Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

AbstractAnimal 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 variations 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 subject 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 that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease 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.

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Effects of Early Rearing Environment on Stress Response, Immune Function, and Disease Resistance in Juvenile Coho (Oncorhynchus kisutch) and Chinook Salmon (O.tshawytscha)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f93-087 ◽

1993 ◽

Vol 50 (4) ◽

pp. 759-766 ◽

Cited By ~ 47

Author(s):

Kira Salonius ◽

George K. Iwama

Keyword(s):

Disease Resistance ◽

Chinook Salmon ◽

Coho Salmon ◽

Vibrio Anguillarum ◽

Oncorhynchus Kisutch ◽

Significant Rise ◽

Wild Fish ◽

Handling Stress ◽

Hatchery Fish ◽

Natural Water Body

Coho (Oncorhynchus kisutch) and chinook salmon (0. tshawytscha) from aquaculture and wild environments were subjected to handling (30–60 s of netting and aerial emersion) and disease challenges. Plasma cortisol concentrations ([cortisol]pl) in both coho and chinook salmon from wild environments were significantly elevated 4 h after handling. Colonized coho salmon (hatchery-reared fish, transported into a natural water body as fry) responded in a similar fashion to wild fish, while those reared entirely in the hatchery showed no significant rise in [cortisol]pl. The responses to handling stress were retained in wild and colonized coho salmon after 7 mo of hatchery rearing. A transient increase in the leukocyte to red blood cell ratio in both wild and hatchery-reared chinook salmon occurred 4 h after handling. Handling signficantly decreased the antibody-producing cell (APC) number in wild fish and elevated their [cortisol]plrelative to hatchery fish. Wild fish had the highest APC number among the three groups before the handling. No difference in resistance to Vibrio anguillarum was apparent in coho and chinook salmon among the different rearing environments, although chinook salmon were generally more susceptible; disease resistance was reduced in wild coho salmon after 7 mo of rearing in a hatchery.

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Genome-wide association study and genomic predictions for resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing

10.1101/124099 ◽

2017 ◽

Cited By ~ 3

Author(s):

Agustín Barría ◽

Kris A. Christensen ◽

Katharina Correa ◽

Ana Jedlicki ◽

Jean P. Lhorente ◽

...

Keyword(s):

Genomic Selection ◽

Genetic Improvement ◽

Coho Salmon ◽

Association Studies ◽

Oncorhynchus Kisutch ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Selection Models ◽

Genome Wide ◽

Piscirickettsia Salmonis

ABSTRACTPiscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming. Current treatments have been ineffective for the control of the disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) which were experimentally challenged against P. salmonis were sequenced using ddRAD sequencing. A total of 4,174 SNP markers were identified in the population. These markers were used to perform a GWAS and testing genomic selection models. One SNP related with iron availability was genome-wide significantly associated with resistance to P. salmonis defined as day of death. Genomic selection models showed similar accuracies and predictive abilities than traditional pedigree-based best linear unbiased prediction (PBLUP) method.

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Comparison of growth rates between growth hormone transgenic and selectively-bred domesticated strains of coho salmon (Oncorhynchus kisutch) assessed under different culture conditions

Aquaculture ◽

10.1016/j.aquaculture.2020.735468 ◽

2020 ◽

Vol 528 ◽

pp. 735468 ◽

Cited By ~ 1

Author(s):

Leigh P. Gaffney ◽

Rosalind A. Leggatt ◽

Annette F. Muttray ◽

Dionne Sakhrani ◽

Carlo A. Biagi ◽

...

Keyword(s):

Growth Hormone ◽

Growth Rates ◽

Coho Salmon ◽

Oncorhynchus Kisutch ◽

Culture Conditions

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Genome-wide analysis reveals signatures of selection for gait traits in Yili horse

10.1101/471797 ◽

2018 ◽

Author(s):

Ling-Ling Liu ◽

Chao Fang ◽

Jun Meng ◽

Johann Detilleux ◽

Wu-Jun Liu ◽

...

Keyword(s):

Breeding Programs ◽

Genotyping Array ◽

Genome Wide ◽

Locomotory Behavior ◽

Genome Array ◽

Signatures Of Selection ◽

Selection For ◽

The Moment ◽

Genomic Regions ◽

First Time

AbstractHigh quality gaits play an important role in many breeding programs, but the genes of gait were limited at the moment. Here, we present an analysis of genomic selection signatures in 53 individuals from two breeds, using genotype data from the Affymetrix Equine 670K SNP genotyping array. The 11 selection regions of Yili horse were identified using an FST statistic and XP-EHH calculated in 200-kb windows across the genome. In total, 50 genes could be found in the 11 regions, and two candidate genes related to locomotory behavior (CLN6, FZD4). The genome of Yili horse and Russian horse were shaped by natural and artificial selection. Our results suggest that gait trait of Yili horse may related to two genes. This is the first time when whole genome array data is utilized to study genomic regions affecting gait in Yili horse breed.

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Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster

10.1101/2021.11.09.467935 ◽

2021 ◽

Author(s):

Claire Burny ◽

Viola Nolte ◽

Marlies Dolezal ◽

Christian Schl&oumltterer

Keyword(s):

Synergistic Effects ◽

Culture Conditions ◽

Selection Signatures ◽

Laboratory Adaptation ◽

Adaptive Architecture ◽

Temperature Regimes ◽

Fitness Consequences ◽

Genome Wide ◽

Founder Populations ◽

Selected Traits

Experimental evolution combined with whole-genome sequencing is a powerful approach to study the adaptive architecture of selected traits, in particular when replicated experimental populations evolving in opposite selective conditions (e.g. hot vs. cold temperature) are compared. Nevertheless, such comparisons could be affected by environmental effects shared between selective regimes (e.g. laboratory adaptation), which complicate the interpretation of selection signatures. Here, we used an experimental design, which takes advantage of the simplicity of selection signatures from founder populations with reduced variation, to study the fitness consequences of the laboratory environment (culture conditions) at two temperature regimes. After 20 generations of adaptation at 18°C and 29°C, strong genome-wide selection signatures were observed. About one third of the selection signatures can be either attributed to temperature effects, laboratory adaptation or the joint effects of both. The fitness consequences reflecting the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions, fitting the pattern of larger expression differences between founders at 29°C. We propose that evolve and resequence (E&R) with reduced genetic variation allows to study genome-wide fitness consequences driven by the interaction of multiple environmental factors.

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Genome-Wide Association Mapping and Gene Expression Analyses Reveal Genetic Mechanisms of Disease Resistance Variations in Cynoglossus semilaevis

Frontiers in Genetics ◽

10.3389/fgene.2019.01167 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 6

Author(s):

Qian Zhou ◽

Zhencheng Su ◽

Yangzhen Li ◽

Yang Liu ◽

Lei Wang ◽

...

Keyword(s):

Gene Expression ◽

Disease Resistance ◽

Association Mapping ◽

Cynoglossus Semilaevis ◽

Genome Wide Association ◽

Genome Wide ◽

Gene Expression Analyses ◽

Genetic Mechanisms

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Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules

Animals ◽

10.3390/ani10060980 ◽

2020 ◽

Vol 10 (6) ◽

pp. 980

Author(s):

Shan Gao ◽

Hojjat Asadollahpour Nanaei ◽

Bin Wei ◽

Yu Wang ◽

Xihong Wang ◽

...

Keyword(s):

Alternative Splicing ◽

Transcriptome Profiling ◽

Muscular Endurance ◽

Breeding Programs ◽

Future Studies ◽

Genome Wide ◽

Genetic Mechanisms ◽

Productive Traits ◽

Genome Wide Gene Expression ◽

Profiling Analysis

Heterosis has been widely exploited in animal and plant breeding programs to enhance the productive traits of hybrid progeny from two breeds or species. However, its underlying genetic mechanisms remain enigmatic. Transcriptome profiling analysis can be used as a method for exploring the mechanism of heterosis. Here, we performed genome-wide gene expression and alternative splicing (AS) analyses in different tissues (muscle, brain, and skin) from crosses between donkeys and horses. Our results indicated that 86.1% of the differentially expressed genes (DEGs) and 87.2% of the differential alternative splicing (DAS) genes showed over-dominance and dominance in muscle. Further analysis showed that the “muscle contraction” pathway was significantly enriched for both the DEGs and DAS genes in mule muscle tissue. Taken together, these DEGs and DAS genes could provide an index for future studies of the genetic and molecular mechanism of heterosis in the hybrids of donkey and horse.

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