Genome-wide identification of loci associated with growth in rainbow trout
Abstract Background Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout. Results A previously developed 50 K gene-transcr...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6617-x |
| _version_ | 1818148577319321600 |
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| author | Ali Ali Rafet Al-Tobasei Daniela Lourenco Tim Leeds Brett Kenney Mohamed Salem |
| author_facet | Ali Ali Rafet Al-Tobasei Daniela Lourenco Tim Leeds Brett Kenney Mohamed Salem |
| author_sort | Ali Ali |
| collection | DOAJ |
| description | Abstract Background Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout. Results A previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R 2 = 0.09). Conclusion The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs. |
| first_indexed | 2024-12-11T12:53:21Z |
| format | Article |
| id | doaj.art-1e3fd4ef57e04f45ac3ba38e373d51c5 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T12:53:21Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1e3fd4ef57e04f45ac3ba38e373d51c52022-12-22T01:06:39ZengBMCBMC Genomics1471-21642020-03-0121111610.1186/s12864-020-6617-xGenome-wide identification of loci associated with growth in rainbow troutAli Ali0Rafet Al-Tobasei1Daniela Lourenco2Tim Leeds3Brett Kenney4Mohamed Salem5Department of Animal and Avian Sciences, University of MarylandComputational Science Program, Middle Tennessee State UniversityDepartment of Animal and Dairy Science, University of GeorgiaUnited States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research ServiceDivision of Animal and Nutritional Sciences, West Virginia UniversityDepartment of Animal and Avian Sciences, University of MarylandAbstract Background Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout. Results A previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R 2 = 0.09). Conclusion The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.http://link.springer.com/article/10.1186/s12864-020-6617-xBody weightFishGenomic selectionQTLGWASWssGBLUP |
| spellingShingle | Ali Ali Rafet Al-Tobasei Daniela Lourenco Tim Leeds Brett Kenney Mohamed Salem Genome-wide identification of loci associated with growth in rainbow trout BMC Genomics Body weight Fish Genomic selection QTL GWAS WssGBLUP |
| title | Genome-wide identification of loci associated with growth in rainbow trout |
| title_full | Genome-wide identification of loci associated with growth in rainbow trout |
| title_fullStr | Genome-wide identification of loci associated with growth in rainbow trout |
| title_full_unstemmed | Genome-wide identification of loci associated with growth in rainbow trout |
| title_short | Genome-wide identification of loci associated with growth in rainbow trout |
| title_sort | genome wide identification of loci associated with growth in rainbow trout |
| topic | Body weight Fish Genomic selection QTL GWAS WssGBLUP |
| url | http://link.springer.com/article/10.1186/s12864-020-6617-x |
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