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Semenov GA, Sonnenberg BR, Branch CL, Heinen VK, Welklin JF, Padula SR, Patel AM, Bridge ES, Pravosudov VV, Taylor SA. Genes and gene networks underlying spatial cognition in food-caching chickadees. Curr Biol 2024; 34:1930-1939.e4. [PMID: 38636515 DOI: 10.1016/j.cub.2024.03.058] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
Substantial progress has been made in understanding the genetic architecture of phenotypes involved in a variety of evolutionary processes. Behavioral genetics remains, however, among the least understood. We explore the genetic architecture of spatial cognitive abilities in a wild passerine bird, the mountain chickadee (Poecile gambeli). Mountain chickadees cache thousands of seeds in the fall and require specialized spatial memory to recover these caches throughout the winter. We previously showed that variation in spatial cognition has a direct effect on fitness and has a genetic basis. It remains unknown which specific genes and developmental pathways are particularly important for shaping spatial cognition. To further dissect the genetic basis of spatial cognitive abilities, we combine experimental quantification of spatial cognition in wild chickadees with whole-genome sequencing of 162 individuals, a new chromosome-scale reference genome, and species-specific gene annotation. We have identified a set of genes and developmental pathways that play a key role in creating variation in spatial cognition and found that the mechanism shaping cognitive variation is consistent with selection against mildly deleterious non-coding mutations. Although some candidate genes were organized into connected gene networks, about half do not have shared regulation, highlighting that multiple independent developmental or physiological mechanisms contribute to variation in spatial cognitive abilities. A large proportion of the candidate genes we found are associated with synaptic plasticity, an intriguing result that leads to the hypothesis that certain genetic variants create antagonism between behavioral plasticity and long-term memory, each providing distinct benefits depending on ecological context.
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Affiliation(s)
- Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA.
| | - Benjamin R Sonnenberg
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Carrie L Branch
- Department of Psychology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Virginia K Heinen
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Joseph F Welklin
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Sara R Padula
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Ajay M Patel
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Eli S Bridge
- Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, USA
| | - Vladimir V Pravosudov
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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2
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Lin R, Li J, Zhao F, Zhou M, Wang J, Xiao T. Transcriptome analysis of genes potentially associated with white and black plumage formation in Chinese indigenous ducks ( Anas platyrhynchos). Br Poult Sci 2022; 63:466-474. [PMID: 35094630 DOI: 10.1080/00071668.2022.2035676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1. Plumage colour is an important recognisable characteristic of duck (Anas platyrhynchos), but the coloration mechanisms remain largely unknown. To elucidate the molecular mechanisms underlying the formation of black and white plumage, the following study applied RNA sequencing (RNA-Seq) to catalogue the global gene expression profiles in the duck feather bulbs of black and white colours.2. Black feather bulbs were collected from Putian Black ducks (B-PTB) and black Longsheng Jade-green ducks (B-LS), while white feather bulbs were collected from Putian White ducks (W-PTW), Putian Black ducks (W-PTB) and Longsheng Jade-green ducks (W-LS). Sixteen cDNA libraries were constructed and sequenced for transcriptional analysis. Three comparison groups were employed to analyse differentially expressed genes (DEGs), including W-PTB versus B-PTB, W-PTW versus B-PTB and W-LS versus B-LS.3. The results showed 180 DEGs between W-PTB and B-PTB, 303 DEGs between W-PTW and B-PTB, and 108 DEGs between W-LS and B-LS. Further analysis showed that 18 DEGs were directly involved in the pigmentation process and melanogenesis signalling pathway. Additionally, the distribution of DEGs varied amongst groups whereby ASIP appeared only in the W-LS versus B-LS group, GNAI1 and ZEB2 appeared only in the W-PTW versus B-PTB group, and KITLG, EDN3 and FZD4 appeared only in W-PTB versus B-PTB.4. The findings suggested that the mechanism of feather albinism may differ between duck breeds. This study provided new information for discovering genes that are important for feather pigmentation and helps elucidate molecular mechanisms involved in black and white plumage in ducks.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaquan Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fanglu Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mai Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junhui Wang
- The Animal Husbandry Station in Fujian Province, Fuzhou, China
| | - Tianfang Xiao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
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3
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Kulikova IV. Molecular Mechanisms and Gene Regulation of Melanic Plumage Coloration in Birds. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542108007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Sello CT, Liu C, Sun Y, Msuthwana P, Hu J, Sui Y, Chen S, Zhou Y, Lu H, Xu C, Sun Y, Liu J, Li S, Yang W. De Novo Assembly and Comparative Transcriptome Profiling of Anser anser and Anser cygnoides Geese Species' Embryonic Skin Feather Follicles. Genes (Basel) 2019; 10:genes10050351. [PMID: 31072014 PMCID: PMC6562822 DOI: 10.3390/genes10050351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Geese feather production and the quality of downy feathers are additional economically important traits in the geese industry. However, little information is available about the molecular mechanisms fundamental to feather formation and the quality of feathers in geese. This study conducted de novo transcriptome sequencing analysis of two related geese species using the Illumina 4000 platform to determine the genes involved in embryonic skin feather follicle development. A total of 165,564,278 for Anser anser and 144,595,262 for Anser cygnoides clean reads were generated, which were further assembled into 77,134 unigenes with an average length of 906 base pairs in Anser anser and 66,041 unigenes with an average length of 922 base pairs in Anser cygnoides. To recognize the potential regulatory roles of differentially expressed genes (DEGs) during geese embryonic skin feather follicle development, the obtained unigenes were annotated to Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analysis. In both species, GO and KOG had shown similar distribution patterns during functional annotation except for KEGG, which showed significant variation in signaling enrichment. Anser asnser was significantly enriched in the calcium signaling pathway, whereas Anser cygnoides was significantly enriched with glycerolipid metabolism. Further analysis indicated that 14,227 gene families were conserved between the species, among which a total of 20,715 specific gene families were identified. Comparative RNA-Seq data analysis may reveal inclusive knowledge to assist in the identification of genetic regulators at a molecular level to improve feather quality production in geese and other poultry species.
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Affiliation(s)
- Cornelius Tlotliso Sello
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Chang Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Changchun 130118, China.
| | - Petunia Msuthwana
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Jingtao Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yujian Sui
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, Beijing 100107, China.
| | - Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Hongtao Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Chenguang Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Yue Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Jing Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Shengyi Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Wei Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
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Robic A, Morisson M, Leroux S, Gourichon D, Vignal A, Thebault N, Fillon V, Minvielle F, Bed’Hom B, Zerjal T, Pitel F. Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotypes in Japanese quail. Genet Sel Evol 2019; 51:12. [PMID: 30987584 PMCID: PMC6466734 DOI: 10.1186/s12711-019-0458-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn-2/beige mutation (assumed to be caused by a different structural modification). RESULTS For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the ASIP gene. Thus, we hypothesize that the 5' region of the ITCH-ASIP fusion gene leads to a higher transcription level than the 5' region of the ASIP gene. CONCLUSIONS We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the ASIP locus. Both of the associated mutations fawn-2/beige and yellow lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of ASIP depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5' region of the ASIP gene itself has additional impacts, especially for the fawn-2/beige mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the ASIP coding sequences has been reported, which supports our hypothesis that repressors in the 5' region of ASIP are absent in the fawn-2/beige mutant.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | - Sophie Leroux
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | | | - Alain Vignal
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | - Noémie Thebault
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | - Valérie Fillon
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
| | - Francis Minvielle
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bertrand Bed’Hom
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Tatiana Zerjal
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, 31326 Castanet-Tolosan, France
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6
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Abolins-Abols M, Kornobis E, Ribeca P, Wakamatsu K, Peterson MP, Ketterson ED, Milá B. Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis
). Mol Ecol 2018; 27:4501-4515. [DOI: 10.1111/mec.14878] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Mikus Abolins-Abols
- Department of Animal Biology; University of Illinois; Urbana Illinois
- Department of Biology; Indiana University; Bloomington Indiana
| | - Etienne Kornobis
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | | | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | | | | | - Borja Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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