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Morris KM, Sutton K, Girma M, Sánchez-Molano E, Solomon B, Esatu W, Dessie T, Vervelde L, Psifidi A, Hanotte O, Banos G. Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia. Front Genet 2024; 15:1383609. [PMID: 38706792 PMCID: PMC11066160 DOI: 10.3389/fgene.2024.1383609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background In sub-Saharan Africa, 80% of poultry production is on smallholder village farms, where chickens are typically reared outdoors in free-ranging conditions. There is limited knowledge on chickens' phenotypic characteristics and genetics under these conditions. Objective The present is a large-scale study set out to phenotypically characterise the performance of tropically adapted commercial chickens in typical smallholder farm conditions, and to examine the genetic profile of chicken phenotypes associated with growth, meat production, immunity, and survival. Methods A total of 2,573 T451A dual-purpose Sasso chickens kept outdoors in emulated free-ranging conditions at the poultry facility of the International Livestock Research Institute in Addis Ababa, Ethiopia, were included in the study. The chickens were raised in five equally sized batches and were individually monitored and phenotyped from the age of 56 days for 8 weeks. Individual chicken data collected included weekly body weight, growth rate, body and breast meat weight at slaughter, Newcastle Disease Virus (NDV) titres and intestinal Immunoglobulin A (IgA) levels recorded at the beginning and the end of the period of study, and survival rate during the same period. Genotyping by sequencing was performed on all chickens using a low-coverage and imputation approach. Chicken phenotypes and genotypes were combined in genomic association analyses. Results We discovered that the chickens were phenotypically diverse, with extensive variance levels observed in all traits. Batch number and sex of the chicken significantly affected the studied phenotypes. Following quality assurance, genotypes consisted of 2.9 million Single Nucleotide Polymorphism markers that were used in the genomic analyses. Results revealed a largely polygenic mode of genetic control of all phenotypic traits. Nevertheless, 15 distinct markers were identified that were significantly associated with growth, carcass traits, NDV titres, IgA levels, and chicken survival. These markers were located in regions harbouring relevant annotated genes. Conclusion Results suggest that performance of chickens raised under smallholder farm conditions is amenable to genetic improvement and may inform selective breeding programmes for enhanced chicken productivity in sub-Saharan Africa.
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Affiliation(s)
- Katrina M. Morris
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Kate Sutton
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Mekonnen Girma
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | | | - Bersabhe Solomon
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Wondmeneh Esatu
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Lonneke Vervelde
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Androniki Psifidi
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Royal Veterinary College, Hatfield, United Kingdom
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Georgios Banos
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Scotland’s Rural College (SRUC), Animal and Veterinary Sciences, Midlothian, United Kingdom
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Seo YJ, Lim B, Kim DY, Lim KS, Kim JM. Regulation of Swine Growth by Backfat Tissue during Growing and Finishing Stages. Animals (Basel) 2021; 11:ani11123511. [PMID: 34944286 PMCID: PMC8698142 DOI: 10.3390/ani11123511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Swine have a large influence on livestock animals. In particular, Korean native pigs (KNPs) have unique traits in their body composition including lipids and proteins. In this study, we performed RNA-sequencing analysis to identify porcine transcriptomic changes during growing and finishing stages in the backfat tissue of KNP and Yorkshire pig crossbreeds. Enrichment analysis revealed that differentially expressed genes (DEGs) were significantly influenced by lipid metabolism and hormonal changes. Network analysis showed that the LEP and ACTC1 genes were connected with significant terminologies which resulted from up- and down-regulated DEGs. The results of our analysis indicate that backfat tissue could regulate swine biology during stages of growth. Consequently, our analysis provided comprehensive understanding for transcriptomic changes during growth periods. Abstract Recently, interest in the function of pig backfat (BF) has increased in the field of livestock animals, and many transcriptome-based studies using commercial pig breeds have been conducted. However, there is a lack of comprehensive studies regarding the biological mechanisms of Korean native pigs (KNPs) and Yorkshire pig crossbreeds. In this study, therefore, BF samples of F1 crossbreeds of KNPs and Yorkshire pigs were investigated to identify differentially expressed genes (DEGs) and their related terms using RNA-sequencing analysis. DEG analysis identified 611 DEGs, of which 182 were up-regulated and 429 were down-regulated. Lipid metabolism was identified in the up-regulated genes, whereas growth and maturation-related terminologies were identified in the down-regulated genes. LEP and ACTC1 were identified as highly connected core genes during functional gene network analysis. Fat tissue was observed to affect lipid metabolism and organ development due to hormonal changes driven by transcriptional alteration. This study provides a comprehensive understanding of BF contribution to crossbreeds of KNPs and Yorkshire pigs during growth periods.
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Affiliation(s)
- Young-Jun Seo
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (Y.-J.S.); (B.L.); (D.-Y.K.)
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (Y.-J.S.); (B.L.); (D.-Y.K.)
| | - Do-Young Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (Y.-J.S.); (B.L.); (D.-Y.K.)
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA;
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea; (Y.-J.S.); (B.L.); (D.-Y.K.)
- Correspondence: ; Tel.: +82-31-670-3263; Fax: +82-31-675-3108
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Balatsky VN, Oliinychenko YK, Buslyk TV, Bankovska IB, Korinnyi SN, Saienko AM, Pochernyaev KF. Associations of QTL Region Genes of Chromosome 2 with Meat Quality Traits and Productivity of the Ukrainian Large White Pig Breed. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Velez-Irizarry D, Casiro S, Daza KR, Bates RO, Raney NE, Steibel JP, Ernst CW. Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs. BMC Genomics 2019; 20:3. [PMID: 30606113 PMCID: PMC6319002 DOI: 10.1186/s12864-018-5386-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
Background Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, little is known about the genes and molecular mechanisms involved in this process. Evaluating transcriptomic profiles of skeletal muscle during the initial steps leading to the conversion of muscle to meat can identify key regulators of polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker genotypes allows identification of genomic regions that control gene expression, referred to as expression quantitative trait loci (eQTL). In this study, we perform eQTL analyses to identify potential candidate genes and molecular markers regulating growth and meat quality traits in pigs. Results Messenger RNA transcripts obtained with RNA-seq of longissimus dorsi muscle from 168 F2 animals from a Duroc x Pietrain pig resource population were used to estimate gene expression variation subject to genetic control by mapping eQTL. A total of 339 eQTL were mapped (FDR ≤ 0.01) with 191 exhibiting local-acting regulation. Joint analysis of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for meat quality, carcass composition and growth traits. Ten of these pQTL were for meat quality phenotypes that co-localized with one eQTL on SSC2 (8.8-Mb region) and 11 eQTL on SSC15 (121-Mb region). Biological processes identified for co-localized eQTL genes include calcium signaling (FERM, MRLN, PKP2 and CHRNA9), energy metabolism (SUCLG2 and PFKFB3) and redox hemostasis (NQO1 and CEP128), and results support an important role for activation of the PI3K-Akt-mTOR signaling pathway during the initial conversion of muscle to meat. Conclusion Co-localization of eQTL with pQTL identified molecular markers significantly associated with both economically important phenotypes and gene transcript abundance. This study reveals candidate genes contributing to variation in pig production traits, and provides new knowledge regarding the genetic architecture of meat quality phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-018-5386-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sebastian Casiro
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Kaitlyn R Daza
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Ronald O Bates
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
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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: 17] [Impact Index Per Article: 2.8] [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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Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Trop Anim Health Prod 2017; 49:1657-1662. [PMID: 28801813 DOI: 10.1007/s11250-017-1373-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022]
Abstract
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
| | - Ayoub Farhadi
- Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, P.O. Box -578, Sari, Iran
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