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Rajawat D, Nayak SS, Jain K, Sharma A, Parida S, Sahoo SP, Bhushan B, Patil DB, Dutt T, Panigrahi M. Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds. Mamm Genome 2024:10.1007/s00335-024-10047-2. [PMID: 39014170 DOI: 10.1007/s00335-024-10047-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Karan Jain
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
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2
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Sun S, Guan B, Xing Y, Li X, Liu L, Li Y, Jia L, Ye S, Dossa K, Zheng L, Luan Y. Genome-wide association analysis and transgenic characterization for amylose content regulating gene in tuber of Dioscorea zingiberensis. BMC PLANT BIOLOGY 2024; 24:524. [PMID: 38853253 PMCID: PMC11163818 DOI: 10.1186/s12870-024-05122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Amylose, a prebiotic found in yams is known to be beneficial for the gut microflora and is particularly advantageous for diabetic patients' diet. However, the genetic machinery underlying amylose production remains elusive. A comprehensive characterization of the genetic basis of amylose content in yam tubers is a prerequisite for accelerating the genetic engineering of yams with respect to amylose content variation. RESULTS To uncover the genetic variants underlying variation in amylose content, we evaluated amylose content in freshly harvested tubers from 150 accessions of Dioscorea zingibensis. With 30,000 high-quality single nucleotide polymorphisms (SNP), we performed a genome-wide association analysis (GWAS). The population structure analysis classified the D. zingiberensis accessions into three groups. A total of 115 significant loci were detected on four chromosomes. Of these, 112 significant SNPs (log10(p) = 5, q-value < 0.004) were clustered in a narrow window on the chromosome 6 (chr6). The peak SNP at the position 75,609,202 on chr6 could explain 63.15% of amylose variation in the population and fell into the first exon of the ADP-glucose pyrophosphorylase (AGPase) small subunit gene, causing a non-synonymous modification of the resulting protein sequence. Allele segregation analysis showed that accessions with the rare G allele had a higher amylose content than those harboring the common A allele. However, AGPase, a key enzyme precursor of amylose biosynthesis, was not expressed differentially between accessions with A and G alleles. Overexpression of the two variants of AGPase in Arabidopsis thaliana resulted in a significantly higher amylose content in lines transformed with the AGPase-G allele. CONCLUSIONS Overall, this study showed that a major genetic variant in AGPase probably enhances the enzyme activity leading to high amylose content in D. zingiberensis tuber. The results provide valuable insights for the development of amylose-enriched genotypes.
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Affiliation(s)
- Shixian Sun
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, 650224, China
| | - Binbin Guan
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Yue Xing
- Department of Life Science, Southwest Forestry University, Kunming, 650224, China
| | - Xiang Li
- The First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine, Kunming, 650021, China
| | - Lanlan Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Yanmei Li
- Department of Life Technology Teaching and Research, School of Life Science, Southwest Forestry University, Kunming, 650224, China
| | - Lu Jia
- Department of Life Technology Teaching and Research, School of Life Science, Southwest Forestry University, Kunming, 650224, China
| | - Shili Ye
- Faculty of Mathematics and Physics, Southwest Forestry University, Kunming, 650224, China
| | - Komivi Dossa
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, 34398, France
| | - Li Zheng
- Eco-development Academy, Southwest Forestry University, Kunming, 650224, China.
| | - Yunpeng Luan
- The First Affiliated Hospital of Yunnan University of Traditional Chinese Medicine, Kunming, 650021, China.
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
- Engineering Research Center for inheritance and innovation of Traditional Chinese Medicine, Kunming, 650034, China.
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3
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Colombi D, Rovelli G, Luigi-Sierra MG, Ceccobelli S, Guan D, Perini F, Sbarra F, Quaglia A, Sarti FM, Pasquini M, Amills M, Lasagna E. Population structure and identification of genomic regions associated with productive traits in five Italian beef cattle breeds. Sci Rep 2024; 14:8529. [PMID: 38609445 PMCID: PMC11014930 DOI: 10.1038/s41598-024-59269-z] [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: 12/07/2023] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
Italy has a long history in beef production, with local breeds such as Marchigiana, Chianina, Romagnola, Maremmana, and Podolica which produce high-quality meat. Selection has improved meat production, precocity, growth ability and muscle development, but the genetic determinism of such traits is mostly unknown. Using 33K SNPs-data from young bulls (N = 4064) belonging to these five Italian breeds, we demonstrated that the Maremmana and Podolica rustic breeds are closely related, while the specialised Marchigiana, Chianina, and Romagnola breeds are more differentiated. A genome-wide association study for growth and muscle development traits (average daily gain during the performance test, weight at 1 year old, muscularity) was conducted in the five Italian breeds. Results indicated a region on chromosome 2, containing the myostatin gene (MSTN), which displayed significant genome-wide associations with muscularity in Marchigiana cattle, a breed in which the muscle hypertrophy phenotype is segregating. Moreover, a significant SNP on chromosome 14 was associated, in the Chianina breed, to muscularity. The identification of diverse genomic regions associated with conformation traits might increase our knowledge about the genomic basis of such traits in Italian beef cattle and, eventually, such information could be used to implement marker-assisted selection of young bulls tested in the performance test.
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Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
- Department of Animal Science, University of California, Davis, CA, 2251, USA
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020, Legnaro, Italy
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Andrea Quaglia
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain.
- Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
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Aggarwal RAK, Kour A, Gandhi RS, Niranjan SK, Paul V, Bhutia TL, Bhutia KD. Characterization of a unique Sikkimese yak population of India: a multivariate approach. Trop Anim Health Prod 2023; 55:208. [PMID: 37199829 DOI: 10.1007/s11250-023-03627-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Native Sikkimese yak in Sikkim state of India is a pastoral treasure being raised through centuries-old transhumance practices and has evolved in response to natural and man-made selection. Currently, the population of Sikkimese yak is at risk with about five thousand total headcounts. Characterization is essential for taking appropriate decisions for conservation of any endangered population. In an attempt to phenotypically characterize the Sikkimese yaks, this study recorded phenotypic morphometric traits information, viz., body length (LG), height at withers (HT), heart girth (HG), paunch girth (PG), horn length (HL), horn circumference (HC), distance between horns (DbH), ear length (EL), face length (FL), face width (FW), and tail length with switch (TL), on 2154 yaks of both sexes. Multiple correlation estimation highlighted that HG and PG, DbH and FW, and EL and FW were highly correlated. Using principal component analysis, LG, HT, HG, PG, and HL were found to be the most important traits for phenotypic characterization of Sikkimese yak animals. Discriminant analysis based on different locations of Sikkim hinted at the existence of two separate clusters, however, broadly, phenotypic uniformity could be observed. Subsequent genetic characterization can offer greater insights and can pave the way for future breed registration and conservation of the population.
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Affiliation(s)
- R A K Aggarwal
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
| | - Aneet Kour
- ICAR-National Research Centre On Yak, Dirang, Arunachal Pradesh, 790101, India
| | - R S Gandhi
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Vijay Paul
- ICAR-National Research Centre On Yak, Dirang, Arunachal Pradesh, 790101, India
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5
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Li S, Lei H, Li J, Sun A, Ahmed Z, Duan H, Chen L, Zhang B, Lei C, Yi K. Analysis of genetic diversity and selection signals in Chaling cattle of southern China using whole-genome scan. Anim Genet 2023; 54:284-294. [PMID: 36864643 DOI: 10.1111/age.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
China has diversified resources of indigenous cattle, which are classified into Northern, Central, and Southern groups according to their geographical distribution. Chaling cattle belong to Southern group. This breed is famous for the production of good quality meat with elite meat grades. To analyze the genetic diversity of Chaling cattle, 20 samples were sequenced using whole-genome resequencing technology, along with 138 published whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle as control. It was found that Chaling cattle originated from Chinese indicine cattle. The genetic diversity of Chaling cattle is higher than that of Indian indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle, but lower than that of Chinese indicine cattle and Xiangxi cattle. Annotating the selection signals obtained by composite likelihood ratio, θπ, FST , π-ratio, and XP-EHH methods, several genes associated with immunity, heat tolerance, reproduction, growth, and meat quality showed strong selection signals. In general, this study provides a theoretical basis for analyzing the genetic mechanism of Chaling cattle with excellent adaptability, rough feeding tolerance, good immune performance, and good meat quality. This work lays a foundation for genetic breeding of Chaling cattle in future.
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Affiliation(s)
- Shuang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Ao Sun
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Science, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Hongfeng Duan
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Lin Chen
- Chaling County Agricultural Development Corporation Ltd, Chaling, Hunan, China
| | - Baizhong Zhang
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
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6
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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7
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Machado PC, Brito LF, Martins R, Pinto LFB, Silva MR, Pedrosa VB. Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems. Animals (Basel) 2022; 12:ani12243526. [PMID: 36552446 PMCID: PMC9774243 DOI: 10.3390/ani12243526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.
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Affiliation(s)
- Pamela C. Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Rafaela Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luis Fernando B. Pinto
- Department of Animal Science, Federal University of Bahia, Av. Adhemar de Barros 500, Ondina, Salvador 40170-110, BA, Brazil
| | - Marcio R. Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes 16700-000, SP, Brazil
| | - Victor B. Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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8
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Wang P, Li X, Zhu Y, Wei J, Zhang C, Kong Q, Nie X, Zhang Q, Wang Z. Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows. Front Vet Sci 2022; 9:932034. [PMID: 36268046 PMCID: PMC9578681 DOI: 10.3389/fvets.2022.932034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/09/2022] [Indexed: 11/04/2022] Open
Abstract
Milk production and body conformation traits are critical economic traits for dairy cows. To understand the basic genetic structure for those traits, a genome wide association study was performed on milk yield, milk fat yield, milk fat percentage, milk protein yield, milk protein percentage, somatic cell score, body form composite index, daily capacity composite index, feed, and leg conformation traits, based on the Illumina Bovine HD100k BeadChip. A total of 57, 12 and 26 SNPs were found to be related to the milk production, somatic cell score and body conformation traits in the Holstein cattle. Genes with pleiotropic effect were also found in this study. Seven significant SNPs were associated with multi-traits and were located on the PLEC, PLEKHA5, TONSL, PTGER4, and LCORL genes. In addition, some important candidate genes, like GPAT3, CEBPB, AGO2, SLC37A1, and FNDC3B, were found to participate in fat metabolism or mammary gland development. These results can be used as candidate genes for milk production, somatic cell score, and body conformation traits of Holstein cows, and are helpful for further gene function analysis to improve milk production and quality.
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Affiliation(s)
- Peng Wang
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Xue Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yihao Zhu
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Jiani Wei
- School of mathematics, University of Edinburgh, Edinburgh, United Kingdom
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Qingfang Kong
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Xu Nie
- Heilongjiang Animal Husbandry Service, Harbin, China
| | - Qi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,Bioinformatics Center, Northeast Agricultural University, Harbin, China,*Correspondence: Zhipeng Wang
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9
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Luo X, Li J, Xiao C, Sun L, Xiang W, Chen N, Lei C, Lei H, Long Y, Long T, Suolang Q, Yi K. Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures. Front Genet 2022; 13:816379. [PMID: 35711927 PMCID: PMC9196905 DOI: 10.3389/fgene.2022.816379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023] Open
Abstract
Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, FST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.
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Affiliation(s)
- Xiaoyu Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Chentong Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Weixuan Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,School of Life Science, University of Bristol, Bristol, United Kingdom
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Yun Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Ting Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
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10
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Waters DL, Clark SA, Moghaddar N, van der Werf JH. Genomic analysis of the slope of the reaction norm for body weight in Australian sheep. Genet Sel Evol 2022; 54:40. [PMID: 35659541 PMCID: PMC9164502 DOI: 10.1186/s12711-022-00734-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Selection of livestock based on their robustness or sensitivity to environmental variation could help improve the efficiency of production systems, particularly in the light of climate change. Genetic variation in robustness arises from genotype-by-environment (G × E) interactions, with genotypes performing differently when animals are raised in contrasted environments. Understanding the nature of this genetic variation is essential to implement strategies to improve robustness. In this study, our aim was to explore the genetics of robustness in Australian sheep to different growth environments using linear reaction norm models (RNM), with post-weaning weight records of 22,513 lambs and 60 k single nucleotide polymorphisms (SNPs). The use of scale-corrected genomic estimated breeding values (GEBV) for the slope to account for scale-type G × E interactions was also investigated. Results Additive genetic variance was observed for the slope of the RNM, with genetic correlations between low- and high-growth environments indicating substantial re-ranking of genotypes (0.44–0.49). The genetic variance increased from low- to high-growth environments. The heritability of post-weaning body weight ranged from 0.28 to 0.39. The genetic correlation between intercept and slope of the reaction norm for post-weaning body weight was low to moderate when based on the estimated (co)variance components but was much higher when based on back-solved SNP effects. An initial analysis suggested that a region on chromosome 11 affected both the intercept and the slope, but when the GEBV for the slope were conditioned on the GEBV for the intercept to remove the effect of scale-type G × E interactions on SNP effects for robustness, a single genomic region on chromosome 7 was found to be associated with robustness. This region included genes previously associated with growth traits and disease susceptibility in livestock. Conclusions This study shows a significant genetic variation in the slope of RNM that could be used for selecting for increased robustness of sheep. Both scale-type and rank-type G × E interactions contributed to variation in the slope. The correction for scale effects of GEBV for the slope should be considered when analysing robustness using RNM. Overall, robustness appears to be a highly polygenic trait. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00734-6.
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Affiliation(s)
- Dominic L Waters
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - Sam A Clark
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Nasir Moghaddar
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Julius H van der Werf
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
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11
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Why and How European Farmers Are Dedicated to Breeding the Dwarf Dahomey Cattle. Animals (Basel) 2022; 12:ani12030377. [PMID: 35158700 PMCID: PMC8833708 DOI: 10.3390/ani12030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The introduction of high productive cattle breeds in Africa is well known, but the contribution of African breeds to livestock biodiversity in Europe is generally overlooked. This study reports, for the first time, European farmers’ interests in keeping the Dahomey cattle, and characterizes their management practices. The Dahomey cattle from Benin (West Africa) are the smallest cattle in the world, and they were introduced to Europe in the early 1900s. The findings revealed that European farmers are increasingly interested in keeping Dahomey cattle, because of their suitability for grassland maintenance and meat production, as well as their low management requirements (with regard to feeding, preventive and curative health care and reproduction management). Overall, the study displays the agricultural importance and ecological utilization of Dahomey cattle in European countries. It shows how small-sized cattle can support the promotion of sustainable livestock production and the management of ecosystems, including faunistic and floristic diversity. Abstract This study investigates the motivations and breeding practices of farmers keeping Dahomey cattle in European countries. Data were collected using a web-based open-closed questionnaire survey targeting 55 farmers from Germany, Switzerland and Austria. Descriptive analyses revealed that the earliest European Dahomey herds were established in 2005. Moreover, interest in the breed recently increased as 63.7% of the investigated farmers established their herds between 2016 and 2020. The average herd size comprises seven Dahomey cattle, kept for managing grassland (59.3%), for production of meat or as breeding stock (32.1%) and for a hobby (8.6%). The animals are mostly kept in grazing systems throughout the year, partly fattened with supplement feeds. The low disease incidence and no need for extra health care in the herds indicate the robustness of the breed. Furthermore, meat quality, calving ease, small size, calm character and low feed requirements of Dahomey cattle were valued by the farmers. For the preservation of these features, farmers confirmed their enthusiasm to support any breeding and conservation program of this smallholder breed in Europe and Benin. This study highlights the importance of small-sized cattle for sustainable breeding systems and with regard to ecosystem management practices.
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12
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Mancin E, Tuliozi B, Pegolo S, Sartori C, Mantovani R. Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification. Front Genet 2022; 12:746665. [PMID: 35058966 PMCID: PMC8764395 DOI: 10.3389/fgene.2021.746665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
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Vanvanhossou SFU, Giambra IJ, Yin T, Brügemann K, Dossa LH, König S. First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants. Genes (Basel) 2021; 12:1702. [PMID: 34828308 PMCID: PMC8625544 DOI: 10.3390/genes12111702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
This study investigated polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. Considering 67 animals, DNA sequencing of the genes' exons, flanking regions and parts of the 5'-upstream regions identified 1058 genetic variants including 731 previously unknown. In addition, four novel milk protein variants were detected, including CSN3K (p.Ala66Val), LALBAF (p.Arg58Trp), LGBB1 (p.Ala134Val) and LGBK (p.Thr92Asnfs*13). CSN3K is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas LALBAF and LGBB1 are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding LGBK, a frameshift insertion of one adenine residue at BTA11:103257980 (exon 3) induces a premature translation termination resulting in a 46% reduction of the reference protein sequence. The casein polymorphisms formed five main CSN1S1-CSN2-CSN1S2-CSN3 haplotypes including B-A1-A-B, B-A1-A-A and C-A2-A-B which are predominant in the investigated cattle breeds. Moreover, in silico analyses of polymorphisms within the 5'- and 3'- untranslated regions of all six milk proteins revealed effects on microRNA and transcription factor binding sites. This study suggests a large genetic variation of milk protein genes in Beninese cattle, which should be investigated in further studies for their effects on milk production, including quality and yield traits.
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Affiliation(s)
- Sèyi Fridaïus Ulrich Vanvanhossou
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Isabella Jasmin Giambra
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Abomey-Calavi, 03 BP 2819 Jéricho Cotonou, Benin;
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - 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; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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15
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Palombo V, D’Andrea M, Licastro D, Dal Monego S, Sgorlon S, Sandri M, Stefanon B. Single-Step Genome Wide Association Study Identifies QTL Signals for Untrimmed and Trimmed Thigh Weight in Italian Crossbred Pigs for Dry-Cured Ham Production. Animals (Basel) 2021; 11:ani11061612. [PMID: 34072469 PMCID: PMC8227816 DOI: 10.3390/ani11061612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Along with the traditional traits, swine breeding programs for Italian dry-cured ham production have recently aimed to include novel phenotypes. The identification of the genomic regions underlying such new traits helps to untangle their genetic architecture and may provide useful information to be integrated in genetic selection. With this aim, we estimated genetic parameters and conducted a single step genome wide association studies (GWAS) on untrimmed and trimmed thigh weight considering two pig crossbred lines approved for Italian Protected Designation of Origin ham production. Quantitative trait loci (QTLs) were characterized based on the variance of 10-SNP sliding windows genomic estimated breeding values. In particular, we identified interesting QTL signals on several chromosomes, notably on chromosome 4, 6, 7 and 15. A high heritability and genetic correlation were observed for the two traits under investigation and although independent studies including other pig populations are required to disentangle the possible effects of specific linkage disequilibrium in our population, our findings suggest that such QTL could be investigated in future pig breeding programs to improve the reliability of genomic estimated breeding values for the dry-cured ham production. Abstract Protected Designation of Origin (PDO) dry-cured ham is the most important product in the Italian pig breeding industry, mainly oriented to produce heavy pig carcasses to obtain hams of the right weight and maturity. Recently, along with the traditional traits swine breeding programs have aimed to include novel carcass traits. The identification at the genome level of quantitative trait loci (QTLs) affecting such new traits helps to reveal their genetic determinism and may provide information to be integrated in prediction models in order to improve prediction accuracy as well as to identify candidate genes underlying such traits. This study aimed to estimate genetic parameters and perform a single step genome wide association studies (ssGWAS) on novel carcass traits such as untrimmed (UTW) and trimmed thigh weight (TTW) in two pig crossbred lines approved for the ham production of the Italian PDO. With this purpose, phenotypes were collected from ~1800 animals and 240 pigs were genotyped with Illumina PorcineSNP60 Beadchip. The single-step genomic BLUP procedure was used for the heritability estimation and to implement the ssGWAS. QTL were characterized based on the variance of 10-SNP sliding window genomic estimated breeding values. Moderate heritabilities were detected and QTL signals were identified on chromosome 1, 4, 6, 7, 11 and 15 for both traits. As expected, the genetic correlation among the two traits was very high (~0.99). The QTL regions encompassed a total of 249 unique candidate genes, some of which were already reported in association with growth, carcass or ham weight traits in pigs. Although independent studies are required to further verify our findings and disentangle the possible effects of specific linkage disequilibrium in our population, our results support the potential use of such new QTL information in future breeding programs to improve the reliability of genomic prediction.
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Affiliation(s)
- Valentino Palombo
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via de Sanctis Snc, 86100 Campobasso, Italy;
| | - Mariasilvia D’Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via de Sanctis Snc, 86100 Campobasso, Italy;
- Correspondence: ; Tel.: +39-0874-404671
| | - Danilo Licastro
- ARGO Open Lab Platform for Genome Sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Simeone Dal Monego
- ARGO Open Lab Platform for Genome Sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Sandy Sgorlon
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, Università di Udine, Via Delle Scienze, 208, 33100 Udine, Italy; (S.S.); (M.S.); (B.S.)
| | - Misa Sandri
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, Università di Udine, Via Delle Scienze, 208, 33100 Udine, Italy; (S.S.); (M.S.); (B.S.)
| | - Bruno Stefanon
- Dipartimento di Scienze Agroambientali, Alimentari e Animali, Università di Udine, Via Delle Scienze, 208, 33100 Udine, Italy; (S.S.); (M.S.); (B.S.)
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16
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Tahir MS, Porto-Neto LR, Gondro C, Shittu OB, Wockner K, Tan AWL, Smith HR, Gouveia GC, Kour J, Fortes MRS. Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle. Genes (Basel) 2021; 12:768. [PMID: 34069992 PMCID: PMC8157873 DOI: 10.3390/genes12050768] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75-0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10-6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes-BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3-are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus-pituitary-ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.
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Affiliation(s)
- Muhammad S. Tahir
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Laercio R. Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Brisbane, QLD 4072, Australia;
| | - Cedric Gondro
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Olasege B. Shittu
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Kimberley Wockner
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Andre W. L. Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Hugo R. Smith
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Gabriela C. Gouveia
- Animal Science Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Jagish Kour
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland Australia, Brisbane, QLD 4072, Australia; (M.S.T.); (O.B.S.); (K.W.); (A.W.L.T.); (H.R.S.); (J.K.)
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Aikins-Wilson S, Bohlouli M, König S. Maternal and direct genetic parameters for tail length, tail lesions, and growth traits in pigs. J Anim Sci 2021; 99:skaa398. [PMID: 33320242 PMCID: PMC7819635 DOI: 10.1093/jas/skaa398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Tail length and tail lesions are the major triggers for tail biting in pigs. Against this background, 2 datasets were analyzed to estimate genetic parameters for tail characteristics and growth traits. Dataset 1 considered measurements for trait tail length (T-LEN) and for the growth traits birth weight (BW), weaning weight (WW), postweaning weight (PWW), and average daily gain (ADG) from 9,348 piglets. Piglets were born in the period from 2015 to 2018 and kept on the university Gießen research station. Dataset 2 included 4,943 binary observations from 1,648 pigs from the birth years 2016 to 2019 for tail lesions (T-LES) as indicators for nail necrosis, tail abnormalities, or tail biting. T-LES were recorded at 30 ± 7 d after entry for rearing (T-Les-1), at 50 ± 7 d after entry for rearing (end of the rearing period, T-LES-2), and 130 ± 20 d after entry for rearing (end of fattening period, T-LES-3). Genetic statistical model evaluation for dataset 1 based on Akaike's information criterion and likelihood ration tests suggested multiple-trait animal models considering covariances between direct and maternal genetic effects. The direct heritability for T-LEN was 0.42 (±0.03), indicating the potential for genetic selection on short tails. The maternal genetic heritability for T-LEN was 0.05 (±0.04), indicating the influence of uterine characteristics on morphological traits. The negative correlation between direct and maternal effects for T-LEN of -0.35 (±0.13), as well as the antagonistic relationships (i.e., positive direct genetic correlations in the range from 0.03 to 0.40) between T-LEN with the growth traits BW, WW, PWW, and ADG, complicate selection strategies and breeding goal definitions. The correlations between direct effects for T-LEN and maternal effects for breeding goal traits, and vice versa, were positive but associated with a quite large SE. The heritability for T-LES when considering the 3 repeated measurements was 0.23 (±0.04) from the linear (repeatability of 0.30) and 0.21 (±0.06; repeatability of 0.29) from the threshold model. The breeding value correlations between T-LES-3 with breeding values from the repeatability models were quite large (0.74 to 0.90), suggesting trait lesion recording at the end of the rearing period. To understand all genetic mechanisms in detail, ongoing studies are focusing on association analyses between T-LEN and T-LES, and the identification of tail biting from an actor's perspective.
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Affiliation(s)
- Sheila Aikins-Wilson
- Institute of Animal Breeding and Genetics, University of Giessen, Giessen, Germany
| | - Mehdi Bohlouli
- Institute of Animal Breeding and Genetics, University of Giessen, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, University of Giessen, Giessen, Germany
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