Genetic architecture and genomic selection of female reproduction traits in rainbow trout

Abstract Background Rainbow trout is a significant fish farming industry under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits. Results A pedigreed population of 1,343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits. Conclusions Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.

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Genomic selection for female reproduction in Australian tropically adapted beef cattle

Animal Production Science ◽

10.1071/an13016 ◽

2014 ◽

Vol 54 (1) ◽

pp. 16 ◽

Cited By ~ 18

Author(s):

Y. D. Zhang ◽

D. J. Johnston ◽

S. Bolormaa ◽

R. J. Hawken ◽

B. Tier

Keyword(s):

Genomic Selection ◽

Cross Validation ◽

Population Data ◽

Northern Australia ◽

Female Reproduction ◽

Genetic Complexity ◽

Reproduction Traits ◽

Experimental Populations ◽

Snp Panels ◽

Genomic Predictions

The usefulness of genomic selection was assessed for female reproduction in tropically adapted breeds in northern Australia. Records from experimental populations of Brahman (996) and Tropical Composite (1097) cattle that had had six calving opportunities were used to derive genomic predictions for several measures of female fertility. These measures included age at first corpus luteum (AGECL), at first calving and subsequent postpartum anoestrous interval and measures of early and lifetime numbers of calves born or weaned. In a second population, data on pregnancy and following status (anoestrous or pregnancy) were collected from 27 commercial herds from northern Australia to validate genomic predictions. Cows were genotyped with a variety of single nucleotide polymorphism (SNP) panels and, where necessary, genotypes imputed to the highest density (729 068 SNPs). Genetic parameters of subsets of the complete data were estimated. These subsets were used to validate genomic predictions using genomic best linear unbiased prediction using both univariate cross-validation and bivariate analyses. Estimated heritability ranged from 0.56 for AGECL to 0.03 for lifetime average calving rate in the experimental cows, and from 0.09 to 0.25 for early life reproduction traits in the commercial cows. Accuracies of predictions were generally low, reflecting the limited number of data in the experimental populations. For AGECL and postpartum anoestrous interval, the highest accuracy was 0.35 for experimental Brahman cows using five-fold univariate cross-validation. Greater genetic complexity in the Tropical Composite cows resulted in the corresponding accuracy of 0.23 for AGECL. Similar level of accuracies (from univariate and bivariate analyses) were found for some of the early measures of female reproduction in commercial cows, indicating that there is potential for genomic selection but it is limited by the number of animals with phenotypes.

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Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

BMC Genomics ◽

10.1186/s12864-021-08062-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Carole Blay ◽

Pierrick Haffray ◽

Jonathan D’Ambrosio ◽

Enora Prado ◽

Nicolas Dechamp ◽

...

Keyword(s):

Raman Spectroscopy ◽

Fatty Acid ◽

Rainbow Trout ◽

Linoleic Acid ◽

Genomic Selection ◽

Candidate Genes ◽

Genetic Architecture ◽

Large Scale ◽

Fat Deposition ◽

Fa Composition

Abstract Background In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection. Results Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait. Conclusion This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species.

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Temperature Selection of Rainbow Trout (Salmo gairdneri) Fingerlings in Vertical and Horizontal Gradients

Journal of the Fisheries Research Board of Canada ◽

10.1139/f71-266 ◽

1971 ◽

Vol 28 (11) ◽

pp. 1801-1804 ◽

Cited By ~ 31

Author(s):

R. W. McCauley ◽

W. L. Pond

Keyword(s):

Rainbow Trout ◽

Salmo Gairdneri ◽

Temperature Preference ◽

Temperature Selection ◽

Horizontal Gradients ◽

Significant Difference ◽

Preferred Temperatures ◽

Laboratory Investigations ◽

Horizontal Temperature Gradients ◽

Selection Of

Preferred temperatures of underyearling rainbow trout (Salmo gairdneri) were determined in both vertical and horizontal temperature gradients. No statistically significant difference was found between the preferred temperatures by the two different methods. This suggests that the nature of the gradient plays a lesser role than generally believed in laboratory investigations of temperature preference.

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Analysis of microsatellite DNA of rainbow trout (Parasalmo (Oncorhynchus) mykiss) of Kamchatka: Selection of loci and optimization of the method

Russian Journal of Genetics ◽

10.1134/s1022795410070161 ◽

2010 ◽

Vol 46 (7) ◽

pp. 894-897 ◽

Cited By ~ 3

Author(s):

A. V. Semenova ◽

G. A. Rubtsova ◽

K. I. Afanas’ev ◽

S. D. Pavlov

Keyword(s):

Rainbow Trout ◽

Oncorhynchus Mykiss ◽

Microsatellite Dna ◽

Selection Of

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Prospects and challenges for genome-wide association and genomic selection in oilseed Brassica speciesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Genome ◽

10.1139/g10-087 ◽

2010 ◽

Vol 53 (11) ◽

pp. 1024-1028 ◽

Cited By ~ 8

Author(s):

W.A. Cowling ◽

E. Balázs

Keyword(s):

Genomic Selection ◽

Genetic Improvement ◽

Genome Wide Association ◽

Sustainable Farming ◽

Genome Wide ◽

Oilseed Brassicas ◽

Selection Of

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Genotyping-by-sequencing for genomic selection of perennial ryegrass (Lolium perenne)

Acta Horticulturae ◽

10.17660/actahortic.2018.1203.2 ◽

2018 ◽

pp. 9-16

Author(s):

J. Jacobs ◽

M. Faville ◽

A. Griffiths ◽

M. Cao ◽

R. Tan ◽

...

Keyword(s):

Genomic Selection ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Genotyping By Sequencing ◽

Selection Of

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Quantitative Genomic Dissection of Soybean Yield Components

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400896 ◽

2019 ◽

Vol 10 (2) ◽

pp. 665-675

Author(s):

Alencar Xavier ◽

Katy M. Rainey

Keyword(s):

Genomic Prediction ◽

Yield Components ◽

Genetic Architecture ◽

Breeding Strategy ◽

Genotype By Environment ◽

Field Crops ◽

Common Parent ◽

Data Collections ◽

Enhanced Yield ◽

Selection Of

Soybean is a crop of major economic importance with low rates of genetic gains for grain yield compared to other field crops. A deeper understanding of the genetic architecture of yield components may enable better ways to tackle the breeding challenges. Key yield components include the total number of pods, nodes and the ratio pods per node. We evaluated the SoyNAM population, containing approximately 5600 lines from 40 biparental families that share a common parent, in 6 environments distributed across 3 years. The study indicates that the yield components under evaluation have low heritability, a reasonable amount of epistatic control, and partially oligogenic architecture: 18 quantitative trait loci were identified across the three yield components using multi-approach signal detection. Genetic correlation between yield and yield components was highly variable from family-to-family, ranging from -0.2 to 0.5. The genotype-by-environment correlation of yield components ranged from -0.1 to 0.4 within families. The number of pods can be utilized for indirect selection of yield. The selection of soybean for enhanced yield components can be successfully performed via genomic prediction, but the challenging data collections necessary to recalibrate models over time makes the introgression of QTL a potentially more feasible breeding strategy. The genomic prediction of yield components was relatively accurate across families, but less accurate predictions were obtained from within family predictions and predicting families not observed included in the calibration set.

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