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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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Zhang X, Zhao J, Zhou C, Li W, Liu Y, Wei C, Wang Y, Hong X, Zhu X, Liu X. Assessing and Screening of Female Fertility in Artificially Bred Asian Yellow Pond Turtles ( Mauremys mutica) Based on Parentage Assignment. Animals (Basel) 2024; 14:479. [PMID: 38338122 PMCID: PMC10854808 DOI: 10.3390/ani14030479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
The Asian yellow pond turtle (Mauremys mutica) is widely traded in China, and its artificial breeding has now become a major industry. However, the insufficient offspring supply and reproductive decline of farmed turtles make the wild turtles more vulnerable. The present study was mainly designed to quantify the fecundity of M. mutica and attempt to screen for good reproductive performance in females. The genetic variability of the population and its genetic structure were also analysed. The parent-offspring relationships of all offspring in four consecutive years were confirmed using sixteen microsatellite loci. The genetic variability between the parents and offspring was low, and offspring of different years also showed little variability. We summarised the reproductive results of all females and counted the annual number of offspring and the variation in the number of offspring. The females were then divided into three types (stable, undulating and levelling off) according to the continuity. We selected seven females with good reproductive ability, which provided 16.94% of the annual contributions, while there were two females that had no offspring in four years. We also analysed the possible reasons for this difference and the importance of carrying out a family survey. This research can provide the basis and materials for the creation of a good reproductive group and the study of the reproductive biology of turtles in M. mutica aquaculture.
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Affiliation(s)
- Xincheng Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Jian Zhao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Chenyao Zhou
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
- School of Fishery, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Yihui Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (J.Z.); (C.Z.); (W.L.); (Y.L.); (C.W.); (Y.W.); (X.H.)
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3
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Gvoždíková Javůrková V, Doležal P, Fraňková A, Horák M, Chodová D, Langrová I, Tůmová E. Effects of genotype, sex, and feed restriction on the biochemical composition of chicken preen gland secretions and their implications for commercial poultry production. J Anim Sci 2022; 101:6956961. [PMID: 36547363 PMCID: PMC9923712 DOI: 10.1093/jas/skac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Preen gland secretions spread on the feathers contain various chemical compounds dominated by fatty acids (FAs) and volatile organic compounds (VOCs). These chemicals may significantly affect plumage condition, microbial and ectoparasitic load on feathers, and chemical communication of birds. However, how chemical composition of preen secretions varies in commercially produced chickens with respect to their genotype, sex, and feeding regime remain largely unknown, as well as the welfare implications for farmed poultry. We found that while polyunsaturated fatty acids in chicken preen secretions differed significantly with genotype (P << 0.001), saturated fatty acids and monounsaturated fatty acids varied with genotype-dependent preen gland volume (P < 0.01). Chickens of meat-type fast-growing Ross 308 genotype had reduced preen gland volume and lower proportions of all FA categories in their preen secretions compared with dual-purpose slow-growing ISA Dual chickens. A total of 34 FAs and 77 VOCs with tens of unique FAs were detected in preen secretions of both genotypes. While differences in the relative proportion of 6 of the 10 most dominant VOCs in chicken preen gland secretions were related to genotype (P < 0.001), only 1 of the 10 most dominant VOCs showed a sex effect (P < 0.01), and only 2 of the 10 most dominant VOCs showed a genotype-dependent effect of feed restriction (P < 0.05). Feed restriction had no effect on the relative proportion of any of the FAs in chicken preen gland secretions. Moreover, we found that meat-type Ross 308 preen secretions were dominated by VOCs, which are proven attractants for poultry red mite and may also increase infestation with other ectoparasites and negatively influence overall odor-mediated intraspecific communication and welfare. This study shows that no feeding management, but long-term genetic selection in commercial breeding may be the main cause of the differences in the biochemistry and function of chicken preen secretions. This might have negative consequences for chemosignaling, antiparasitic, and antimicrobial potential of preen secretions and can lead to increased susceptibility to ectoparasites, plumage care disorders, and can affect the overall condition, welfare, and productivity of commercially bred chickens. Selection-induced preen gland impairments must therefore be considered and compensated by proper management of the chicken farm and increased care about animal well-being.
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Affiliation(s)
| | - Petr Doležal
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic,Department of Agroenvironmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
| | - Adéla Fraňková
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
| | - Monika Horák
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
| | - Darina Chodová
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
| | - Iva Langrová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
| | - Eva Tůmová
- Department of Animal Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague 6 - Suchdol, Czech Republic
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4
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Bakovic V, Höglund A, Martin Cerezo ML, Henriksen R, Wright D. Genomic and gene expression associations to morphology of a sexual ornament in the chicken. G3 GENES|GENOMES|GENETICS 2022; 12:6633936. [PMID: 35801935 PMCID: PMC9434260 DOI: 10.1093/g3journal/jkac174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 11/12/2022]
Abstract
How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.
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Affiliation(s)
- Vid Bakovic
- IFM Biology, University of Linköping , Linköping 581 83, Sweden
| | - Andrey Höglund
- Science for Life Laboratory, Department of Environmental Science, Stockholm University , Stockholm 106 91, Sweden
| | | | - Rie Henriksen
- IFM Biology, University of Linköping , Linköping 581 83, Sweden
| | - Dominic Wright
- IFM Biology, University of Linköping , Linköping 581 83, Sweden
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5
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Goto T, Shimamoto S, Takaya M, Sato S, Takahashi K, Nishimura K, Morii Y, Kunishige K, Ohtsuka A, Ijiri D. Impact on genetic differences among various chicken breeds on free amino acid contents of egg yolk and albumen. Sci Rep 2021; 11:2270. [PMID: 33500483 PMCID: PMC7838262 DOI: 10.1038/s41598-021-81660-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Eggs play important roles as food resources and nutraceuticals, to alleviate malnutrition and to improve health status in the world. Since free amino acids contribute to the nutritional values and food tastes, we investigated a total of 81 eggs from five chicken breeds, which are Australorp, Nagoya (NGY), Rhode Island Red (RIR), Shamo (SHA), Ukokkei, and two F1 hybrids (NGYxRIR and SHAxRIR) to test impact on genetic differences in 10 egg traits, 20 yolk amino acid traits, and 18 albumen amino acid traits. One-way ANOVA revealed significant breed effects on 10 egg traits, 20 yolk amino acid traits, and 15 albumen amino acid traits. Moreover, a significant heterosis effect on yolk aspartic acid was identified. In addition, positive correlations were found broadly among traits within each trait category (egg traits, yolk amino acid traits, and albumen amino acid traits), whereas there were basically no or weak correlations among the trait categories. These results suggest that almost all traits can be dramatically modified by genetic factor, and there will be partially independent production systems of amino acids into yolk and albumen. Since there will be typical quantitative genetic architecture of egg contents, further genetic analyses will be needed.
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Affiliation(s)
- Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan. .,Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.
| | - Saki Shimamoto
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan.,Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Masahiro Takaya
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.,Hokkaido Tokachi Area Regional Food Processing Technology Center, Tokachi Foundation, Obihiro, Hokkaido, 080-2462, Japan
| | - Shun Sato
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kanna Takahashi
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kenji Nishimura
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Yasuko Morii
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kyoko Kunishige
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Akira Ohtsuka
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
| | - Daichi Ijiri
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
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6
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Effects of Observed Incubation Behavior on Egg Production in Laying Hens of a Commercial Chicken Breed and Detection of Single-Nucleotide Polymorphisms Associated with the Incubation Behavior. J Poult Sci 2021; 59:121-128. [PMID: 35528377 PMCID: PMC9039150 DOI: 10.2141/jpsa.0210037] [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: 03/22/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022] Open
Abstract
Upon contact with laid eggs, avians initiate incubation behavior and stop laying additional eggs. This phenomenon suggests that the productivity of laying hens in free-range facilities may decrease because of frequent contact with laid eggs. Here, we examined whether hens of a commercial breed exhibit incubation behavior in a free-range facility and whether egg productivity subsequently decreases. One-hour observations were performed twice weekly for 3 weeks, during which 9 of 129 hens (7.0%) exhibited incubation behavior (i.e., sitting on eggs) in the free-range facility and were defined as incubating hens. During 4 d of continuous behavioral observation, incubating and non-incubating hens laid the same number of eggs statistically (4.6 and 3.6, on average, respectively); however, incubating hens spent significantly more time on average incubating the eggs (2071.9 min) than did the non-incubating hens (20.9 min; P<0.05), indicating a clear behavioral difference. Subsequently, the incubation behavior and egg productivity of incubating hens and a Silkie Fowl breed hen, which is known to exhibit typical incubation behavior and cessation of laying, were continuously compared for 27 d. The average minutes spent incubating eggs during the observation period increased in both the incubating hens and Silkie Fowl hen and the total time was almost the same (18,088.5 and 23,092 min, respectively). However, the Silkie Fowl hen stopped laying on day 17 after laying 17 eggs, whereas the incubating hens continued laying throughout the observation period. Incubating hens laid an average of 24.5 eggs, indicating that some hens (at least those of the commercial breed used in our study) can continue laying while exhibiting incubation behavior. A single-nucleotide polymorphism associated with incubation behavior was detected on chromosome 4 through genome-wide association analysis.
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Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
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Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
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8
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Laine VN, Verhagen I, Mateman AC, Pijl A, Williams TD, Gienapp P, van Oers K, Visser ME. Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird. BMC Genomics 2019; 20:693. [PMID: 31477015 PMCID: PMC6720064 DOI: 10.1186/s12864-019-6043-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression. RESULTS Birds from the selection lines differed in expression especially for one gene with clear reproductive functions, zona pellucida glycoprotein 4 (ZP4), which has also been shown to be under selection in these lines. Genes were differentially expressed at different time points in all tissues and most of the differentially expressed genes between the two temperature treatments were found in the liver. We identified a set of hub genes from all the tissues which showed high association to hormonal functions, suggesting that they have a core function in timing of breeding. We also found ample differentially expressed genes with largely unknown functions in birds. CONCLUSIONS We found differentially expressed genes associated with selection line and temperature treatment. Interestingly, the latter mainly in the liver suggesting that temperature effects on egg-laying date may happen down-stream in the physiological pathway. These findings, as well as our datasets, will further the knowledge of the mechanisms of tissue-specific avian seasonality in the future.
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Affiliation(s)
- Veronika N. Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - A. Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Agata Pijl
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Tony D. Williams
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Marcel E. Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
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10
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Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses. Genetics 2018; 210:1509-1525. [PMID: 30341085 PMCID: PMC6283156 DOI: 10.1534/genetics.118.301311] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/16/2018] [Indexed: 01/25/2023] Open
Abstract
Phenotypic complexity is caused by the contributions of environmental factors and multiple genetic loci, interacting or acting independently. Studies of yeast and Arabidopsis often find that the majority of natural variation across phenotypes is attributable to independent additive quantitative trait loci (QTL). Detected loci in these organisms explain most of the estimated heritable variation. By contrast, many heritable components underlying phenotypic variation in metazoan models remain undetected. Before the relative impacts of additive and interactive variance components on metazoan phenotypic variation can be dissected, high replication and precise phenotypic measurements are required to obtain sufficient statistical power to detect loci contributing to this missing heritability. Here, we used a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to detect loci underlying responses to 16 different toxins, including heavy metals, chemotherapeutic drugs, pesticides, and neuropharmaceuticals. Using linkage mapping, we identified 82 QTL that underlie variation in responses to these toxins, and predicted the relative contributions of additive loci and genetic interactions across various growth parameters. Additionally, we identified three genomic regions that impact responses to multiple classes of toxins. These QTL hotspots could represent common factors impacting toxin responses. We went further to generate near-isogenic lines and chromosome substitution strains, and then experimentally validated these QTL hotspots, implicating additive and interactive loci that underlie toxin-response variation.
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11
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Johnsson M, Henriksen R, Höglund A, Fogelholm J, Jensen P, Wright D. Genetical genomics of growth in a chicken model. BMC Genomics 2018; 19:72. [PMID: 29361907 PMCID: PMC5782384 DOI: 10.1186/s12864-018-4441-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants of small effect. This complicates genetic mapping of growth and body mass. Experimental intercrosses between individuals from divergent populations allows us to map naturally occurring genetic variants for selected traits, such as body mass by linkage mapping. By simultaneously measuring traits and intermediary molecular phenotypes, such as gene expression, one can use integrative genomics to search for potential causative genes. RESULTS In this study, we use linkage mapping approach to map growth traits (N = 471) and liver gene expression (N = 130) in an advanced intercross of wild Red Junglefowl and domestic White Leghorn layer chickens. We find 16 loci for growth traits, and 1463 loci for liver gene expression, as measured by microarrays. Of these, the genes TRAK1, OSBPL8, YEATS4, CEP55, and PIP4K2B are identified as strong candidates for growth loci in the chicken. We also show a high degree of sex-specific gene-regulation, with almost every gene expression locus exhibiting sex-interactions. Finally, several trans-regulatory hotspots were found, one of which coincides with a major growth locus. CONCLUSIONS These findings not only serve to identify several strong candidates affecting growth, but also show how sex-specificity and local gene-regulation affect growth regulation in the chicken.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.,Department of Animal Breeding and Genetics, The Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden.
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12
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Goto T, Tsudzuki M. Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review. J Poult Sci 2017; 54:1-12. [PMID: 32908402 PMCID: PMC7477176 DOI: 10.2141/jpsa.0160121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.
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Affiliation(s)
- Tatsuhiko Goto
- Genetics, Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Present address: Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
| | - Masaoki Tsudzuki
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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13
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Johnsson M, Gering E, Willis P, Lopez S, Van Dorp L, Hellenthal G, Henriksen R, Friberg U, Wright D. Feralisation targets different genomic loci to domestication in the chicken. Nat Commun 2016; 7:12950. [PMID: 27686863 PMCID: PMC5056458 DOI: 10.1038/ncomms12950] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/18/2016] [Indexed: 12/03/2022] Open
Abstract
Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.
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Affiliation(s)
- M. Johnsson
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - E. Gering
- Department of Zoology, Michigan University, Michigan 48824, USA
| | - P. Willis
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8P 5C2
| | - S. Lopez
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - L. Van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Centre for Mathematics, Physics and Engineering in the Life Sciences and EXperimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - G. Hellenthal
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - R. Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - U. Friberg
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - D. Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
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