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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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Wang S, Raza SHA, Zhang K, Mei C, Alamoudi MO, Aloufi BH, Alshammari AM, Zan L. Selection signatures of Qinchuan cattle based on whole-genome sequences. Anim Biotechnol 2023; 34:1483-1491. [PMID: 35152846 DOI: 10.1080/10495398.2022.2033252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on Fst, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that KMT2E, LTBP1 and NIPBL were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. ARIH2, DACT1 and DNM2, et al. are related to meat quality. Meanwhile, TBXA2R can be used as a gene associated with reproductive function, and USH2A affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.
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Affiliation(s)
- Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Muna O Alamoudi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | - Bandar H Aloufi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
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3
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Fernández-Barroso MÁ, García-Casco JM, Núñez Y, Ramírez-Hidalgo L, Matos G, Muñoz M. Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile. Anim Genet 2022; 53:352-367. [PMID: 35355298 PMCID: PMC9314091 DOI: 10.1111/age.13195] [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: 07/01/2021] [Revised: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 11/30/2022]
Abstract
Meat color is the first perceived sensory feature and one of the most important quality traits. Myoglobin is the main pigment in meat, giving meat its characteristic cherry‐red color, highly appreciated by the consumers. In the current study, we used the RNA‐seq technique to characterize the longissimus dorsi muscle transcriptome in two groups of Iberian pigs with divergent breeding values for myoglobin content. As a result, we identified 57 differentially expressed genes and transcripts (DEGs). Moreover, we have validated the RNA‐seq expression of a set of genes by quantitative PCR (qPCR). Functional analyses revealed an enrichment of DEGs in biological processes related to oxidation (HBA1), lipid metabolism (ECH1, PLA2G10, PLD2), inflammation (CHST1, CD209, PLA2G10), and immune system (CD209, MX2, LGALS3, LGALS9). The upstream analysis showed a total of five transcriptional regulatory factors and eight master regulators that could moderate the expression of some DEGs, highlighting SPI1 and MAPK1, since they regulate the expression of DEGs involved in immune defense and inflammatory processes. Iberian pigs with high myoglobin content also showed higher expression of the HBA1 gene and both molecules, myoglobin and hemoglobin, have been described as having a protective effect against oxidative and inflammatory processes. Therefore, the HBA1 gene is a very promising candidate gene to harbor polymorphisms underlying myoglobin content, whereby further studies should be carried out for its potential use in an Iberian pig selection program.
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Affiliation(s)
- Miguel Ángel Fernández-Barroso
- Centro Nacional de I+D del Cerdo Ibérico, INIA-CSIC, Zafra, Spain.,Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - Juan María García-Casco
- Centro Nacional de I+D del Cerdo Ibérico, INIA-CSIC, Zafra, Spain.,Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | | | - Gema Matos
- Sánchez Romero Carvajal-Jabugo, SRC, Huelva, Spain
| | - María Muñoz
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
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Hidalgo J, Cesarani A, Garcia A, Sumreddee P, Larios N, Mancin E, García JG, Núñez R, Ramírez R. Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico. Animals (Basel) 2021; 11:ani11020321. [PMID: 33525405 PMCID: PMC7911603 DOI: 10.3390/ani11020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The objective of this study was to evaluate the genetic background and inbreeding depression in the Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH). Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals; 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. A 1% increase in inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to sustainable breeding programs for the Mexican Romosinuano cattle breed. Abstract The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.
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Affiliation(s)
- Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Alberto Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Andre Garcia
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (J.H.); (A.C.); (A.G.)
| | - Pattarapol Sumreddee
- Department of Livestock Development, Bureau of Biotechnology in Livestock Production, Pathum Thani 12000, Thailand;
| | - Neon Larios
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment-DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy;
| | - José Guadalupe García
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
- Correspondence:
| | - Rafael Núñez
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
| | - Rodolfo Ramírez
- Departamento de Zootecnia, Posgrado en Producción Animal, Universidad Autónoma Chapingo, Chapingo 56230, Mexico; (N.L.); (R.N.); (R.R.)
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Mei C, Gui L, Hong J, Raza SHA, Aorigele C, Tian W, Garcia M, Xin Y, Yang W, Zhang S, Zan L. Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:959-967. [PMID: 33614243 PMCID: PMC7868925 DOI: 10.1016/j.omtn.2020.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.
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Affiliation(s)
- Chugang Mei
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
| | - Linsheng Gui
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Qinghai University, Xining 810008, China
| | - Jieyun Hong
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Yunnan Agricultural University, Kunming 650031, China
| | | | - Chen Aorigele
- Inner Mongolia Agricultural University, Hohhot 010000, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling 712100, China
| | | | - Yaping Xin
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wucai Yang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Song Zhang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linsen Zan
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
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6
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Silva DBS, Fonseca LFS, Pinheiro DG, Magalhães AFB, Muniz MMM, Ferro JA, Baldi F, Chardulo LAL, Schnabel RD, Taylor JF, Albuquerque LG. Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality. Sci Rep 2020; 10:14701. [PMID: 32895448 PMCID: PMC7477197 DOI: 10.1038/s41598-020-71783-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/04/2020] [Indexed: 01/31/2023] Open
Abstract
Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3′ splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.
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Affiliation(s)
- Danielly B S Silva
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
| | - Larissa F S Fonseca
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Daniel G Pinheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ana F B Magalhães
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Maria M M Muniz
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Jesus A Ferro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil
| | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil
| | - Luis A L Chardulo
- School of Veterinary and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil. .,National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil.
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Zhao Z, Tian H, Shi B, Jiang Y, Liu X, Hu J. Transcriptional Regulation of the Bovine Fatty Acid Transport Protein 1 Gene by Krüppel-Like Factors 15. Animals (Basel) 2019; 9:ani9090654. [PMID: 31491871 PMCID: PMC6769441 DOI: 10.3390/ani9090654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The nutritional value and qualities of beef are enhanced when the unsaturated fatty acid content is increased. Fatty acid transport protein 1 (FATP1), also called SLC27A1, an integral membrane protein that facilitates long-chain fatty acid influx, is involved in the genetic network for oleic acid synthesis in beef. Polymorphisms in bovine SLC27A1 gene are most significantly associated with oleic acid. Its expression exhibits significant positive correlations with bovine intramuscular fat content in the longissimus thoracis muscle. However, the transcription factors that contribute to the control and regulation of its expression have not been characterized extensively. In this study, we determined the tissue distribution of SLC27A1 mRNA and found that bovine SLC27A1 was highly expressed in subcutaneous adipose tissue and the longissimus thoracis muscle. Furthermore, we analyzed the molecular mechanisms involved in SLC27A1 regulation and found that the transcriptional activity of SLC27A1 gene was dependent on KLF15 transcription factor. These results may lead to an enhanced understanding of the regulation of SLC27A1 expression in other models, as well as provide new insights into the regulatory mechanism and biological functions of the SLC27A1 gene in determining the lipid composition in beef. Abstract Oleic acid is a major monounsaturated fatty acid, which accounts for about 33% of the fatty acid content in beef and is considered to have the least negative effect on serum cholesterol levels. Fatty acid transport protein 1 (FATP1), an integral membrane protein that facilitates long-chain fatty acid (LCFA) influx, is involved in the genetic network for oleic acid synthesis in beef. Its expression exhibits significant positive correlations with intramuscular fat (IMF) content in the longissimus thoracis. However, the expression mechanism of SLC27A1 or FATP1 is still unclear. To elucidate the molecular mechanisms involved in bovine SLC27A1 regulation, we cloned and characterized the promoter region of SLC27A1. By applying 5′-rapid amplification of cDNA end analysis, we identified two alternative splice variants of this gene. Using a series of 5′ deletion promoter plasmids in luciferase reporter assays, we found that the core promoter was 96 base pairs upstream from the transcription initiation site. Electrophoretic mobility shift assay combined with a site-directed mutation experiment demonstrated that KLF15 binding to the promoter region drives the SLC27A1 transcription. KLF15 plays an essential role in adipogenesis and skeletal muscle lipid flux. Thus, these results might provide further information on the regulatory roles of SLC27A1 gene in mediating the lipid composition in beef.
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Affiliation(s)
- Zhidong Zhao
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Hongshan Tian
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Bingang Shi
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yanyan Jiang
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xiu Liu
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiang Hu
- College of Animal Science and Technology & Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China.
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Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L. Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics 2019; 112:831-836. [PMID: 31145994 DOI: 10.1016/j.ygeno.2019.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chuping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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9
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Bertolini F, Servin B, Talenti A, Rochat E, Kim ES, Oget C, Palhière I, Crisà A, Catillo G, Steri R, Amills M, Colli L, Marras G, Milanesi M, Nicolazzi E, Rosen BD, Van Tassell CP, Guldbrandtsen B, Sonstegard TS, Tosser-Klopp G, Stella A, Rothschild MF, Joost S, Crepaldi P. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genet Sel Evol 2018; 50:57. [PMID: 30449276 PMCID: PMC6240954 DOI: 10.1186/s12711-018-0421-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Claire Oget
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Gennaro Catillo
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Roberto Steri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
| | | | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
| | | | - Gwenola Tosser-Klopp
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Alessandra Stella
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - the AdaptMap consortium
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), 2800 Lyngby, Denmark
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326 Castanet Tolosan, France
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Recombinetics Inc, St Paul, 55104 MN USA
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015 Monterotondo, Roma, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, 29100 Piacenza, Italy
- Fondazione Parco Tecnologico Padano (PTP), 26900 Lodi, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD 20705 USA
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830 Tjele, Denmark
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10
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Magalhães AFB, de Camargo GMF, Fernandes GA, Gordo DGM, Tonussi RL, Costa RB, Espigolan R, Silva RMDO, Bresolin T, de Andrade WBF, Takada L, Feitosa FLB, Baldi F, Carvalheiro R, Chardulo LAL, de Albuquerque LG. Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle. PLoS One 2016; 11:e0157845. [PMID: 27359122 PMCID: PMC4928802 DOI: 10.1371/journal.pone.0157845] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/06/2016] [Indexed: 01/19/2023] Open
Abstract
The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.
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Affiliation(s)
- Ana F. B. Magalhães
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Gregório M. F. de Camargo
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Gerardo A. Fernandes
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Daniel G. M. Gordo
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael L. Tonussi
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Raphael B. Costa
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael Espigolan
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Rafael M. de O. Silva
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Tiago Bresolin
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Willian B. F. de Andrade
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Luciana Takada
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Fabieli L. B. Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
| | - Luis A. L. Chardulo
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
- Departamento de Melhoramento e Nutrição Animal, Faculdade de Medicina Veterinária e Zootecnia, Botucatu, São Paulo, Brazil
| | - Lucia G. de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Jaboticabal, São Paulo, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, Brasília, Distrito Federal, Brazil
- * E-mail:
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11
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Jiang Z, Wang H, Michal JJ, Zhou X, Liu B, Woods LCS, Fuchs RA. Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development. Int J Biol Sci 2016; 12:100-8. [PMID: 26722221 PMCID: PMC4679402 DOI: 10.7150/ijbs.13498] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/07/2015] [Indexed: 12/04/2022] Open
Abstract
Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are used for whole genome sequencing or resequencing. In order to improve the cost-effectiveness of the process, however, the research community has mainly focused on developing genome-wide sampling sequencing (GWSS) methods, a collection of reduced genome complexity sequencing, reduced genome representation sequencing and selective genome target sequencing. Here we review the major steps involved in library preparation, the types of adapters used for ligation and the primers designed for amplification of ligated products for sequencing. Unfortunately, currently available GWSS methods have their drawbacks, such as inconsistency in the number of reads per sample library, the number of sites/targets per individual, and the number of reads per site/target, all of which result in missing data. Suggestions are proposed here to improve library construction, genotype calling accuracy, genome-wide marker density and read mapping rate. In brief, optimized GWSS library preparation should generate a unique set of target sites with dense distribution along chromosomes and even coverage per site across all individuals.
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Affiliation(s)
- Zhihua Jiang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Hongyang Wang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA; ; 2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jennifer J Michal
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Xiang Zhou
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Bang Liu
- 2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Leah C Solberg Woods
- 3. Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rita A Fuchs
- 4. Department of Integrative Physiology and Neuroscience, Washington State University College of Veterinary Medicine, Pullman, WA 99164-7620, USA
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12
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Wei S, Du M, Jiang Z, Duarte MS, Fernyhough-Culver M, Albrecht E, Will K, Zan L, Hausman GJ, Elabd EMY, Bergen WG, Basu U, Dodson MV. Bovine dedifferentiated adipose tissue (DFAT) cells: DFAT cell isolation. Adipocyte 2013; 2:148-59. [PMID: 23991361 PMCID: PMC3756103 DOI: 10.4161/adip.24589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 12/15/2022] Open
Abstract
Dedifferentiated fat cells (DFAT cells) are derived from lipid-containing (mature) adipocytes, which possess the ability to symmetrically or asymmetrically proliferate, replicate, and redifferentiate/transdifferentiate. Robust cell isolation and downstream culture methods are needed to isolate large numbers of DFAT cells from any (one) adipose depot in order to establish population dynamics and regulation of the cells within and across laboratories. In order to establish more consistent/repeatable methodology here we report on two different methods to establish viable DFAT cell cultures: both traditional cell culture flasks and non-traditional (flat) cell culture plates were used for ceiling culture establishment. Adipocytes (maternal cells of the DFAT cells) were easier to remove from flat culture plates than flasks and the flat plates also allowed cloning rings to be utilized for cell/cell population isolation. While additional aspects of usage of flat-bottomed cell culture plates may yet need to be optimized by definition of optimum bio-coating to enhance cell attachment, utilization of flat plate approaches will allow more efficient study of the dedifferentiation process or the DFAT progeny cells. To extend our preliminary observations, dedifferentiation of Wagyu intramuscular fat (IMF)-derived mature adipocytes and redifferentiation ability of DFAT cells utilizing the aforementioned isolation protocols were examined in traditional basal media/differentiation induction media (DMI) containing adipogenic inducement reagents. In the absence of treatment approximately 10% isolated Wagyu IMF-mature adipocytes dedifferentiated spontaneously and 70% DFAT cells displayed protracted adipogenesis 12 d after confluence in vitro. Lipid-free intracellular vesicles in the cytoplasm (vesicles possessing an intact membrane but with no any observable or stainable lipid inside) were observed during redifferentiation. One to 30% DFAT cells redifferentiated into lipid-assimilating adipocytes in the DMI media, with distinct lipid-droplets in the cytoplasm and with no observable lipid-free vesicles inside. Moreover, a high confluence level promoted the redifferentiation efficiency of DFAT cells. Wagyu IMF dedifferentiated DFAT cells exhibited unique adipogenesis modes in vitro, revealing a useful cell model for studying adipogenesis and lipid metabolism.
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