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Suárez-Mesa R, Ros-Freixedes R, Laghouaouta H, Pena RN, Hernández-Ortiz B, Rondón-Barragán I, Estany J. Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing. Trop Anim Health Prod 2023; 55:154. [PMID: 37041265 PMCID: PMC10089996 DOI: 10.1007/s11250-023-03557-9] [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: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
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Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Houda Laghouaouta
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Byron Hernández-Ortiz
- Research and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
| | - Joan Estany
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
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Hou X, Zhang R, Yang M, Niu N, Wu J, Shu Z, Zhang P, Shi L, Zhao F, Wang L, Wang L, Zhang L. Metabolomics and lipidomics profiles related to intramuscular fat content and flavor precursors between Laiwu and Yorkshire pigs. Food Chem 2023; 404:134699. [DOI: 10.1016/j.foodchem.2022.134699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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Chen J, You R, Lv Y, Liu H, Yang G. Conjugated linoleic acid regulates adipocyte fatty acid binding protein expression via peroxisome proliferator-activated receptor α signaling pathway and increases intramuscular fat content. Front Nutr 2022; 9:1029864. [DOI: 10.3389/fnut.2022.1029864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Intramuscular fat (IMF) is correlated positively with meat tenderness, juiciness and taste that affected sensory meat quality. Conjugated linoleic acid (CLA) has been extensively researched to increase IMF content in animals, however, the regulatory mechanism remains unclear. Adipocyte fatty acid binding protein (A-FABP) gene has been proposed as candidates for IMF accretion. The purpose of this study is to explore the molecular regulatory pathways of CLA on intramuscular fat deposition. Here, our results by cell lines indicated that CLA treatment promoted the expression of A-FABP through activated the transcription factor of peroxisome proliferator-activated receptor α (PPARα). Moreover, in an animal model, we discovered that dietary supplemental with CLA significantly enhanced IMF deposition by up-regulating the mRNA and protein expression of PPARα and A-FABP in the muscle tissues of mice. In addition, our current study also demonstrated that dietary CLA increased mRNA expression of genes and enzymes involved in fatty acid synthesis and lipid metabolism the muscle tissues of mice. These findings suggest that CLA mainly increases the expression of A-FABP through PPARα signaling pathway and regulates the expression of genes and enzymes related to IMF deposition, thus increasing IMF content. These results contribute to better understanding the molecular mechanism of IMF accretion in animals for the improvement of meat quality.
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Malgwi IH, Halas V, Grünvald P, Schiavon S, Jócsák I. Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics. Animals (Basel) 2022; 12:ani12020150. [PMID: 35049772 PMCID: PMC8772548 DOI: 10.3390/ani12020150] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals. Abstract Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.
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Affiliation(s)
- Isaac Hyeladi Malgwi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
- Correspondence: ; Tel.: +39-33-17566768
| | - Veronika Halas
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Petra Grünvald
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
| | - Ildikó Jócsák
- Institute of Agronomy, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary;
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Association Between ATP Citrate Lyase (ACLY) Gene Polymorphism and Fattening, Slaughter and Pork Quality Traits in Polish Pigs. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The primary aim of this study was to estimate the relationship between ATP citrate lyase (ACLY) gene polymorphism (c.*523 T>C) and fattening and pork quality traits. Investigations were carried out on 526 pigs represented by three breeds: Polish Landrace (n=269), Polish Large White (n=189) and Puławska (n=68). ACLY genotypes were determined by PCR–RFLP method. It was demonstrated that the analyzed polymorphism had significant influence (P<0.05 and P≤0.01) on several economically important traits in pigs, e.g. average daily gain, average backfat thickness, lean meat percentage. The results obtained allow for application of c.*523 T>C polymorphism in breeding programs to improve the pig population in terms of fattening and slaughter traits. However, this breeding program may have a slight negative effect on meat texture parameters.
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Wang L, Zhang Y, Zhang B, Zhong H, Lu Y, Zhang H. Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs. BMC Genomics 2021; 22:441. [PMID: 34118873 PMCID: PMC8201413 DOI: 10.1186/s12864-021-07764-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Background Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation. Results A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR). Conclusions This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07764-2.
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Affiliation(s)
- Liyuan Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.,National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Yunfeng Lu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.
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Pothakam N, Supakankul P, Norseeda W, Liu G, Teltathum T, Naraballobh W, Khamlor T, Sringarm K, Mekchay S. Association of adipocytokine IL-1A and IL-6 genes with intramuscular fat content and fatty acid composition in pigs. Meat Sci 2021; 179:108554. [PMID: 34000609 DOI: 10.1016/j.meatsci.2021.108554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/22/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
Several adipocytokines are involved in inflammatory and immune responses as well as regulated fat deposition and lipid metabolism in mammals. This study aimed to verify the polymorphisms of the porcine interleukin 1A (IL-1A) and interleukin 6 (IL-6) genes and to assess their association with intramuscular fat (IMF) content and fatty acid (FA) composition in commercial crossbred pigs. Two single nucleotide polymorphisms (SNPs) of the porcine IL-1A g.43722547A>G and IL-6 g.91508173C>T loci were found to be segregating in these crossbred pigs. Furthermore, the porcine IL-1A g.43722547A>G polymorphism was found to be significantly associated with myristic, palmitic, palmitoleic, and eicosadienoic acid levels. Moreover, the porcine IL-6 g.91508173C>T polymorphism was significantly associated with IMF content and homolinolenic acid levels. These results suggest that the polymorphisms of the porcine IL-1A and IL-6 genes correlated with lipid content and FA composition and confirmed the importance of the adipocytokine IL-1A and IL-6 genes as candidate genes for fatty acid composition in the muscles of pigs.
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Affiliation(s)
- Nanthana Pothakam
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Worrarak Norseeda
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand.
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Pena RN, Noguera JL, García-Santana MJ, González E, Tejeda JF, Ros-Freixedes R, Ibáñez-Escriche N. Five genomic regions have a major impact on fat composition in Iberian pigs. Sci Rep 2019; 9:2031. [PMID: 30765794 PMCID: PMC6375979 DOI: 10.1038/s41598-019-38622-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content.
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Affiliation(s)
- R N Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - J L Noguera
- IRTA, Genètica i Millora Animal, 25198, Lleida, Spain
| | | | - E González
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - J F Tejeda
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - R Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain.,The Roslin Institute, Edinburgh University, Easter Bush, EH25 9RG, UK
| | - N Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain.
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Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, García-Casco J, Alves E, Škrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández AI, Óvilo C. Diversity across major and candidate genes in European local pig breeds. PLoS One 2018; 13:e0207475. [PMID: 30458028 PMCID: PMC6245784 DOI: 10.1371/journal.pone.0207475] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.
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Affiliation(s)
- María Muñoz
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | | | - Fabián García
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Jose M. Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | | | - Joan Tibau
- Programa de Genética y Mejora Animal, IRTA, Barcelona, Spain
| | - Goran Kušec
- University of Osijek, Faculty of Agrobiotechnical Sciences, Osijek, Croatia
| | | | | | - Juliette Riquet
- Génétique Physiologie et Système d’Elevage, INRA, Castanet-Tolosan, France
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Jose P. Araujo
- Instituto Politecnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Čedomir Radović
- Institute for Animal Husbandry-Pig Research Department, Belgrade-Zemun, Serbia
| | - Radomir Savić
- University of Belgrade, Faculty of agriculture, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of animal science, Faculty of agriculture, University of Zagreb, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy
| | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Cristina Óvilo
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
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Martínez-Montes ÁM, Fernández A, Muñoz M, Noguera JL, Folch JM, Fernández AI. Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed. PLoS One 2018. [PMID: 29522525 PMCID: PMC5844516 DOI: 10.1371/journal.pone.0190184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.
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Affiliation(s)
- Ángel M. Martínez-Montes
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Almudena Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - María Muñoz
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- Centro de I+D en Cerdo Ibérico, Zafra, Badajoz, Spain
| | - Jose Luis Noguera
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Lleida, Spain
| | - Josep M. Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Ana I. Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- * E-mail:
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Fernández AI, Óvilo C, Barragán C, Carmen Rodríguez M, Silió L, Folch JM, Fernández A. Validating porcine SCD haplotype effects on fatty acid desaturation and fat deposition in different genetic backgrounds. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Suzuki K. Genome-wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population. Anim Sci J 2017; 88:1482-1490. [PMID: 28402008 DOI: 10.1111/asj.12793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/15/2017] [Indexed: 12/24/2022]
Abstract
The aim of the present study was to detect quantitative trait loci affecting fatty acid composition in back fat and intramuscular fat in a Duroc pig population comprising seventh-generation pedigrees using genome-wide association studies (GWAS). In total, 305 animals were genotyped using single nucleotide polymorphisms (SNPs) array and five selected SNPs from regions containing known candidate genes related to fatty acid synthesis or metabolism. In total, 24 genome-wide significant SNP regions were detected in 12 traits, and 76 genome-wide suggestive SNP regions were detected in 33 traits. The Sus scrofa chromosome (SSC) 7 at 10.3 Mb was significantly associated with C17:0 in intramuscular fat, while the SSC9 at 13.6 Mb was significantly associated with C14:0 in intramuscular fat. The SSC12 at 1.0 Mb was significantly associated with C14:0 in back fat and the SSC14 at 121.0 Mb was significantly associated with C18:0 in intramuscular fat. These regions not only replicated previously reported loci containing some candidate genes involved in fatty acid composition (fatty acid synthase and stearoyl-CoA desaturase) but also included several additional related loci.
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Affiliation(s)
- Shuji Sato
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | | | - Takashi Kikuchi
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Sachiko Egawa
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, Japan
| | - Kimiko Kohira
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Tomomi Saito
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Hironori Sakuma
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Satoshi Miyashita
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, Japan
| | - Shinji Arata
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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Park HB, Han SH, Yoo CK, Lee JB, Kim JH, Baek KS, Son JK, Shin SM, Lim HT, Cho IC. Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F 2 intercross between Landrace and Korean native pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1061-1065. [PMID: 28111443 PMCID: PMC5494477 DOI: 10.5713/ajas.16.0562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/25/2016] [Accepted: 12/29/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F2 intercross between Landrace and Korean native pigs. METHODS Eighteen FA composition traits were measured in more than 960 F2 progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes. RESULTS We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10-39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance. CONCLUSION Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.
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Affiliation(s)
- Hee-Bok Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju 63243, Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea
| | - Ji-Hyang Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Kwang-Soo Baek
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Jun-Kyu Son
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Sang-Min Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea.,Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
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Choi JS, Jin SK, Jeong YH, Jung YC, Jung JH, Shim KS, Choi YI. Relationships between Single Nucleotide Polymorphism Markers and Meat Quality Traits of Duroc Breeding Stocks in Korea. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1229-38. [PMID: 27507182 PMCID: PMC5003982 DOI: 10.5713/ajas.16.0158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/09/2016] [Accepted: 08/10/2016] [Indexed: 11/27/2022]
Abstract
This study was conducted to determine the relationships of five intragenic single nucleotide polymorphism (SNP) markers (protein kinase adenosine monophosphate-activated γ3 subunit [PRKAG3], fatty acid synthase [FASN], calpastatin [CAST], high mobility group AT-hook 1 [HMGA1], and melanocortin-4 receptor [MC4R]) and meat quality traits of Duroc breeding stocks in Korea. A total of 200 purebred Duroc gilts from 8 sires and 40 dams at 4 pig breeding farms from 2010 to 2011 reaching market weight (110 kg) were slaughtered and their carcasses were chilled overnight. Longissimus dorsi muscles were removed from the carcass after 24 h of slaughter and used to determine pork properties including carcass weight, backfat thickness, moisture, intramuscular fat, pH24h, shear force, redness, texture, and fatty acid composition. The PRKAG3, FASN, CAST, and MC4R gene SNPs were significantly associated with the meat quality traits (p<0.003). The meats of PRKAG3 (A 0.024/G 0.976) AA genotype had higher pH, redness and texture than those from PRKAG3 GG genotype. Meats of FASN (C 0.301/A 0.699) AA genotype had higher backfat thickness, texture, stearic acid, oleic acid and polyunsaturated fatty acid than FASN CC genotype. While the carcasses of CAST (A 0.373/G 0.627) AA genotype had thicker backfat, and lower shear force, palmitoleic acid and oleic acid content, they had higher stearic acid content than those from the CAST GG genotype. The MC4R (G 0.208/A 0.792) AA genotype were involved in increasing backfat thickness, carcass weight, moisture and saturated fatty acid content, and decreasing unsaturated fatty acid content in Duroc meat. These results indicated that the five SNP markers tested can be a help to select Duroc breed to improve carcass and meat quality properties in crossbred pigs.
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Affiliation(s)
- J S Choi
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea.,Department of Animal Resources Technology and Swine Science & Technology Center, Gyeongnam National University of Science and Technology, Jinju 660-758, Korea
| | - S K Jin
- Department of Animal Resources Technology and Swine Science & Technology Center, Gyeongnam National University of Science and Technology, Jinju 660-758, Korea
| | - Y H Jeong
- Hanwoo Department, Korea Animal Improvement Association, Seoul 137-871, Korea
| | - Y C Jung
- Jung P&C Institute, Yongin 446-982, Korea
| | - J H Jung
- Jung P&C Institute, Yongin 446-982, Korea
| | - K S Shim
- Department of Animal Biotechnology, Chunbuk National University, Jeonju 561-756, Korea
| | - Y I Choi
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
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15
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Association of NLK polymorphisms with intramuscular fat content and fatty acid composition traits in pigs. Meat Sci 2016; 118:61-5. [DOI: 10.1016/j.meatsci.2016.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
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16
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Pig fatness in relation to FASN and INSIG2 genes polymorphism and their transcript level. Mol Biol Rep 2016; 43:381-9. [PMID: 26965892 PMCID: PMC4831998 DOI: 10.1007/s11033-016-3969-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/03/2016] [Indexed: 02/02/2023]
Abstract
Fat content and fatty acid (FA) profile influence meat quality in pigs. These parameters are important for consumers due to their preferences for healthy, high quality meat. The aim of this study was searching for polymorphisms and transcript levels of two positional and functional candidate genes, FASN and INSIG2, encoding proteins which take part in lipid metabolism. The molecular findings were analyzed in relation to fatness traits. Pigs of four commercial breeds were included: Polish Landrace (PL), Polish Large White (PLW), Duroc and Pietrain. DNA sequencing, 5′RACE technique and real time PCR and association analysis were applied. In total, 20 polymorphisms in 5′-flanking, 5′UTR and 3′UTR regions of FASN (12 novel polymorphisms) and INSIG2 (seven novel ones and one known) genes were found. Association study with fatness traits (PL n = 225, PLW n = 179) revealed that four polymorphisms (c.-2908G>A, c.-2335C>T, c.*42_43insCCCCA and c.*264A>G) of the FASN gene were associated with back fat thickness in PL and PLW. Since the polymorphisms were identified in regulatory sequences of the both genes also their transcript levels were studied in PLW (n = 23), PL (n = 22), Pietrain (n = 17) and Duroc (n = 23). The INSIG2 transcript level was positively correlated with monounsaturated FA contents in the longissimus thoracis et lumborum muscle. Several correlations were also found between three polymorphisms (c.*264A>G and c.-2335C>T in FASN, and c.-5527C>G in INSIG2) and the FA content. Our study showed that the FASN gene is a promising marker for subcutaneous fat tissue accumulation, while INSIG2 is a promising marker for FA composition.
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17
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Molnár J, Nagy T, Stéger V, Tóth G, Marincs F, Barta E. Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary. BMC Genomics 2014; 15:761. [PMID: 25193519 PMCID: PMC4162939 DOI: 10.1186/1471-2164-15-761] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/02/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs. RESULTS More than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes. CONCLUSIONS Genome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs.
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Affiliation(s)
| | | | | | | | - Ferenc Marincs
- Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, NARIC, Gödöllő, Hungary.
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18
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Lee KT, Lee YM, Alam M, Choi BH, Park MR, Kim KS, Kim TH, Kim JJ. A Whole Genome Association Study on Meat Quality Traits Using High Density SNP Chips in a Cross between Korean Native Pig and Landrace. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:1529-39. [PMID: 25049513 PMCID: PMC4093033 DOI: 10.5713/ajas.2012.12474] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 09/28/2012] [Accepted: 09/27/2012] [Indexed: 11/27/2022]
Abstract
A whole genome association (WGA) study was performed to detect significant polymorphisms for meat quality traits in an F2 cross population (N = 478) that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001), a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL) were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs), in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.
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Affiliation(s)
- K-T Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - Y-M Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - M Alam
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - B H Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - M R Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - T-H Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - J-J Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
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19
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Analysis of g.265T>C SNP of fatty acid synthase gene and expression study in skeletal muscle and backfat tissues of Italian Large White and Italian Duroc pigs. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Muñoz M, Rodríguez MC, Alves E, Folch JM, Ibañez-Escriche N, Silió L, Fernández AI. Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics 2013; 14:845. [PMID: 24295214 PMCID: PMC4046688 DOI: 10.1186/1471-2164-14-845] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 11/25/2013] [Indexed: 01/15/2023] Open
Abstract
Background Porcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to point out different genetic control of fatty acid composition conditional on the fat deposits. Those studies have been conducted using simple approaches and most of them focused on one single tissue. The first objective of the present study was to identify tissue-specific and tissue-consistent QTLs for fatty acid composition in backfat and intramuscular fat, combining linkage mapping and GWAS approaches and conducted under single and multitrait models. A second aim was to identify powerful candidate genes for these tissue-consistent QTLs, using microarray gene expression data and following a targeted genetical genomics approach. Results The single model analyses, linkage and GWAS, revealed over 30 and 20 chromosomal regions, 24 of them identified here for the first time, specifically associated to the content of diverse fatty acids in BF and IMF, respectively. The analyses with multitrait models allowed identifying for the first time with a formal statistical approach seven different regions with pleiotropic effects on particular fatty acids in both fat deposits. The most relevant were found on SSC8 for C16:0 and C16:1(n-7) fatty acids, detected by both linkage and GWAS approaches. Other detected pleiotropic regions included one on SSC1 for C16:0, two on SSC4 for C16:0 and C18:2, one on SSC11 for C20:3 and the last one on SSC17 for C16:0. Finally, a targeted eQTL scan focused on regions showing tissue-consistent effects was conducted with Longissimus and fat gene expression data. Some powerful candidate genes and regions were identified such as the PBX1, RGS4, TRIB3 and a transcription regulatory element close to ELOVL6 gene to be further studied. Conclusions Complementary genome scans have confirmed several chromosome regions previously associated to fatty acid composition in backfat and intramuscular fat, but even more, to identify new ones. Although most of the detected regions were tissue-specific, supporting the hypothesis that the major part of genes affecting fatty acid composition differs among tissues, seven chromosomal regions showed tissue-consistent effects. Additional gene expression analyses have revealed powerful target regions to carry the mutation responsible for the pleiotropic effects. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-845) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Muñoz
- INIA, Mejora Genética Animal, 28040 Madrid, Spain.
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21
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Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics 2013; 14:843. [PMID: 24289474 PMCID: PMC3879068 DOI: 10.1186/1471-2164-14-843] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/25/2013] [Indexed: 01/18/2023] Open
Abstract
Background In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particularly involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). Results High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. Conclusions These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases.
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Stachowiak M, Nowacka-Woszuk J, Szydlowski M, Switonski M. The ACACA and SREBF1 genes are promising markers for pig carcass and performance traits, but not for fatty acid content in the longissimus dorsi muscle and adipose tissue. Meat Sci 2013; 95:64-71. [DOI: 10.1016/j.meatsci.2013.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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Muñoz M, Fernández AI, Benítez R, Pena RN, Folch JM, Rodríguez MDC, Silió L, Alves E. Disentangling Two QTL on Porcine Chromosome 12 for Backfat Fatty Acid Composition. Anim Biotechnol 2013; 24:168-86. [DOI: 10.1080/10495398.2012.763130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Casellas J, Vidal O, Pena RN, Gallardo D, Manunza A, Quintanilla R, Amills M. Genetics of serum and muscle lipids in pigs. Anim Genet 2013; 44:609-19. [DOI: 10.1111/age.12049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 01/31/2023]
Affiliation(s)
- J. Casellas
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - R. N. Pena
- Departament de Producció Animal; Universitat de Lleida; Lleida 25198 Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | | | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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Rohrer G, Nonneman D, Miller R, Zerby H, Moeller S. Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs. Meat Sci 2012; 92:511-8. [DOI: 10.1016/j.meatsci.2012.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 04/10/2012] [Accepted: 05/18/2012] [Indexed: 11/28/2022]
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Abstract
Fat affects meat quality, value and production efficiency as well as providing energy reserves for pregnancy and lactation in farm livestock. Leptin, the adipocyte product of the obese (ob) gene, was quickly seen as a predictor of body fat content in animals approaching slaughter and an aid to assessing reproductive readiness in females. Its participation in inflammation and immune responses that help animals survive infection and trauma has clear additional relevance to meat and milk production. Furthermore, almost a decade of discoveries of nucleotide polymorphisms in the leptin and leptin receptor genes has suggested useful applications relating to feed intake regulation, the efficiency of feed use, the composition of growth, the timing of puberty, mammogenesis and mammary gland function and fertility in cattle, pigs and poultry. The current review attempts to summarise where research has taken us in each of these aspects and speculates on where future research might lead.
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Muñoz M, Alves E, Corominas J, Folch JM, Casellas J, Noguera JL, Silió L, Fernández AI. Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data. Front Genet 2012; 2:101. [PMID: 22303395 PMCID: PMC3262226 DOI: 10.3389/fgene.2011.00101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 12/14/2011] [Indexed: 11/13/2022] Open
Abstract
Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content.
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Affiliation(s)
- María Muñoz
- Departament Mejora Genética Animal, Instituto Nacional de Investigaciones Agrarias Madrid, Spain
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Quintanilla R, Pena RN, Gallardo D, Cánovas A, Ramírez O, Díaz I, Noguera JL, Amills M. Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects1. J Anim Sci 2011; 89:2963-71. [DOI: 10.2527/jas.2011-3974] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Kim SW, Choi YI, Choi JS, Kim JJ, Choi BH, Kim TH, Kim KS. Porcine Fatty Acid Synthase Gene Polymorphisms Are Associated with Meat Quality and Fatty Acid Composition. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.3.356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Maharani D, Jo CR, Jeon JT, Lee JH. Quantitative Trait Loci and Candidate Genes Affecting Fatty Acid Composition in Cattle and Pig. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.3.325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Uemoto Y, Soma Y, Sato S, Ishida M, Shibata T, Kadowaki H, Kobayashi E, Suzuki K. Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Anim Genet 2011; 43:27-34. [DOI: 10.1111/j.1365-2052.2011.02218.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dervishi E, Serrano C, Joy M, Serrano M, Rodellar C, Calvo JH. The effect of feeding system in the expression of genes related with fat metabolism in semitendinous muscle in sheep. Meat Sci 2011; 89:91-7. [PMID: 21543161 DOI: 10.1016/j.meatsci.2011.04.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/05/2011] [Accepted: 04/06/2011] [Indexed: 12/30/2022]
Abstract
The effect of feeding system on the expression of LPL, ACACA, FASN, FABP4, DGAT1, SCD, CPT1B, PRKAA2, LEP, SREBP1, PPARG, PPARA and CEBPB genes in semitendinous muscle was studied. Forty-four single born male lambs of the Rasa Aragonesa breed, allocated to four different dietary treatments, were used: grazing alfalfa, grazing alfalfa with supplement for lambs, indoor lambs with grazing ewes and drylot. Significant differences were found in the expression of genes LPL, ACACA, FASN, FABP4, CPT1B and SCD. Genes related to adipogenesis (LPL, ACACA, FASN, FABP4, and SCD) are up-regulated in the intensive groups. In grazing groups CPT1B gene expression, related to β-oxidation process, is up-regulated. The relative expression of CPT1B was 1.54 fold higher in ALF+S, and 0.43 and 0.37 fold lower in IND- GRE and IND, respectively. The results support the hypothesis that changes in fatty acid profile due to feeding system implicate changes in the mRNA expression level of genes related with fat metabolism. Feeding strategy is an important tool to manipulate intramuscular fatty acid profile in meat through altering gene expression of enzymes related with fat metabolism.
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Affiliation(s)
- E Dervishi
- Unidad de Tecnología en Producción Animal, CITA, Zaragoza, Spain.
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García-Fernández M, Gutiérrez-Gil B, Garcia-Gámez E, Arranz JJ. Identification of single nucleotide polymorphisms in the ovine acetyl-CoA carboxylase-alpha gene. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2009.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Tian J, Wang S, Wang Q, Leng L, Hu X, Li H. A single nucleotide polymorphism of chicken acetyl-CoA carboxylase A gene associated with fatness traits. Anim Biotechnol 2010; 21:42-50. [PMID: 20024786 DOI: 10.1080/10495390903347009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Acetyl-CoA carboxylase alpha (ACCalpha) is a major rate-limiting enzyme in the biogenesis of long-chain fatty acids. It can catalyze the carboxylation of acetyl-CoA to form malonyl-CoA that plays a key role in the regulation of fatty acid metabolism. The objective of the present study was to investigate the associations of ACCalpha gene polymorphisms with chicken growth and body composition traits. The Northeast Agricultural University broiler lines divergently selected for abdominal fat content and the Northeast Agricultural University F(2) Resource Population were used in the current study. Body weight and body composition traits were measured in the aforementioned two populations. A synonymous mutation was detected in the exon 19 region of ACCalpha gene, then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to genotype all the individuals derived from the aforementioned populations. Association analysis revealed that the polymorphism was associated with abdominal fat weight and percentage of abdominal fat in the two populations. The results suggested that ACCalpha gene could be a candidate locus or linked to a major gene that affects abdominal fat content in the chicken.
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Affiliation(s)
- Jianwei Tian
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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García-Fernández M, Gutiérrez-Gil B, García-Gámez E, Sánchez JP, Arranz JJ. The identification of QTL that affect the fatty acid composition of milk on sheep chromosome 11. Anim Genet 2009; 41:324-8. [PMID: 19968648 DOI: 10.1111/j.1365-2052.2009.02000.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we analysed 11 genetic markers localized on OAR11 in a commercial population of Spanish Churra sheep to detect QTL that underlie milk fatty acid (FA) composition traits. Following a daughter design, we analysed 799 ewes distributed in 15 half-sib families. Eight microsatellite markers and three novel SNPs identified in two genes related to fatty acid metabolism, acetyl-CoA carboxylase alpha (ACACA) and fatty acid synthase (FASN), were genotyped in the whole population under study. The phenotypic traits considered in the study included 22 measurements related to the FA composition of the milk and three other milk production traits (milk protein percentage, milk fat percentage and milk yield). Across-family regression analysis revealed four significant QTL at the 5% chromosome-wise level influencing contents of capric acid (C10:0), lauric acid (C12:0), linoleic conjugated acid (CLA) and polyunsaturated fatty acids (PUFA) respectively. The peaks of the QTL affecting C10:0 and PUFA contents in milk map close to the FASN gene, which has been evaluated as a putative positional candidate for these QTL. The QTL influencing C12:0 content reaches its maximum significance at 58 cM, close to the gene coding for the glucose-dependent insulinotropic polypeptide. We were not able to find any candidate genes related to fat metabolism at the QTL influencing CLA content, which is located at the proximal end of the chromosome. Further research efforts will be needed to confirm and refine the QTL locations reported here.
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Affiliation(s)
- M García-Fernández
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, 24071, León, Spain
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Uemoto Y, Sato S, Ohnishi C, Terai S, Komatsuda A, Kobayashi E. The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan × Duroc crossbred population. J Anim Sci 2009; 87:3470-6. [DOI: 10.2527/jas.2009-1917] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gallardo D, Quintanilla R, Varona L, Díaz I, Ramírez O, Pena RN, Amills M. Polymorphism of the pigacetyl-coenzyme A carboxylase αgene is associated with fatty acid composition in a Duroc commercial line. Anim Genet 2009; 40:410-7. [DOI: 10.1111/j.1365-2052.2009.01854.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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A critical analysis of production-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig. Mamm Genome 2008; 19:591-617. [PMID: 18836775 DOI: 10.1007/s00335-008-9141-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
Abstract
Increasing productivity is one of the main objectives in animal production. Traditional breeding methods have led to increased gains in some traits but gains are not easily attainable in traits with low heritabilities. Exploiting the genetic variations underlying desired phenotypes is the goal of today's animal producers. Such positive genetic variants must, however, be known before possible application. Consequently, candidate genes of traits of interest have been searched for possible relationships with such traits or to explain reported quantitative trait loci (QTL) for such traits. DNA variants or polymorphisms have been identified in many such genes and their relationships with production traits determined. However, only a few genes have been evaluated, given the wealth of information on reported QTL for production traits, and in most cases genes are only partially investigated. This review presents available information on DNA variants for production traits and discusses steps that are required for effective utilization of this information for successful marker-assisted selection programs.
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