1
|
Parakkunnel R, K BN, Vanishree G, George A, Kv S, Yr A, K UB, Anandan A, Kumar S. Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops. BMC Genomics 2024; 25:653. [PMID: 38956471 PMCID: PMC11218257 DOI: 10.1186/s12864-024-10527-4] [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: 02/12/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Oil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism providing energy to the germinating seeds. Major LD-associated proteins are lipoxygenases, phospholipaseD, oleosins, TAG-lipases, steroleosins, caleosins and SEIPINs; involved in facilitating germination and enhancing peroxidation resulting in off-flavours. However, how natural selection is balancing contradictory processes in lipid-rich seeds remains evasive. The present study was aimed at the prediction of selection signatures among orthologous clades in major oilseeds and the correlation of selection effect with gene expression. RESULTS The LD-associated genes from the major oil-bearing crops were analyzed to predict natural selection signatures in phylogenetically close-knit ortholog clusters to understand adaptive evolution. Positive selection was the major force driving the evolution and diversification of orthologs in a lineage-specific manner. Significant positive selection effects were found in 94 genes particularly in oleosin and TAG-lipases, purifying with excess of non-synonymous substitution in 44 genes while 35 genes were neutral to selection effects. No significant selection impact was noticed in Brassicaceae as against LOX genes of oil palm. A heavy load of deleterious mutations affecting selection signatures was detected in T-lineage oleosins and LOX genes of Arachis hypogaea. The T-lineage oleosin genes were involved in mainly anther, tapetum and anther wall morphogenesis. In Ricinus communis and Sesamum indicum > 85% of PLD genes were under selection whereas selection pressures were low in Brassica juncea and Helianthus annuus. Steroleosin, caleosin and SEIPINs with large roles in lipid droplet organization expressed mostly in seeds and were under considerable positive selection pressures. Expression divergence was evident among paralogs and homeologs with one gene attaining functional superiority compared to the other. The LOX gene Glyma.13g347500 associated with off-flavor was not expressed during germination, rather its paralog Glyma.13g347600 showed expression in Glycine max. PLD-α genes were expressed on all the tissues except the seed,δ genes in seed and meristem while β and γ genes expressed in the leaf. CONCLUSIONS The genes involved in seed germination and lipid metabolism were under strong positive selection, although species differences were discernable. The present study identifies suitable candidate genes enhancing seed oil content and germination wherein directional selection can become more fruitful.
Collapse
Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India.
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Anjitha George
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sripathy Kv
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Aruna Yr
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - A Anandan
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, 275103, Uttar Pradesh, India
| |
Collapse
|
2
|
Paul K, Restoux G, Phocas F. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Genet Sel Evol 2024; 56:13. [PMID: 38389056 PMCID: PMC10882880 DOI: 10.1186/s12711-024-00884-9] [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: 03/09/2023] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. RESULTS Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). CONCLUSIONS Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.
Collapse
Affiliation(s)
- Katy Paul
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gwendal Restoux
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| |
Collapse
|
3
|
Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
Collapse
Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| |
Collapse
|
4
|
Sui J, Luan S, Cao J, Dai P, Meng X, Luo K, Chen B, Tan J, Fu Q, Kong J. Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei. Front Genet 2022; 13:929889. [PMID: 36105098 PMCID: PMC9465174 DOI: 10.3389/fgene.2022.929889] [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: 04/27/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
Penaeusvannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future.
Collapse
Affiliation(s)
- Juan Sui
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiawang Cao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping Dai
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianhong Meng
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Baolong Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Tan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiang Fu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Jie Kong,
| |
Collapse
|
5
|
Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
6
|
Yáñez JM, Xu P, Carvalheiro R, Hayes B. Genomics applied to livestock and aquaculture breeding. Evol Appl 2022; 15:517-522. [PMID: 35505887 PMCID: PMC9046759 DOI: 10.1111/eva.13378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- José M. Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Roberto Carvalheiro
- Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista Jaboticabal, São Paulo Brazil
- CSIRO Agriculture & Food Hobart Tasmania Australia
| | - Ben Hayes
- Centre for Animal Science Queensland Alliance for Agriculture and Food Innovation The University of Queensland Australia
| |
Collapse
|
7
|
Besnier F, Ayllon F, Skaala Ø, Solberg MF, Fjeldheim PT, Anderson K, Knutar S, Glover KA. Introgression of domesticated salmon changes life history and phenology of a wild salmon population. Evol Appl 2022; 15:853-864. [PMID: 35603027 PMCID: PMC9108307 DOI: 10.1111/eva.13375] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- F. Besnier
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - F. Ayllon
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - Ø. Skaala
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - M. F. Solberg
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | | | - K. Anderson
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - S. Knutar
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - K. A. Glover
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
| |
Collapse
|
8
|
Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [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: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
Collapse
Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| |
Collapse
|
9
|
Lu Y, Shi C, Jin X, He J, Yin Z. Domestication of farmed fish via the attenuation of stress responses mediated by the hypothalamus-pituitary-inter-renal endocrine axis. Front Endocrinol (Lausanne) 2022; 13:923475. [PMID: 35937837 PMCID: PMC9353172 DOI: 10.3389/fendo.2022.923475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/29/2022] [Indexed: 12/13/2022] Open
Abstract
Human-directed domestication of terrestrial animals traditionally requires thousands of years for breeding. The most prominent behavioral features of domesticated animals include reduced aggression and enhanced tameness relative to their wild forebears, and such behaviors improve the social tolerance of domestic animals toward both humans and crowds of their own species. These behavioral responses are primarily mediated by the hypothalamic-pituitary-adrenal (inter-renal in fish) (HPA/I) endocrine axis, which is involved in the rapid conversion of neuronal-derived perceptual information into hormonal signals. Over recent decades, growing evidence implicating the attenuation of the HPA/I axis during the domestication of animals have been identified through comprehensive genomic analyses of the paleogenomic datasets of wild progenitors and their domestic congeners. Compared with that of terrestrial animals, domestication of most farmed fish species remains at early stages. The present review focuses on the application of HPI signaling attenuation to accelerate the domestication and genetic breeding of farmed fish. We anticipate that deeper understanding of HPI signaling and its implementation in the domestication of farmed fish will benefit genetic breeding to meet the global demands of the aquaculture industry.
Collapse
Affiliation(s)
- Yao Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chuang Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xia Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jiangyan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Zhan Yin,
| |
Collapse
|
10
|
López ME, Cádiz MI, Rondeau EB, Koop BF, Yáñez JM. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Sci Rep 2021; 11:9685. [PMID: 33958603 PMCID: PMC8102513 DOI: 10.1038/s41598-021-86154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.
Collapse
Affiliation(s)
- M E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - M I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - E B Rondeau
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - B F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - J M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile. .,Núcleo Milenio INVASAL, Concepción, Chile.
| |
Collapse
|
11
|
Orbán L, Shen X, Phua N, Varga L. Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? Front Genet 2021; 12:506754. [PMID: 33968125 PMCID: PMC8097054 DOI: 10.3389/fgene.2021.506754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.
Collapse
Affiliation(s)
- László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllõ, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllõ, Hungary
| |
Collapse
|
12
|
Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. Sci Rep 2021; 11:2466. [PMID: 33510350 PMCID: PMC7844035 DOI: 10.1038/s41598-021-81932-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.
Collapse
|