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Baltazar-Soares M, Karell P, Wright D, Nilsson JÅ, Brommer JE. Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls. Mol Ecol 2024; 33:e17247. [PMID: 38173194 DOI: 10.1111/mec.17247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Feathers comprise a series of evolutionary innovations but also harbour colour, a key biological trait known to co-vary with life history or complex traits. Those relationships are particularly true in melanin-based pigmentation species due to known pleiotropic effects of the melanocortin pathway - originating from melanin-associated phenotypes. Here, we explore the molecular basis of melanin colouration and expected co-variation at the molecular level in the melanin-based, colour polymorphic system of the tawny owl (Strix aluco). An extensive body of literature has revealed that grey and brown tawny owl colour morphs differ in a series of life history and behavioural traits. Thus, it is plausible to expect co-variation also at molecular level between colour morphs. To investigate this possibility, we assembled the first draft genome of the species against which we mapped ddRADseq reads from 220 grey and 150 brown morphs - representing 10 years of pedigree data from a population in Southern Finland - and explored genome-wide associations with colour phenotype. Our results revealed putative molecular signatures of cold adaptation strongly associated with the grey phenotype, namely, a non-synonymous substitution in MCHR1, plus 2 substitutions in non-coding regions of FTCD and FAM135A whose genotype combinations obtained a predictive power of up to 100% (predicting grey colour). These suggest a molecular basis of cold environment adaptations predicted to be grey-morph specific. Our results potentially reveal part of the molecular machinery of melanin-associated phenotypes and provide novel insights towards understanding the functional genomics of colour polymorphism in melanin-based pigmented species.
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Affiliation(s)
| | - Patrik Karell
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
- Department of Ecology and Genetics, University of Uppsala, Uppsala, Sweden
- Department of Bioeconomy, Novia University of Applied Sciences, Ekenäs, Finland
| | | | - Jan-Åke Nilsson
- Department of Biology, Section of Evolutionary Ecology, Lund University, Lund, Sweden
| | - Jon E Brommer
- Department of Biology, University of Turku, Turku, Finland
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2
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Heo S, Cho S, Dinh PTN, Park J, Jin DH, Cha J, Kim YK, Koh YJ, Lee SH, Lee JH. A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach. Anim Genet 2023; 54:355-362. [PMID: 36855963 DOI: 10.1111/age.13303] [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: 07/25/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 03/02/2023]
Abstract
Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult. In this study, we developed a method to quantify and classify colour using an F2 population crossed from two pure lines: White Leghorn and the Korean indigenous breed Yeonsan Ogye. Using red, green, and blue values in the cropped body region, we identified significant genomic regions on chromosomes 33:3 160 480-7 447 197 and Z:78 748 287-79 173 793. Furthermore, we identified two potential candidate genes (PMEL and MTAP) that might have significant effects on melanin-based plumage pigmentation. Our study presents a new phenotyping method using a computer vision approach and provides new insights into the genetic basis of melanin-based feather colouration in chickens.
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Affiliation(s)
- Seonyeong Heo
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea
| | - Sunghyun Cho
- Research and Development Center, Insilicogen Inc., Yongin, South Korea
| | | | - Jongho Park
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea
| | - Dae-Hyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang, South Korea
| | - Jihye Cha
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
| | - Young-Kuk Kim
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Department of Computer Science & Engineering, Chungnam National University, Daejeon, South Korea
| | - Yeong Jun Koh
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Department of Computer Science & Engineering, Chungnam National University, Daejeon, South Korea
| | - Seung Hwan Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, South Korea.,Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
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3
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Sun D, Qi X, Wen H, Li C, Li J, Chen J, Tao Z, Zhu M, Zhang X, Li Y. The genetic basis and potential molecular mechanism of yellow-albino northern snakehead ( Channa argus). Open Biol 2023; 13:220235. [PMID: 36789536 PMCID: PMC9929503 DOI: 10.1098/rsob.220235] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Body colour is an important economic trait for commercial fishes. Recently, a new colour morph displaying market-favoured yellow skin (termed as yellow-mutant, YM) of northern snakehead (Channa argus) was discovered in China. We confirmed that YM snakehead is an albino with complete loss of melanin in the skin and eyes by histological and ultrastructural observations, and inherited as a recessive Mendelian trait. By applying genomic analysis approaches, in combination with gene knockdown and rescue experiments, we suggested a non-sense mutation in slc45a2 (c.383G > A) is the causation for the YM snakehead. Notably, significantly higher levels of key melanogenesis genes (tyr, tyrp1, dct and pmel) and phospho-MITF protein were detected in YM snakehead than those in wild-type individuals, and the underlying mechanism was further investigated by comparative transcriptomic analysis. Results revealed that differential expressed genes involved in pathways like MAPK, WNT and calcium signalling were significantly induced in YM snakehead, which might account for the increased amount of melanogenesis elements, and presumably be stimulated by fibroblast-derived melanogenic factors in a paracrine manner. Our study clarified the genetic basis of colour variation in C. argus and provided the preliminary clue indicating the potential involvement of fibroblasts in pigmentation in fish.
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Affiliation(s)
- Donglei Sun
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xin Qi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Haishen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Jianlong Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Jiwei Chen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zexin Tao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Mingxin Zhu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
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4
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Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA. A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy. Nat Commun 2022; 13:1233. [PMID: 35264556 PMCID: PMC8907176 DOI: 10.1038/s41467-022-28895-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis. Extreme colour pattern variation in male Trinidadian guppies are influenced by natural selection and sexual selection. Here, the authors phenotype and genotype four guppy lineages finding that colour pattern is associated with a diverse haplotype on an autosome.
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Affiliation(s)
- Josephine R Paris
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - James R Whiting
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Mitchel J Daniel
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32304, USA
| | - Joan Ferrer Obiol
- Departament de Microbiologia, Genètica i Estadística and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Paul J Parsons
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mijke J van der Zee
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | | | - Kimberly A Hughes
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32304, USA
| | - Bonnie A Fraser
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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5
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Zhu T, Liu M, Peng S, Zhang X, Chen Y, Lv X, Yang W, Li K, Zhang J, Wang H, Li H, Ning Z, Wang L, Qu L. A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken. Genes (Basel) 2022; 13:genes13020327. [PMID: 35205371 PMCID: PMC8872211 DOI: 10.3390/genes13020327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Chicken plumage colour is a complex trait controlled by many genes. Herein, through Rhode Island Red (RIR) and White Leghorn (WL) F1 cross populations, the segregation of plumage color was observed in females, showing white in males, and dark red (DR) and light yellow (LY) in females. The white has been found to be caused by dominant white alleles (I) and the DR phenotype is attributed to a sex-linked recessive silver allele (S∗S). LY is a derived feather colour phenotype and the genetic mechanism of this is unclear. In order to explore the genetic basis for LY, we randomly selected 40 DR and 39 LY chickens for paired-end sequencing. Through the use of association analysis, we found the LY phenotype is caused by a 7.6 kb non-coding deletion near the SOX10 gene. This mutation has been reported to be responsible for dark brown plumage in chicken, and subsequent diagnostic PCR tests showed that the length of the long-range non-coding deletion is 7.6 kb instead of 8.3 kb as previously reported.
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Affiliation(s)
- Tao Zhu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Mengchao Liu
- Beijing Municipal Bureau of Agriculture and Rural Affairs, Beijing 100005, China;
| | - Shan Peng
- Guiyang Municipal General Station of Animal Science, Guizhou 550081, China; (S.P.); (L.W.)
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Kaiyang Li
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Jianwei Zhang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China; (Y.C.); (X.L.); (W.Y.); (K.L.); (J.Z.)
| | - Huie Wang
- College of Animal Science, Tarim University, Alar 843300, China;
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumchi 830000, China;
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
| | - Liang Wang
- Guiyang Municipal General Station of Animal Science, Guizhou 550081, China; (S.P.); (L.W.)
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (T.Z.); (X.Z.); (Z.N.)
- Correspondence:
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6
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Davoodi P, Ehsani A, Vaez Torshizi R, Masoudi AA. New insights into genetics underlying of plumage color. Anim Genet 2021; 53:80-93. [PMID: 34855995 DOI: 10.1111/age.13156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 01/12/2023]
Abstract
Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10-6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.
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Affiliation(s)
- P Davoodi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - R Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A A Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
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7
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Fallahshahroudi A, Johnsson M, Sorato E, Ubhayasekera SJKA, Bergquist J, Altimiras J, Jensen P. Effects of the domestic thyroid stimulating hormone receptor (TSHR) variant on the hypothalamic-pituitary-thyroid axis and behavior in chicken. Genetics 2021; 217:1-9. [PMID: 33683367 DOI: 10.1093/genetics/iyaa050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Domestic chickens are less fearful, have a faster sexual development, grow bigger, and lay more eggs than their primary ancestor, the red junglefowl. Several candidate genetic variants selected during domestication have been identified, but only a few studies have directly linked them with distinct phenotypic traits. Notably, a variant of the thyroid stimulating hormone receptor (TSHR) gene has been under strong positive selection over the past millennium, but it's function and mechanisms of action are still largely unresolved. We therefore assessed the abundance of the domestic TSHR variant and possible genomic selection signatures in an extensive data set comprising multiple commercial and village chicken populations as well as wild-living extant members of the genus Gallus. Furthermore, by mean of extensive backcrossing we introgressed the wild-type TSHR variant from red junglefowl into domestic White Leghorn chickens and investigated gene expression, hormone levels, cold adaptation, and behavior in chickens possessing either the wild-type or domestic TSHR variant. While the domestic TSHR was the most common variant in all studied domestic populations and in one of two red junglefowl population, it was not detected in the other Gallus species. Functionally, the individuals with the domestic TSHR variant had a lower expression of the TSHR in the hypothalamus and marginally higher in the thyroid gland than wild-type TSHR individuals. Expression of TSHB and DIO2, two regulators of sexual maturity and reproduction in birds, was higher in the pituitary gland of the domestic-variant chickens. Furthermore, the domestic variant was associated with higher activity in the open field test. Our findings confirm that the spread of the domestic TSHR variant is limited to domesticated chickens, and to a lesser extent, their wild counterpart, the red junglefowl. Furthermore, we showed that effects of genetic variability in TSHR mirror key differences in gene expression and behavior previously described between the red junglefowl and domestic chicken.
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Affiliation(s)
- Amir Fallahshahroudi
- Department of Medical Biochemistry and Microbiology, Biomedical Center (BMC), Uppsala University, Uppsala 752 37, Sweden
| | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Enrico Sorato
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
| | | | - Jonas Bergquist
- Department of Chemistry, Biomedical Center (BMC), Uppsala University, Uppsala 75124, Sweden
| | - Jordi Altimiras
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
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