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dos Santos CA, Eler JP, Oliveira ECDM, Espigolan R, Giacomini G, Ferraz JBS, Paim TDP. Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation. PLoS One 2024; 19:e0301937. [PMID: 38662691 PMCID: PMC11045132 DOI: 10.1371/journal.pone.0301937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Genomic regions related to tropical adaptability are of paramount importance for animal breeding nowadays, especially in the context of global climate change. Moreover, understanding the genomic architecture of these regions may be very relevant for aiding breeding programs in choosing the best selection scheme for tropical adaptation and/or implementing a crossbreeding scheme. The composite MONTANA TROPICAL® population was developed by crossing cattle of four different biological types to improve production in harsh environments. Pedigree and genotype data (51962 SNPs) from 3215 MONTANA TROPICAL® cattle were used to i) characterize the population structure; ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to each selected region. The population structure based on principal components had a weak relationship with the genetic contribution of the different biological types. Clustering analyses (ADMIXTURE) showed different clusters according to the number of generations within the composite population. Considering results of both selection signatures approaches, we identified only one consensus region on chromosome 20 (35399405-40329703 bp). Genes in this region are related to immune function, regulation of epithelial cell differentiation, and cell response to ionizing radiation. This region harbors the slick locus which is related to slick hair and epidermis anatomy, both of which are related to heat stress adaptation. Also, QTLs in this region were related to feed intake, milk yield, mastitis, reproduction, and slick hair coat. The signatures of selection detected here arose in a few generations after crossbreeding between contrasting breeds. Therefore, it shows how important this genomic region may be for these animals to thrive in tropical conditions. Further investigations on sequencing this region can identify candidate genes for animal breeding and/or gene editing to tackle the challenges of climate change.
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Affiliation(s)
- Camila Alves dos Santos
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
| | - Joanir Pereira Eler
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Rafael Espigolan
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Gabriela Giacomini
- Associação Internacional de criadores de Montana, Mogi Mirim, São Paulo, Brazil
| | - José Bento Sterman Ferraz
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Tiago do Prado Paim
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
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Ward JA, Ng'ang'a SI, Randhawa IAS, McHugo GP, O'Grady JF, Flórez JM, Browne JA, Pérez O’Brien AM, Landaeta-Hernández AJ, Garcia JF, Sonstegard TS, Frantz LAF, Salter-Townshend M, MacHugh DE. Genomic insights into the population history and adaptive traits of Latin American Criollo cattle. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231388. [PMID: 38571912 PMCID: PMC10990470 DOI: 10.1098/rsos.231388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/04/2024] [Accepted: 01/31/2024] [Indexed: 04/05/2024]
Abstract
Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.
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Affiliation(s)
- James A. Ward
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Said I. Ng'ang'a
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - Gillian P. McHugo
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - John F. O'Grady
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Julio M. Flórez
- Acceligen, Eagan, MN55121, USA
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - John A. Browne
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | | | - Antonio J. Landaeta-Hernández
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Jóse F. Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | - Laurent A. F. Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD04 V1W8, Ireland
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Baazaoui I, Bedhiaf-Romdhani S, Mastrangelo S, Lenstra JA, Da Silva A, Benjelloun B, Ciani E. Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data. Front Vet Sci 2024; 11:1339321. [PMID: 38487707 PMCID: PMC10938946 DOI: 10.3389/fvets.2024.1339321] [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: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. Methods In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. Results and discussion We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.
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Affiliation(s)
- Imen Baazaoui
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Sonia Bedhiaf-Romdhani
- Laboratory of Animal and Fodder Production, National Institute of Agronomic Research of Tunisia, Ariana, Tunisia
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Da Silva
- Faculté des Sciences et Techniques de Limoges, E2LIM, Limoges, France
| | - Badr Benjelloun
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, Beni Mellal, Morocco
| | - Elena Ciani
- Dipartamento Bioscienze, Biotecnologie, Biofarmaceutica, University of Bari Aldo Moro, Bari, Italy
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Ben-Jemaa S, Adam G, Boussaha M, Bardou P, Klopp C, Mandonnet N, Naves M. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle. Sci Rep 2023; 13:12155. [PMID: 37500674 PMCID: PMC10374910 DOI: 10.1038/s41598-023-38774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.
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Affiliation(s)
- Slim Ben-Jemaa
- INRAE, ASSET, 97170, Petit-Bourg, France.
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia.
| | | | - Mekki Boussaha
- AgroParisTech, GABI, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Philippe Bardou
- GenPhySE, Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA, Université de Toulouse, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
- Sigenae, INRAE, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Christophe Klopp
- Genotoul Bioinfo, BioInfoMics, MIAT UR875, Sigenae, INRAE, Castanet-Tolosan, France
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. BIOLOGY 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
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Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
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Rojas-Espinoza R, Macedo R, Suaña A, Delgado A, Manrique YP, Rodríguez H, Quispe YM, Perez-Guerra UH, Pérez-Durand MG, García-Herreros M. Phenotypic Characterization of Creole Cattle in the Andean Highlands Using Bio-Morphometric Measures and Zoometric Indices. Animals (Basel) 2023; 13:1843. [PMID: 37417307 DOI: 10.3390/ani13111843] [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: 04/11/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 07/08/2023] Open
Abstract
Several Creole cattle biotypes can be found in the Andean highlands, and most of them are considered as being in risk of extinction. The main aim of the present study was to perform a phenotypic characterization of the Creole cattle in the Andean highlands using bio-morphometric measures and zoometric indices. Individuals from three different biotypes (Black 'Negro' (n = 57), Colour-Sided 'Callejón' (n = 20), and Brindle 'Atigrado' (n = 18)) from an experimental research center located in the Peruvian highlands were enrolled in the study. In total, seventeen morphometric parameters were evaluated and ten zoometric indices were calculated in each biotype. To test the relationship between biometric traits, correlation analyses were carried out between morphometric parameters. Differences were observed regarding different morphometric variables such as head length (HL) and rump length (RL) among cattle biotypes (p ≤ 0.05). The coefficient of variation (CV; %) regarding different morphometric parameters ranged between 11.32 for neck length (NL) and 3.63 for height at withers (HaW), which indicated low-moderate variability among morphometric variables. Differences were observed in the longitudinal pelvic index (LPI) when different zoometric indices were compared among biotypes (p ≤ 0.05). The CV regarding different zoometric indices, which ranged between 10.78 for the cephalic index (CEI) and 5.05 for LPI, indicated low variability among indices. No differences were observed in any other morphometric parameter or zoometric index among cattle biotypes or genders (p > 0.05). Finally, multiple correlations were observed between morphometric variables (p ≤ 0.05). In conclusion, it was determined that Peruvian Andean Creole cattle can be considered as a dairy-related biotype with a slight tendency for beef production (dual-purpose). The great homogeneity regarding zoometric characteristics among biotypes and genders may indicate that the Andean Creole cattle have been maintained quite isolated, avoiding the genetic influence of other foreign breeds. Finally, the phenotypic characterization including bio-morphometric measurements and zoometric indices obtained from the different Creole bovine biotypes is crucial in order to begin different conservation programs to preserve cattle breeds in the Peruvian Andean highlands.
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Affiliation(s)
- Rolando Rojas-Espinoza
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Rassiel Macedo
- Facultad de Ciencias Agrarias, Universidad Nacional San Antonio Abad del Cusco, Cusco 08000, Peru
| | - Alex Suaña
- Independent Researcher, Puno 21001, Peru
| | - Alfredo Delgado
- Facultad de Medicina Veterinária, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Yan P Manrique
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Halley Rodríguez
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | | | - Uri H Perez-Guerra
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Manuel G Pérez-Durand
- Facultad de Medicina Veterinária y Zootecnia, Universidad Nacional del Altiplano, Puno 21001, Peru
| | - Manuel García-Herreros
- National Institute for Agricultural and Veterinary Research (INIAV), 2005-048 Santarém, Portugal
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Hirano T, Saito T, Ito S, Ye B, Linscott TM, Do VT, Dong Z, Chiba S. Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia. Mol Phylogenet Evol 2023; 182:107728. [PMID: 36804427 DOI: 10.1016/j.ympev.2023.107728] [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: 02/15/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.
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Affiliation(s)
- Takahiro Hirano
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan.
| | - Takumi Saito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Shun Ito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - T Mason Linscott
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Zhengzhong Dong
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
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8
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Sánchez-Arroyo E, Vargas-Romero JM, Rosendo-Ponce A, Hernández-Mendo O, Pérez-Chabela ML, Pro-Martínez A, Becerril-Pérez CM. Growth performance, carcass, and meat quality traits of Tropical Milking criollo bulls fed with two energy-level diets. Trop Anim Health Prod 2023; 55:62. [PMID: 36729241 DOI: 10.1007/s11250-023-03469-8] [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: 07/14/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
The aim of this study was to determine the effect of two energy-level diets on the beef performance of Tropical Milking criollo bulls grouped by weight and age in three periods: initial, middle, and final. Evidence on intensive beef production from Tropical Milking criollo cattle breeds are unknown, and productive alternatives for dairy producers in the hot tropics are needed. Bulls were fed in each period with low (LE, 2.2 Mcal ME/kg DM) and high (HE, 2.9 Mcal ME/kg DM) energy diets and content phase feeding protein of 14.5, 12.0, and 10.3%, respectively. For each period, ten bulls were randomly assigned to diets. In all periods, growth performance for final body weight, average daily gain, feed intake, and feed conversion were all superior in HE (p ≤ 0.05). For the final period, slaughter body, hot and cold carcass weights, and dressing were also superior in HE (p ≤ 0.05); for meat quality traits, differences were observed in muscles Longissimus dorsi, Semimembranosus, Infraspinatus, and Serratus ventralis for pH and tenderness (p ≤ 0.05), although not for diets. For color L*, a*, and b* system, neither diet nor muscle had effect on L* (p > 0.05); however, the diet-muscle interaction was significant for a* (p ≤ 0.05), and only muscle effect was detected for b* (p ≤ 0.05). Tropical Milking bulls responded positively to a high-energy diet, despite not being a beef breed.
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Affiliation(s)
- Eduardo Sánchez-Arroyo
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km 36.5, 56230, Texcoco, Estado de México, Mexico
| | - Juan Manuel Vargas-Romero
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, San Rafael Atlixco 186, Col. Vicentina, Alcaldía Iztapalapa, 09340, Mexico City, Mexico
| | - Adalberto Rosendo-Ponce
- Colegio de Postgraduados, Campus Veracruz, Programa de Agroecosistemas Tropicales, Carretera Federal Xalapa-Veracruz, Km. 88.5, 94251 Manlio Fabio Altamirano, Veracruz, Mexico
| | - Omar Hernández-Mendo
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km 36.5, 56230, Texcoco, Estado de México, Mexico
| | - María Lourdes Pérez-Chabela
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, San Rafael Atlixco 186, Col. Vicentina, Alcaldía Iztapalapa, 09340, Mexico City, Mexico
| | - Arturo Pro-Martínez
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km 36.5, 56230, Texcoco, Estado de México, Mexico
| | - Carlos Miguel Becerril-Pérez
- Programa de Ganadería, Colegio de Postgraduados, Campus Montecillo, Carretera Federal México-Texcoco Km 36.5, 56230, Texcoco, Estado de México, Mexico. .,Colegio de Postgraduados, Campus Veracruz, Programa de Agroecosistemas Tropicales, Carretera Federal Xalapa-Veracruz, Km. 88.5, 94251 Manlio Fabio Altamirano, Veracruz, Mexico.
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Michiels B, Pardo AM, Ortega Masagué MF, Giovambattista G, Corva PM. Characterization of experimental cattle populations from Argentina with a low-density SNP genotyping panel. Anim Genet 2023; 54:68-72. [PMID: 36464984 DOI: 10.1111/age.13278] [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: 06/06/2022] [Revised: 09/28/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
The objectives of the present experiment were to evaluate a low-density SNP array designed for the molecular characterisation of gene banks and to assess the genetic diversity and population structure of beef cattle herds from an Argentinean research station. Forty-nine animals from three breeds (Angus, Hereford, and Argentinean Creole) were genotyped using the multi-species IMAGE001 60-K SNP array (10 K for cattle). Genotypes of other 19 cattle populations from Argentina, other American countries, and Europe were included in the study. Of special interest was the characterization of the Argentinean Creole, the only autochthonous cattle breed in the country. Due to the merging of different datasets, approximately 5 K SNPs were effectively used. Genetic differentiation (FST ), principal component analysis, neighbour-joining tree of Reynolds distances and ancestry analysis showed that autochthonous American breeds are clearly differentiated, but all have genetic influences of Iberian cattle. The analysed herds of Argentinean Creole showed no evidence of recent admixture and represent a unique genetic pool within local American breeds. An experimental herd and the local commercial Hereford population have also diverged, probably due to the influence of current selection objectives in the breed. Our results illustrate the utility of using low-cost, low density SNP arrays in the evaluation of animal genetic resources. This type of panels could become a very useful resource in developing countries, where most endangered cattle breeds are located. The results also reinforce the importance of experimental herds as reservoir of genetic diversity, particularly in the case of local breeds under-represented in traditional production systems.
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Affiliation(s)
- Brian Michiels
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Alan Maxs Pardo
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina.,Instituto Nacional de Tecnología Agropecuaria (INTA) E.E.A., Balcarce, Argentina
| | - Maria F Ortega Masagué
- Instituto de Investigación Animal del Chaco Semiárido, IIACS-CIAP (INTA), Tucumán, Argentina
| | - Guillermo Giovambattista
- Instituto de Genética Veterinaria (IGEVET, Facultad de Ciencias Veterinarias, UNLP-CONICET), La Plata, Argentina
| | - Pablo M Corva
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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10
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Huang N, Zhao L, Wang J, Jiang Q, Ju Z, Wang X, Yang C, Gao Y, Wei X, Zhang Y, Xiao Y, Liu W, Lu S, Huang J. Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate. J Anim Sci 2023; 101:skad006. [PMID: 36617259 PMCID: PMC9985157 DOI: 10.1093/jas/skad006] [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: 08/14/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023] Open
Abstract
Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.24 °C to 10.3 °C) and heat-adapted (20.2 °C to 24.73 °C) Chinese native cattle breeds. Genomic analyses revealed a set of candidate genes (e.g., UQCR11, DNAJC18, EGR1, and STING1) were functionally associated with thermogenesis and energy metabolism. We also characterized the adaptive loci of cattle exposed to cold temperatures. Our study finds new candidate genes and provides new insights into adaptations to cold climates in cattle.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Lihong Zhao
- Informatic Center, SAAMS, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jinpeng Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Qiang Jiang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Zhihua Ju
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Xiuge Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Chunhong Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaping Gao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaochao Wei
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaran Zhang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Yao Xiao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Wenhao Liu
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Shaoxiong Lu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Jinming Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
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11
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Nazari F, Seyedabadi HR, Noshary A, Emamjomeh-Kashan N, Banabazi MH. A genome-wide scan for signatures of selection in Kurdish horse breed. J Equine Vet Sci 2022; 113:103916. [PMID: 35218903 DOI: 10.1016/j.jevs.2022.103916] [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: 11/10/2021] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
The genetic diversity and genomic regions being under putative natural selection in Kurdish horse population were studied. The samples from 72 horses were genotyped by using GGP Equine 70K SNP arrays. The Ne Slope (NeS) analyses revealed that a sharp decline in Ne has probably occurred around four generations ago, and high frequency of ROH with 2-4 Mbp in length suggested that the inbreeding has probably occurred around 20 generations ago. The effective population size (Ne) was 104 horses up to three generations ago and the average inbreeding (FROH) was 0.047(±0.045). Using de-correlated composite of multiple selection signals (DCMS) and runs of homozygosity (ROH) analyses the genomic regions being under putative selection were detected. By using DCMS, a total of 148 significant SNP (FDR < 0.05) were identified, 40% of which were located on ECA9, where the greatest peak was observed. This genomic region harbors several known QTL which are associated with withers height (body size). Also significant genomic regions (FDR<0.05), harboring QTL associated with insect bite hypersensitivity (IBH), hair density and coat texture, alternate gaits, guttural pouch tympany and temperament were identified. By using outputs of ROH analyses, two hotspot regions (i.e. 30% of individuals was considered as threshold), were identified on ECA7 (50.11-54.36 Mbp) and ECA11 (26.10-29.07 Mbp) harboring QTL associated with withers height, alternate gait and IBH. In summary, the genomic regions being under putative natural selection which harbors known QTL associated with body size and IBH, among others, were introduced. Nevertheless, additional functional and comparative studies are necessary to corroborate their effect on the observed genetic and phenotypic diversity of the Kurdish horses.
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Affiliation(s)
- Faezeh Nazari
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid-Reza Seyedabadi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Alireza Noshary
- Department of Animal Science, Faculty of Agriculture, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Nasser Emamjomeh-Kashan
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohamad-Hosein Banabazi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran; Department of animal breeding and genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala 75007, Sweden
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12
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Yougbaré B, Ouédraogo D, Tapsoba ASR, Soudré A, Zoma BL, Orozco-terWengel P, Moumouni S, Ouédraogo-Koné S, Wurzinger M, Tamboura HH, Traoré A, Mwai OA, Sölkner J, Khayatzadeh N, Mészáros G, Burger PA. Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso. Front Genet 2021; 12:670390. [PMID: 34646296 PMCID: PMC8504455 DOI: 10.3389/fgene.2021.670390] [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: 02/21/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.
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Affiliation(s)
- Bernadette Yougbaré
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Dominique Ouédraogo
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Arnaud S R Tapsoba
- Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Albert Soudré
- Unité de Formation et de Recherche en Sciences et Technologies, Université Norbert Zongo, Koudougou, Burkina Faso
| | - Bienvenue L Zoma
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,Institut du Développement Rural, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | | | - Sanou Moumouni
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | | | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Hamidou H Tamboura
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Amadou Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.,SUISAG, Sempach, Switzerland
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, Vienna, Austria
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13
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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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14
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Igoshin A, Yudin N, Aitnazarov R, Yurchenko AA, Larkin DM. Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations. Life (Basel) 2021; 11:959. [PMID: 34575108 PMCID: PMC8467296 DOI: 10.3390/life11090959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/30/2022] Open
Abstract
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.
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Affiliation(s)
- Alexander Igoshin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Nikolay Yudin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ruslan Aitnazarov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Andrey A. Yurchenko
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Denis M. Larkin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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15
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Braz CU, Rowan TN, Schnabel RD, Decker JE. Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle. Sci Rep 2021; 11:13335. [PMID: 34172761 PMCID: PMC8233360 DOI: 10.1038/s41598-021-92455-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that G × E contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. G × E genome-wide association analysis (GWAA) detected a large number of G × E loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with G × E effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of G × E genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of G × E underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.
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Affiliation(s)
- Camila U Braz
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
- Genetics Area Program, University of Missouri, Columbia, MO, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
- Genetics Area Program, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Genetics Area Program, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
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16
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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17
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Caivio-Nasner S, López-Herrera A, González-Herrera LG, Rincón JC. Diversity analysis, runs of homozygosity and genomic inbreeding reveal recent selection in Blanco Orejinegro cattle. J Anim Breed Genet 2021; 138:613-627. [PMID: 33783906 DOI: 10.1111/jbg.12549] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/26/2021] [Accepted: 03/16/2021] [Indexed: 01/18/2023]
Abstract
Blanco Orejinegro (BON) cattle have 500 years of adaptation to the Colombian tropic, but little is known about their genetic history. Our aim was to estimate levels of linkage disequilibrium (LD), effective population size (Ne), genomic inbreeding for runs of homozygosity (FROH ), genomic relation matrix (FGRM ), excess of homozygotes (FHOM ) and pedigree information (FPEDCOMP ) and to characterize the runs of homozygosity (ROH), searching for selection signatures. A total of 419 BON animals were genotyped, 70 with a 150K chip and 349 with a 50K chip. Next, an imputation to 50K was performed, and, after editing, databases of 40K were obtained. The PLINK v1.90 and R programs were used to estimate LD, ROH, FROH and FHOM . The SNeP v1.1 program was used to obtain Ne, and PreGSf90 was used to elaborate the scaled G matrix. The MTDFNRM program was used to estimate FPEDCOMP . The LD mean as r2 at 1 Mb was 0.21 (r2 > 0.30 at a distance of 96.72kb), and Ne was 123 ± 1. A total of 7,652 homozygous segments were obtained, with a mean of 18.35 ± 0.55 ROH/animal. Most of the genome was covered by long ROHs (ROH>8 Mb = 4.86%), indicating significant recent inbreeding. The average inbreeding coefficient for FPEDCOM , FGRM , FHOM and FROH was 4.41%, 4.18%, 5.58% and 6.78%, respectively. The highest correlation was observed between FHOM and FROH (0.95). ROH hotspots/islands were defined using the extreme values of a box plot that was generated, and correspond to QTLs related to milk yield (55.11%), external appearance (13.47%), production (13.30%), reproduction (8.15%), health (5.24%) and meat carcass (4.74%).
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Affiliation(s)
- Sindy Caivio-Nasner
- Grupo de Investigación Biomolecular y Pecuaria (BIOPEC), Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Albeiro López-Herrera
- Universidad Nacional de Colombia sede Medellín, Medellín, Colombia.,Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia
| | - Luis G González-Herrera
- Universidad Nacional de Colombia sede Medellín, Medellín, Colombia.,Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan C Rincón
- Grupo de investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia, Bogotá, Colombia.,Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
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Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages. Sci Rep 2021; 11:5865. [PMID: 33712687 PMCID: PMC7971002 DOI: 10.1038/s41598-021-85245-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/22/2021] [Indexed: 12/23/2022] Open
Abstract
Ovary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.
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19
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Gu Z, Pan S, Lin Z, Hu L, Dai X, Chang J, Xue Y, Su H, Long J, Sun M, Ganusevich S, Sokolov V, Sokolov A, Pokrovsky I, Ji F, Bruford MW, Dixon A, Zhan X. Climate-driven flyway changes and memory-based long-distance migration. Nature 2021; 591:259-264. [PMID: 33658718 DOI: 10.1038/s41586-021-03265-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic1, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.
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Affiliation(s)
- Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Li Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Han Su
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Juan Long
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Mengru Sun
- University of the Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | | | - Vasiliy Sokolov
- Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Ekaterinburg, Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia
| | - Ivan Pokrovsky
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia.,Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Laboratory of Ornithology, Institute of Biological Problems of the North FEB RAS, Magadan, Russia
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael W Bruford
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - Andrew Dixon
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Reneco International Wildlife Consultants, Abu Dhabi, United Arab Emirates.,International Wildlife Consultants, Carmarthen, UK
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China. .,University of the Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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20
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Saravanan KA, Panigrahi M, Kumar H, Parida S, Bhushan B, Gaur GK, Dutt T, Mishra BP, Singh RK. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics 2021; 113:955-963. [PMID: 33610795 DOI: 10.1016/j.ygeno.2021.02.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022]
Abstract
Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and FST, to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and FST methods, respectively. We found several candidate genes (e.g., NCR3, ARID5A, HIST1H2BN, DEFB4, DEFB7, HSPA1L, HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production & Management section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - R K Singh
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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21
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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23
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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: 12] [Impact Index Per Article: 4.0] [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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Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle. Sci Rep 2020; 10:19466. [PMID: 33173134 PMCID: PMC7655849 DOI: 10.1038/s41598-020-76576-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistics and 92 outlier markers based on Bayescan test. The 13 outlier windows detected by at least two approaches, harboured genes (e.g. GH1, ACE, ASIC3, HSPH1, MVD, BCL2, HIGD2A, CBFA2T3) that may be involved in physiological adaptations required to cope with environmental stressors that are typical of the North African area such as infectious diseases, extended drought periods, scarce food supply, oxygen scarcity in the mountainous areas and high-intensity solar radiation. Our data also point to candidate genes involved in transcriptional regulation suggesting that regulatory elements had also a prominent role in North African cattle response to environmental constraints. Our study yields novel insights into the unique adaptive capacity in these endangered populations emphasizing the need for the use of whole genome sequence data to gain a better understanding of the underlying molecular mechanisms.
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A Genomic Study of Myxomatous Mitral Valve Disease in Cavalier King Charles Spaniels. Animals (Basel) 2020; 10:ani10101895. [PMID: 33081147 PMCID: PMC7602727 DOI: 10.3390/ani10101895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
Cavalier King Charles spaniels (CKCSs) show the earliest onset and the highest incidence of myxomatous mitral valve disease (MMVD). Previous studies have suggested a polygenic inheritance of the disease in this breed and revealed an association with regions on canine chromosomes 13 and 14. Following clinical and echocardiographic examinations, 33 not-directly-related CKCSs were selected and classified as cases (n = 16) if MMVD was present before 5 years of age or as controls (n = 17) if no or very mild MMVD was present after 5 years of age. DNA was extracted from whole blood and genotyped with a Canine 230K SNP BeadChip instrument. Cases and controls were compared with three complementary genomic analyses (Wright's fixation index-FST, cross-population extended haplotype homozygosity-XP-EHH, and runs of homozygosity-ROH) to identify differences in terms of heterozygosity and regions of homozygosity. The top 1% single-nucleotide polymorphisms (SNPs) were selected and mapped, and the genes were thoroughly investigated. Ten consensus genes were found localized on chromosomes 3-11-14-19, partially confirming previous studies. The HEPACAM2, CDK6, and FAH genes, related to the transforming growth factor β (TGF-β) pathway and heart development, also emerged in the ROH analysis. In conclusion, this work expands the knowledge of the genetic basis of MMVD by identifying genes involved in the early onset of MMVD in CKCSs.
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Zhou Z, Fan Y, Wang G, Lai Z, Gao Y, Wu F, Lei C, Dang R. Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations. Animals (Basel) 2020; 10:ani10101823. [PMID: 33036357 PMCID: PMC7600737 DOI: 10.3390/ani10101823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary After a long period of artificial selection, the donkey now presents a variety of body types and production performance values. In this experiment, we performed selective signal scanning on the second-generation resequencing data of six different varieties. The regions and candidate genes related to artificial selection were identified to provide reference for future breeding. Abstract Donkeys (Equus asinus) are an important farm animal. After long-term natural and artificial selection, donkeys now exhibit a variety of body sizes and production performance values. In this study, six donkey breeds, representing different regions and phenotypes, were used for second-generation resequencing. The sequencing results revealed more than seven million single nucleotide variants (SNVs), with an average of more than four million SNVs per species. We combined two methods, Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values, to analyze the signatures of selection. We mapped 11 selected regions and identified genes associated with coat color, body size, motion capacity, and high-altitude adaptation. These candidate genes included staining (ASIP and KITLG), body type (ACSL4, BCOR, CDKL5, LCOR, NCAPG, and TBX3), exercise (GABPA), and adaptation to low-oxygen environments (GLDC and HBB). We also analyzed the SNVs of the breed-specific genes for their potential functions and found that there are three varieties in the conserved regions with breed-specific mutation sites. Our results provide data to support the establishment of the donkey SNV chip and reference information for the utilization of the genetic resources of Chinese domestic donkeys.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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28
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Peripolli E, Reimer C, Ha NT, Geibel J, Machado MA, Panetto JCDC, do Egito AA, Baldi F, Simianer H, da Silva MVGB. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data. BMC Genomics 2020; 21:624. [PMID: 32917133 PMCID: PMC7488563 DOI: 10.1186/s12864-020-07035-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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Affiliation(s)
- Elisa Peripolli
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Ngoc-Thuy Ha
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Johannes Geibel
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Marco Antonio Machado
- National Council for Scientific and Technological Development (CNPq), Lago Sul, 71605-001, Brazil
- Embrapa Dairy Cattle, Juiz de Fora, 36038-330, Brazil
| | | | | | - Fernando Baldi
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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29
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Eisemann JH, Ashwell MS, Devine TL, Poole DH, Poore MH, Linder KE. Physiological response, function of sweat glands, and hair follicle cycling in cattle in response to fescue toxicosis and hair genotype. J Anim Sci 2020; 98:5717958. [PMID: 31998943 DOI: 10.1093/jas/skaa013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/14/2020] [Indexed: 01/27/2023] Open
Abstract
Fescue toxicosis is a syndrome that results when cattle consume toxic endophyte-infected tall fescue. The objective of this study was to compare the response in physiological variables, sweat gland function, hair follicle cycling, and gene expression to feeding a total mixed ration that included tall fescue haylage and tall fescue seed containing a toxic endophyte (EI) or tall fescue haylage containing a nontoxic novel endophyte (EN) in beef heifers (Angus × Senepol heifers, n = 31) with 2 different hair genotypes. Numbers in each subgroup were as follows: novel endophyte, heterozygous slick (EN-S; n = 8), novel endophyte, homozygous hairy (wild type, EN-W; n = 7), endophyte-infected, heterozygous slick (EI-S; n = 10), and endophyte-infected, homozygous hairy (wild type, EI-W; n = 6). Physiological measurements were taken weekly for 7 wk. Data were analyzed using the MIXED procedure of SAS including dietary fescue treatment (EN vs. EI) and hair genotype (S vs. W) as main effects, day as a repeated measure, and temperature-humidity index (THI) as a covariate. Skin biopsies were taken before treatment initiation and on day 37 of treatment. Average surface temperature (ST) increased as the THI increased (P < 0.0001). Average ST was greater (P < 0.01) for animals fed EI than for animals fed the EN fescue diet, and greater (P < 0.01) for animals with the W genotype compared with animals with the S genotype. The difference between heifers with the S and W genotype was greater at greater THI (genotype × day interaction, P < 0.01). Transepidermal water loss (TEWL) was greater (P < 0.05) for animals with the S genotype compared with the W genotype and greater (P < 0.05) for heifers with the S genotype than for heifers with the W genotype when fed EI (36.7, 38.5, 30.0, and 38.7 g/m2 per hour for EN-W, EN-S, EI-W, and EI-S, respectively). The fraction of follicles in telogen in plucked hair samples for heifers fed EI was greater for animals with the S genotype than the W genotype (fraction in telogen: 0.456, 0.565, 0.297, 0.702 for EN-W, EN-S, EI-W, and EI-S, respectively; diet × genotype interaction, P < 0.05). Fraction of follicles in anagen was the opposite. EI fescue resulted in increased ST, changes in hair follicle cycling that support greater hair growth, and decreased TEWL for heifers with the W genotype compared with S genotype, suggesting greater heat stress in response to EI.
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Affiliation(s)
- Joan H Eisemann
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | - Melissa S Ashwell
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | - Thomas L Devine
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | - Daniel H Poole
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | - Matt H Poore
- Department of Animal Science, North Carolina State University, Raleigh, NC
| | - Keith E Linder
- Department of Population, Health and Pathobiology, North Carolina State University, Raleigh, NC
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30
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Fan R, Gu Z, Guang X, Marín JC, Varas V, González BA, Wheeler JC, Hu Y, Li E, Sun X, Yang X, Zhang C, Gao W, He J, Munch K, Corbett-Detig R, Barbato M, Pan S, Zhan X, Bruford MW, Dong C. Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biol 2020; 21:159. [PMID: 32616020 PMCID: PMC7331169 DOI: 10.1186/s13059-020-02080-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/21/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca. RESULTS Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. CONCLUSIONS The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Zhongru Gu
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Juan Carlos Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bio Bio, Chillán, Chile
| | - Valeria Varas
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias., Universidad Austral de Chile, Valdivia, Chile
| | - Benito A. González
- Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Jane C. Wheeler
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Pachacamac, Lima, Peru
| | - Yafei Hu
- BGI Genomics, BGI, Shenzhen, China
| | - Erli Li
- BGI Genomics, BGI, Shenzhen, China
| | | | | | | | - Wenjun Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Junping He
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Russel Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, Santa Cruz, CA USA
| | - Mario Barbato
- Department of Animal Science, Food and Technology – DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Xiangjiang Zhan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael W. Bruford
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, Wales UK
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
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31
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Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020; 10:ani10061005. [PMID: 32521830 PMCID: PMC7341496 DOI: 10.3390/ani10061005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Abstract Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
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32
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Campos E, Cuéllar J, Salvador O, García-Trejo EA, Pereira F. The genetic diversity and phylogeography of Mexican domestic sheep. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
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Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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Melo TP, Fortes MRS, Fernandes Junior GA, Albuquerque LG, Carvalheiro R. RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1. J Anim Sci 2019; 97:3027-3033. [PMID: 30997484 DOI: 10.1093/jas/skz121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/09/2019] [Indexed: 12/18/2022] Open
Abstract
An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10-4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10-3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.
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Affiliation(s)
- Thaise P Melo
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, FCAV/UNESP - Sao Paulo State University, Jaboticabal, Sao Paulo, Brazil
| | - Marina R S Fortes
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, Australia.,The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Queensland, Australia
| | - Gerardo A Fernandes Junior
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, FCAV/UNESP - Sao Paulo State University, Jaboticabal, Sao Paulo, Brazil
| | - Lucia G Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, FCAV/UNESP - Sao Paulo State University, Jaboticabal, Sao Paulo, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasília, Distrito Federal, Brazil
| | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, FCAV/UNESP - Sao Paulo State University, Jaboticabal, Sao Paulo, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasília, Distrito Federal, Brazil
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Genomic selection strategies for breeding adaptation and production in dairy cattle under climate change. Heredity (Edinb) 2019; 123:307-317. [PMID: 30886391 DOI: 10.1038/s41437-019-0207-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/30/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023] Open
Abstract
Livestock production both contributes to and is affected by global climate change, and substantial modifications will be required to increase its climate resilience. In this context, reliance on dominant commercial livestock breeds, featuring small effective population sizes, makes current production strategies vulnerable if their production is restricted to environments, which may be too costly to support under future climate scenarios. The adaptability of animal populations to future environments will therefore become important. To help evaluate the role of genetics in climate adaptation, we compared selection strategies in dairy cattle using breeding simulations, where genomic selection was used on two negatively correlated traits for production (assumed to be moderately heritable) and adaptation (assumed to have low heritability). Compared with within-population breeding, genomic introgression produced a more positive genetic change for both production and adaptation traits. Genomic introgression from highly adapted but low production value populations into highly productive but low adaptation populations was most successful when the adaptation trait was given a lower selection weight than the production trait. Genomic introgression from highly productive population to highly adapted population was most successful when the adaptation trait was given a higher selection weight than the production trait. Both these genomic introgression schemes had the lowest risk of inbreeding. Our results suggest that both adaptation and production can potentially be improved simultaneously by genomic introgression.
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Kantar MB, Bruford MW, Rieseberg LH. The genomics of domestication special issue editorial. Evol Appl 2019; 12:3-5. [PMID: 30622630 PMCID: PMC6304677 DOI: 10.1111/eva.12693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 08/05/2018] [Indexed: 11/27/2022] Open
Abstract
Domestication has been of major interest to biologists for centuries, whether for creating new plants and animal types or more formally exploring the principles of evolution. Such studies have long used combinations of phenotypic and genetic evidence. Recently, the advent of a large number of genomes and genomic tools across a wide array of domesticated plant and animal species has reinvigorated the study of domestication. These genomic data, which can be easily generated for nearly any species, often provide great insight with or without a reference genome. The comparison of genome wide data from domestic and wild species has ignited a wave of insight into human, plant, and animal history with a new range of questions becoming accessible. With this in mind, this issue of Evolutionary Applications includes eleven papers covering a wide range of perspectives and methodologies relevant to understanding genomic variation under domestication.
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Affiliation(s)
- Michael B. Kantar
- Department of Tropical Plant and Soil SciencesUniversity of Hawai'iHonoluluHawaii
| | - Michael W. Bruford
- School of BiosciencesCardiff UniversityCardiffUK
- Sustainable Places Research InstituteCardiff UniversityCardiffUK
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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