectly regulate feather follicle development and wattle growth. Our study identified both known and novel targets, including several genes not previously implicated in feather development and mesenchymal formation. These findings provide insights into the molecular mechanisms of skin appendage variation in birds and offer potential applications in breeding poultry breeds with unique phenotypes.
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Affiliation(s)
- Xiaotong Zheng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu Province, China
| | - Ying Zhang
- China Agricultural Museum, Beijing 100026, China
| | - Yawen Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu Province, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junying Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changxin Wu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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10
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Du W, Yang Z, Xiao C, Liu Y, Peng J, Li J, Li F, Yang X. Identification of genes involved in regulating the development of feathered feet in chicken embryo. Poult Sci 2023; 102:102837. [PMID: 37390552 PMCID: PMC10331478 DOI: 10.1016/j.psj.2023.102837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 07/02/2023] Open
Abstract
The genetic and developmental factors driving the diverse distribution and morphogenesis of feathers and scales on bird feet are yet unclear. Within a single species, Guangxi domestic chickens exhibit dramatic variety in feathered feet, making them an accessible model for research into the molecular basis of variations in skin appendages. In this study, we used H&E staining to observe the morphogenesis of feathered feet, scaled feet and wings skin at different embryonic stages in Longsheng-Feng chickens and Guangxi Partridge chickens. We selected 4 periods (E6, E7, E8, and E12) that play an important role in feather development and performed transcriptome sequencing to screen for candidate genes associated with feathered feet. Through comparison and analysis of transcriptome data, we identified a set of differently expressed genes (DGEs), which were enriched in appendage organ development, hindlimb morphogenesis, activation of transcription factor binding, and binding of sequence-specific DNA in the cis-regulatory region. In addition, we identified some feathered feet-related genes by analyzing the classical signaling pathways that regulate feather development. Finally, we identified candidate genes that regulate feathered feet formation, which include TBX5, PITX1, ZIC1, FGF20, WNT11, WNT7A, WNT16, and SHH. Interestingly, we found that TBX5 was significantly overexpressed in the skin of the feathered feet and had the highest expression at E7 (P < 0.01), whereas PITX1 expression was significantly reduced at E7(P < 0.01). It is hypothesized that TBX5 and PITX1 regulate the development of hair follicles through the Wnt/β-catenin signaling pathway at E7. Our results provide a theoretical basis for investigating the molecular regulatory mechanisms underlying the formation of chicken feathered feet.
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Affiliation(s)
- Wenya Du
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhuliang Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Cong Xiao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yongcui Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiashuo Peng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jianneng Li
- Guangxi Gangfeng Agriculture & Animal Husbandry Co., Ltd, Guigang 537000, China
| | - Fuqiu Li
- Guangxi Gangfeng Agriculture & Animal Husbandry Co., Ltd, Guigang 537000, China
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China.
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11
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Pan Z, Wang Y, Wang M, Wang Y, Zhu X, Gu S, Zhong C, An L, Shan M, Damas J, Halstead MM, Guan D, Trakooljul N, Wimmers K, Bi Y, Wu S, Delany ME, Bai X, Cheng HH, Sun C, Yang N, Hu X, Lewin HA, Fang L, Zhou H. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. SCIENCE ADVANCES 2023; 9:eade1204. [PMID: 37134160 PMCID: PMC10156120 DOI: 10.1126/sciadv.ade1204] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingshan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Yuzhe Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoning Zhu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Shenwen Gu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Conghao Zhong
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Liqi An
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingzhu Shan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Joana Damas
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
| | - Ye Bi
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Shang Wu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Xuechen Bai
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Hans H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Xiaoxiang Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, DK
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
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12
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Fan Y, Wu X, Li Y, Han H, Zhang Y, Yang J, Liu Y. Effect of polymorphisms in the 5’-flanking sequence of MC1R on feather color in Taihang chickens. Poult Sci 2022; 101:102192. [PMID: 36283141 PMCID: PMC9593195 DOI: 10.1016/j.psj.2022.102192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
MC1R plays an important role in the regulation of the formation, transfer, and deposition of melanin in animals and is important for determining coat color. Many studies have reported on single nucleotide polymorphisms (SNPs) in the coding sequence of MC1R. However, few studies have investigated the polymorphisms in the 5’-flanking sequence of MC1R. In this study, we sequenced 2000 bp of the 5’-flanking sequence of MC1R in 300 Taihang chickens with brown feathers (MTH) and 300 Taihang chickens with black feathers (HTH). The sequencing results showed that 4 SNPs (MC1R g.18838722 G > C, g.18838624 T > C, g.18838694 G > A, and g.18838624 C > T) were located in the 5’-flanking sequence of MC1R between the MTH and HTH groups. Association analysis showed that there was a significant correlation between the 4 SNPs and feather color in Taihang chickens. The correlation between MC1R g.18838624 T >C and feather color of Taihang chicken was 100%, of which the CC (E1) genotype is MTH and the TT (E2) genotype is HTH. Furthermore, there was a significant correlation between MC1R g.18838624 T > C and egg production at 302 d. E1 (184.14 ± 0.674) was significantly higher than that in E2 (181.75 ± 0.577) (P < 0.05). Luciferase reporter assays were used to detect the transcriptional activity of MC1R with different SNP genotypes. The results showed that the luciferase activity of E2 was significantly higher than that of E1 (P < 0.05). In addition, transcription factor-binding site predictions showed that E2 creates a new binding site for ZEB1. RT‒qPCR results revealed that the expression of MC1R in E2 was significantly lower than that in E1 (P < 0.05), and the expression of ZEB1 in E2 was significantly higher than that in E1 (P < 0.05). Overexpression and shRNA experiments demonstrated that ZEB1 regulates the expression of MC1R in DF1 cells. ZEB1 has a negative regulatory effect on the transcriptional activity of MC1R; it inhibits the expression of MC1R and affects the feather color of Taihang chickens. This study provides new insight into the molecular mechanism of feather color formation and the transcriptional regulation of MC1R in Taihang chickens.
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13
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Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides). Gene 2022; 834:146612. [PMID: 35618220 DOI: 10.1016/j.gene.2022.146612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/30/2023]
Abstract
Although graylag geese (A. anser) showed similar plumages of white, grey, and white with grey patches compared to those in swan geese (A. cygnoides), it was believed the substantial molecular mechanism for plumage variations were different. To date, studies on genes responsible for diverse plumages among graylag geese were limited and causal mutations remain unknown. In this study, genomes from 57 individuals belonging to six breeds showing different plumages were sequenced at ∼10X depth. Firstly, the allele frequency differences (AFD) of variants on the scaffold394 (NW_013185915.1) between grey and white goose breeds (A. anser) was calculated and a genomic region between 768,290-779,889 bp was detected to carry candidate variants associated with plumages, including one SNP (g. 775,151G > T, ∼18.6 kb upstream of EDNRB2) found to be fixed in white geese. This region was overlapped with the one detected by the haplotype-based sweep analysis, in which significant signals defined a candidate region of 736,610-820,622 bp on the same scaffold. Results from the transcriptomic data showed that expression levels of EDNRB2 and many other melanogenesis-related genes were significantly decreased among white geese compared to that in grey geese, especially at late embryonic stages (>E15). Modifications at transcriptional levels might result in abnormal melanocyte developments and thus the white plumages when they grow up. In addition, a frameshift mutation (C > -) in exon4 of MLANA gene on scaffold176 (NW_013185876.1) was suggested as the causal mutation for sex-linked dilution phenotype in graylag geese although this requires more demonstration experiments. Together with observed white plumages caused by EDNRB2 mutations in coding regions among swan geese and chicken, our study provided new examples to study the parallel evolution.
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14
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Shao M, Shi K, Zhao Q, Duan Y, Shen Y, Tian J, He K, Li D, Yu M, Lu Y, Tang Y, Feng C. Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens. Genes (Basel) 2022; 13:genes13050798. [PMID: 35627183 PMCID: PMC9140345 DOI: 10.3390/genes13050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.
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Affiliation(s)
- Minghui Shao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Ying Duan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Jinjie Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kun He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Minli Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China;
| | - Yanfei Tang
- Guangxi Fufeng Agricultural and Animal Husbandry Group Co., Ltd., Nanning 530024, China;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
- Correspondence:
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15
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Phenotypic Analysis of Growth and Morphological Traits in Miniature Breeds of Japanese Indigenous Chickens. J Poult Sci 2022; 59:38-47. [PMID: 35125911 PMCID: PMC8791770 DOI: 10.2141/jpsa.0200110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
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16
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Duntsch L, Brekke P, Ewen JG, Santure AW. Who are you? A framework to identify and report genetic sample mix-ups. Mol Ecol Resour 2021; 22:1855-1867. [PMID: 34907643 DOI: 10.1111/1755-0998.13575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022]
Abstract
Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups. However, many recent studies in the field of molecular ecology do not appear to systematically report individual assignment checks as part of their publications. Although checks may be done, lack of consistent reporting means that it is difficult to assess whether sample mix-ups have occurred or been detected. Here, we present an easy-to-follow sample verification framework that can utilise existing metadata, including species, population structure, sex and pedigree information. We demonstrate its application to a dataset representing individuals of a threatened Aotearoa New Zealand bird species, the hihi, genotyped on a 50K SNP array. We detected numerous incorrect genotype-ID associations when comparing observed and genetic sex or comparing to relationships in a verified microsatellite pedigree. The framework proposed here helped to confirm 488 individuals (39%), correct another 20 bird-genotype links, and detect hundreds of incorrect sample IDs, emphasizing the value of routinely checking genetic and genomic datasets for their accuracy. We therefore promote the implementation and reporting of this simple yet effective sample verification framework as a standardized quality control step for studies in the field of molecular ecology.
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Affiliation(s)
- Laura Duntsch
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W Santure
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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17
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Boer EF, Van Hollebeke HF, Maclary ET, Holt C, Yandell M, Shapiro MD. A ROR2 coding variant is associated with craniofacial variation in domestic pigeons. Curr Biol 2021; 31:5069-5076.e5. [PMID: 34551284 PMCID: PMC8612976 DOI: 10.1016/j.cub.2021.08.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/01/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022]
Abstract
Vertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways.1,2 Within species, canalized development typically produces modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon displays radical craniofacial variation within a single species. One of the most striking cases of pigeon craniofacial variation is the short-beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex linked (Ku2 locus).3-5 However, the genetic underpinnings of pigeon craniofacial variation remain unknown. Using geometric morphometrics and quantitative trait locus (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH), we identified a single Z chromosome locus that explains a majority of the variation in beak morphology in the F2 population. Complementary comparative genomic analyses revealed that the same locus is strongly differentiated between breeds with short and medium beaks. Within the Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis.6,7 In humans, ROR2 mutations cause Robinow syndrome, a congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton.8,9 Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.
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Affiliation(s)
- Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
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18
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Li J, Lee MO, Chen J, Davis BW, Dorshorst BJ, Siegel PB, Inaba M, Jiang TX, Chuong CM, Andersson L. Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens. Proc Natl Acad Sci U S A 2021; 118:e2109363118. [PMID: 34607956 PMCID: PMC8521658 DOI: 10.1073/pnas.2109363118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml+/ml+ ) chickens assigned Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agouti-signaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Mi-Ok Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Junfeng Chen
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Benjamin J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Masafumi Inaba
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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19
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Trevisoli PA, Moreira GCM, Boschiero C, Cesar ASM, Petrini J, Margarido GRA, Ledur MC, Mourão GB, Garrick D, Coutinho LL. A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens. Front Genet 2021; 12:698163. [PMID: 34456973 PMCID: PMC8386115 DOI: 10.3389/fgene.2021.698163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.
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Affiliation(s)
- Priscila Anchieta Trevisoli
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Gabriel Costa Monteiro Moreira
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Clarissa Boschiero
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Agri-Food Industry, Food and Nutrition Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Juliana Petrini
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Dorian Garrick
- School of Agriculture, Massey University, Wellington, New Zealand
| | - Luiz Lehmann Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
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20
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Wang K, Hu H, Tian Y, Li J, Scheben A, Zhang C, Li Y, Wu J, Yang L, Fan X, Sun G, Li D, Zhang Y, Han R, Jiang R, Huang H, Yan F, Wang Y, Li Z, Li G, Liu X, Li W, Edwards D, Kang X. The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Mol Biol Evol 2021; 38:5066-5081. [PMID: 34329477 PMCID: PMC8557422 DOI: 10.1093/molbev/msab231] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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Affiliation(s)
- Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chenxi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yiyi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Junfeng Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Lan Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xuewei Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Hetian Huang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Fengbin Yan
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanbin Wang
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
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21
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Bortoluzzi C, Megens HJ, Bosse M, Derks MFL, Dibbits B, Laport K, Weigend S, Groenen MAM, Crooijmans RPMA. Parallel Genetic Origin of Foot Feathering in Birds. Mol Biol Evol 2020; 37:2465-2476. [PMID: 32344429 PMCID: PMC7475038 DOI: 10.1093/molbev/msaa092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.
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Affiliation(s)
- Chiara Bortoluzzi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Kimberly Laport
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Steffen Weigend
- Friedrich-Loeffler-Institut (FLI), Institute of Farm Animal Genetics, Neustadt, Germany
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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