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EL Nagar AG, Heddi I, Sosa-Madrid BS, Blasco A, Hernández P, Ibáñez-Escriche N. Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits. Animals (Basel) 2023; 13:3071. [PMID: 37835677 PMCID: PMC10571580 DOI: 10.3390/ani13193071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from -0.53 to -0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.
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Affiliation(s)
- Ayman G. EL Nagar
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt
| | - Imen Heddi
- Centro Regional de Selección y Reproducción Animal (CERSYRA), Av. del Vino, 10, 13300 Valdepeñas, Spain
| | - Bolívar Samuel Sosa-Madrid
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
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Gajaweera C, Kang DH, Lee DH, Kim YK, Park BH, Chang SS, Kim UH, Lee SH, Chung KY. Development of nutrigenomic based precision management model for Hanwoo steers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:596-610. [PMID: 37332286 PMCID: PMC10271920 DOI: 10.5187/jast.2023.e38] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/25/2023] [Accepted: 04/13/2023] [Indexed: 06/20/2023]
Abstract
Focusing high marble deposition, Hanwoo feedlot system uses high-energy diet over the prolonged fattening period. However, due to the individual genetic variation, around 40% of them are graded into inferior quality grades (QG), despite they utilized the same resources. Therefore, focusing on development of a nutrigenomic based precision management model, this study was to evaluated the response to the divergent selection on genetic merit for marbling score (MS), under different dietary total digestible nutrient (TDN) levels. Total of 111 calves were genotyped and initially grouped according to estimated breeding value (high and low) for marbling score (MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2 × 2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness (BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p > 0.05) on the MS. Furthermore, no genetic-by-nutrition interaction for MS (p > 0.05) was also observed. The present results showed no correlation response on BFT (p > 0.05), which indicates that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1++ and QG1+) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1++ animals among the high-genetic group by further increasing the dietary energy content. Overall, this precision management strategy suggests the importance of adopting an MS based initial genetic grouping system for Hanwoo steers with a subsequent divergent management based on dietary energy level.
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Affiliation(s)
- Chandima Gajaweera
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
- Department of Animal Science, Faculty of Agriculture, University of Ruhuna, Matara 81100, Sri Lanka
| | - Dong Hun Kang
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Yeong-Kuk Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Bo Hye Park
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
| | - Sun Sik Chang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Ui Hyung Kim
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Ki Yong Chung
- Department of Livestock, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea
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Rahayu AP, Hartatik T, Purnomoadi A, Kurnianto E. Association of single nucleotide polymorphisms in the fatty acid synthase, LOC514211, and fat mass and obesity-associated genes with milk traits in Indonesian-Holstein dairy cattle. Vet World 2019; 12:1160-1166. [PMID: 31528048 PMCID: PMC6702549 DOI: 10.14202/vetworld.2019.1160-1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/25/2019] [Indexed: 12/02/2022] Open
Abstract
Aim: The study aimed to identify fatty acid synthase (FASN), LOC514211, and fat mass and obesity-associated (FTO) gene polymorphisms and to investigate their associations with milk traits in an Indonesian-Holstein dairy cow population. Materials and Methods: A total of 100 Indonesian-Holstein cows consisting of 50 heads (0th generation; G0) and 50 heads of their daughters (1st generation; G1) were used. Polymerase chain reaction-restriction fragment length polymorphism was performed to genotype three single nucleotide polymorphisms: rs41919985 in the FASN gene, rs42688595 in the LOC514211 gene, and g.1371T>A in the FTO gene. Results: FASN rs41919985 was associated with milk protein percentage (p<0.05), FTO g.1371T>A was associated with milk fat percentage (p<0.05), and LOC514211 rs42688595 was not associated with any trait (p>0.05). Heterozygote variants showed a higher protein percentage for FASN and the highest fat percentage for FTO. These associations were consistent in the G0 and G1 populations. Conclusion: Our results indicate that the milk protein and fat percentages can be improved by increasing the frequency of the AG genotype of FASN and the AT genotype of FTO, respectively.
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Affiliation(s)
- Amalia Puji Rahayu
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Diponegoro University, Semarang 50275, Indonesia.,Agriculture, Fisheries and Food Center of Semarang Regency, Ungaran 50514, Indonesia
| | - Tety Hartatik
- Department of Animal Breeding and Reproduction, Faculty of Animal Sciences, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Agung Purnomoadi
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Diponegoro University, Semarang 50275, Indonesia
| | - Edy Kurnianto
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Diponegoro University, Semarang 50275, Indonesia
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Deciphering signature of selection affecting beef quality traits in Angus cattle. Genes Genomics 2017; 40:63-75. [PMID: 29892901 DOI: 10.1007/s13258-017-0610-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/14/2017] [Indexed: 12/16/2022]
Abstract
Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.
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Shin S, Hong C, Song S, Ahn K, Chung E. Single nucleotide polymorphisms in exomes of high- and low-marbled meats in Korean cattle. Anim Genet 2016; 47:756-757. [DOI: 10.1111/age.12479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sungchul Shin
- Division of Animal Science and Resources; College of Life Science and Natural Resources; Sangji University; 660 Usnadong Wonju Gangwondo 220-702 Republic of Korea
| | - Changpyo Hong
- Theragen Etex Bio Institute, Theragen Etex; Suwon 443-270 Republic of Korea
| | - Sanghoon Song
- Theragen Etex Bio Institute, Theragen Etex; Suwon 443-270 Republic of Korea
| | - Kung Ahn
- Theragen Etex Bio Institute, Theragen Etex; Suwon 443-270 Republic of Korea
| | - Euiryong Chung
- Division of Animal Science and Resources; College of Life Science and Natural Resources; Sangji University; 660 Usnadong Wonju Gangwondo 220-702 Republic of Korea
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Shin SC, Chung ER. Identification of differentially expressed genes between high and low marbling score grades of the longissimus lumborum muscle in Hanwoo (Korean cattle). Meat Sci 2016; 121:114-118. [PMID: 27305318 DOI: 10.1016/j.meatsci.2016.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 11/25/2022]
Abstract
We conducted DD-RT-PCR analysis to identify differentially expressed genes between high and low marbling score groups with extremely different IMF content of the longissimus lumborum muscles in Hanwoo. We detected 137 DEGs between two marbling score groups. Of these DEGs, 41 DEGs were highly expressed in the high marbling score group, whereas 96 DEGs showed a higher expression in the low marbling score group. Among them, we selected eight DEGs exhibiting the greatest differential expression levels between two marbling score groups. These genes could be classified as five candidate genes according to homology to known genes and biological functions. The expression of four DEGs except for ATP6 gene was confirmed by qRT-PCR. The TPI1 gene was significantly higher expressed at the high marbling group, whereas ACTA1, TNNT1 and MDH2 genes were significantly higher expressed at the low marbling group. Therefore, the TPI1 gene was up-regulated, suggesting that this gene may have an important function related to IMF deposition.
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Affiliation(s)
- S C Shin
- Division of Animal Science and Resources, College of Life Science and Natural Resources, Sangji University, 660 Usnadong, Wonju, Gangwondo 220-702, South Korea
| | - E R Chung
- Division of Animal Science and Resources, College of Life Science and Natural Resources, Sangji University, 660 Usnadong, Wonju, Gangwondo 220-702, South Korea.
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