GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>)
Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping...
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MDPI AG
2022-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/1/114 |
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| author | Charles Sánchez-Roncancio Baltasar García Jousepth Gallardo-Hidalgo José M. Yáñez |
| author_facet | Charles Sánchez-Roncancio Baltasar García Jousepth Gallardo-Hidalgo José M. Yáñez |
| author_sort | Charles Sánchez-Roncancio |
| collection | DOAJ |
| description | Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium <i>Piscirickettsia salmonis</i>, which affects farmed rainbow trout, <i>Oncorhynchus mykiss</i>, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with <i>P. salmonis</i> under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with <i>P. salmonis</i> resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout. |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T12:37:24Z |
| publishDate | 2022-12-01 |
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| series | Genes |
| spelling | doaj.art-ead2de846e4844a496826aaf84307c6b2023-11-30T22:23:45ZengMDPI AGGenes2073-44252022-12-0114111410.3390/genes14010114GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>)Charles Sánchez-Roncancio0Baltasar García1Jousepth Gallardo-Hidalgo2José M. Yáñez3Doctorado en Acuicultura, Programa Cooperativo: Universidad de Chile. Universidad Católica del Norte. Pontificia Universidad Católica de Valparaíso, ChileCenter for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, ChileCenter for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, ChileCenter for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, ChileGenome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium <i>Piscirickettsia salmonis</i>, which affects farmed rainbow trout, <i>Oncorhynchus mykiss</i>, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with <i>P. salmonis</i> under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with <i>P. salmonis</i> resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.https://www.mdpi.com/2073-4425/14/1/114<i>Piscirickettsia salmonis</i>GWASwhole genome sequencingrainbow trout |
| spellingShingle | Charles Sánchez-Roncancio Baltasar García Jousepth Gallardo-Hidalgo José M. Yáñez GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) Genes <i>Piscirickettsia salmonis</i> GWAS whole genome sequencing rainbow trout |
| title | GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) |
| title_full | GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) |
| title_fullStr | GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) |
| title_full_unstemmed | GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) |
| title_short | GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to <i>Piscirickettsia salmonis</i> in Rainbow Trout (<i>Oncorhynchus mykiss</i>) |
| title_sort | gwas on imputed whole genome sequence variants reveal genes associated with resistance to i piscirickettsia salmonis i in rainbow trout i oncorhynchus mykiss i |
| topic | <i>Piscirickettsia salmonis</i> GWAS whole genome sequencing rainbow trout |
| url | https://www.mdpi.com/2073-4425/14/1/114 |
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