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Ulloa PE, Jilberto F, Lam N, Rincón G, Valenzuela L, Cordova-Alarcón V, Hernández AJ, Dantagnan P, Ravanal MC, Elgueta S, Araneda C. Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:754-765. [PMID: 38958822 DOI: 10.1007/s10126-024-10343-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Genetic variability within the same fish species could confer soybean meal (SBM) tolerance in some individuals, thus favoring growth. This study investigates the single-nucleotide polymorphisms (SNPs) in differentially expressed genes (DEGs) favoring SBM tolerance in higher-growth zebrafish (Danio rerio). In a previous work, nineteen families of zebrafish were fed a fish meal diet (100FM control diet) or SBM-based diets supplemented with saponin (50SBM + 2SPN-experimental diet), from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (170 ± 18 mg) or lower (76 ± 10 mg) weight gain on 50SBM + 2SPN in relation to 100FM. Intestinal transcriptomic analysis using RNA-seq revealed six hundred and sixty-five differentially expressed genes in higher-growth fish fed 50SBM + 2SPN diet. In this work, using these results, 47 SNPs in DEGs were selected. These SNPs were genotyped by Sequenom in 340 zebrafish that were fed with a 50SBM + 2SPN diet or with 100FM diet. Marker-trait analysis revealed 4 SNPs associated with growth in 3 immunity-related genes (aif1l, arid3c, and cst14b.2) in response to the 50SBM + 2SPN diet (p-value < 0.05). Two SNPs belonging to aif1l y arid3c produce a positive (+19 mg) and negative (-26 mg) effect on fish growth, respectively. These SNPs can be used as markers to improve the early selection of tolerant fish to SBM diet or other plant-based diets. These genes can be used as biomarkers to identify SNPs in commercial fish, thus contributing to the aquaculture sustainability.
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Affiliation(s)
- Pilar E Ulloa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Avenida Manuel Montt 948, Santiago, 7500975, Chile.
| | - Felipe Jilberto
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | - Natalia Lam
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | | | - Luis Valenzuela
- INRIA Chile, Avenida Apoquindo 2827, piso 12, Santiago, 7550312, Chile
| | - Valentina Cordova-Alarcón
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
| | - Adrián J Hernández
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, 4780000, Chile
| | - Patricio Dantagnan
- Núcleo de Investigación en Producción Alimentaria, Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, 4780000, Chile
| | - Maria Cristina Ravanal
- Instituto de Ciencia y Tecnología de los Alimentos (ICYTAL), Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Isla Teja, Avda. Julio Sarrazín s/n, Valdivia, 5090000, Chile
| | - Sebastian Elgueta
- Facultad de Ciencias Para El Cuidado de La Salud, Universidad San Sebastian, Sede Los Leones, Santiago, Chile
| | - Cristian Araneda
- Food Quality Research Center, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago, 8820808, Chile
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Park J, Na CS. Weighted single-step genome-wide association study to reveal new candidate genes for productive traits of Landrace pig in Korea. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:702-716. [PMID: 39165735 PMCID: PMC11331376 DOI: 10.5187/jast.2024.e104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 08/22/2024]
Abstract
The objective of this study was to identify genomic regions and candidate genes associated with productive traits using a total of 37,099 productive records and 6,683 single nucleotide polymorphism (SNP) data obtained from five Great-Grand-Parents (GGP) farms in Landrace. The estimated of heritabilities for days to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) were 0.49, 0.49, 0.56, and 0.23, respectively. We identified a genetic window that explained 2.05%-2.34% for each trait of the total genetic variance. We observed a clear partitioning of the four traits into two groups, and the most significant genomic region for AGE and ADG were located on the Sus scrofa chromosome (SSC) 1, while BF and EMA were located on SSC 2. We conducted Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), which revealed results in three biological processes, four cellular component, three molecular function, and six KEGG pathway. Significant SNPs can be used as markers for quantitative trait loci (QTL) investigation and genomic selection (GS) for productive traits in Landrace pig.
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Affiliation(s)
- Jun Park
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Chong-Sam Na
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
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Arora D, Park JE, Lim D, Cho IC, Kang KS, Kim TH, Park W. Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed. PLoS One 2022; 17:e0263035. [PMID: 35587479 PMCID: PMC9119490 DOI: 10.1371/journal.pone.0263035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
The porcine immune system has an important role in pre-clinical studies together with understanding the biological response mechanisms before entering into clinical trials. The size distribution of the Korean minipig is an important feature that make this breed ideal for biomedical research and safe practice in post clinical studies. The extremely tiny (ET) minipig serves as an excellent model for various biomedical research studies, but the comparatively frail and vulnerable immune response to the environment over its Large (L) size minipig breed leads to additional after born care. To overcome this pitfall, comparative analysis of the genomic regions under selection in the L type breed could provide a better understanding at the molecular level and lead to the development of an enhanced variety of ET type minipig. In this study, we utilized whole genome sequencing (WGS) to identify traces of artificial selection and integrated them with transcriptome data generated from blood samples to find strongly selected and differentially expressed genes of interest. We identified a total of 35 common genes among which 7 were differentially expressed and showed selective sweep in the L type over the ET type minipig breed. The stabilization of these genes were further confirmed using nucleotide diversity analysis, and these genes could serve as potential biomarkers for the development of a better variety of ET type pig breed.
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Affiliation(s)
- Devender Arora
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, Korea
| | - Kyung Soo Kang
- Department of Animal Sciences, Shingu College, Jungwon-gu, Seongnam-si, Korea
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
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Hu T, Lei Y, Li M, Liu Q, Song L, Zhao D. Dietary Eucommia ulmoides Extract Alleviates the Effect of Cold Stress on Chick Growth Performance, Antioxidant and Immune Ability. Animals (Basel) 2021; 11:3008. [PMID: 34827741 PMCID: PMC8614489 DOI: 10.3390/ani11113008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/09/2021] [Accepted: 10/16/2021] [Indexed: 01/10/2023] Open
Abstract
This study aimed to investigate the protective value of Eucommia ulmoides extract (EUE) on chicks under cold stress. A total of 21 compounds were identified in EUE using mass spectrometry (LC-MS). Ninety chicks were divided into a control group (CS) fed a basal diet and an experimental group supplemented with EUE, exposed to 10 ± 1 °C for 8 h per day. Results showed, compared with the CS group, the body weights (BW) (p < 0.01) and average daily gains ADG (p < 0.05) of the EUE group were increased throughout the study period. Chicks fed EUE had higher AFI (0-7 d, p < 0.001) and lower feed-to-gain ratios (F/G) (0-15 d, p < 0.001). EUE increased the activities of superoxide dismutase (SOD) (15 d, p < 0.05) and glutathione peroxidase (GSH-Px) (7 d, p < 0.05), whereas it decreased malondialdehyde (MDA) (15 d, p < 0.01). The contents of IgA (7 d, p < 0.05), IgG (7 d; 15 d, p < 0.01), and IgM (15 d, p < 0. 001) were higher in the EUE group. Dietary EUE could also reduce chick organ damage. Overall, EUE as a natural feed additive can improve the growth performance, antioxidant capacity, and immune level, and reduce the organ damage of cold-stressed chicks.
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Affiliation(s)
- Ting Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; (T.H.); (Y.L.); (M.L.)
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Yue Lei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; (T.H.); (Y.L.); (M.L.)
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Institute of Subtropical Crops, Xingyi 562400, China
| | - Minxue Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; (T.H.); (Y.L.); (M.L.)
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Qin Liu
- College of Animal Science, Guizhou University, Guiyang 550025, China;
| | - Li Song
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; (T.H.); (Y.L.); (M.L.)
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Degang Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China; (T.H.); (Y.L.); (M.L.)
- Guizhou Key Lab of Agro-Bioengineering, Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Academy of Agricultural Science, Guiyang 550006, China
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Khan SA, He J, Deng S, Zhang H, Liu G, Li S, Tang D, Zhang J, Shu Y, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between fast- and slow-growing king ratsnakes (Elaphe carinata). Comp Biochem Physiol B Biochem Mol Biol 2020; 248-249:110482. [DOI: 10.1016/j.cbpb.2020.110482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/18/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
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