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Münzbergová Z, Šurinová M, Biscarini F, Níčová E. Genetic response of a perennial grass to warm and wet environments interacts and is associated with trait means as well as plasticity. J Evol Biol 2024; 37:704-716. [PMID: 38761114 DOI: 10.1093/jeb/voae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/15/2024] [Accepted: 05/17/2024] [Indexed: 05/20/2024]
Abstract
The potential for rapid evolution is an important mechanism allowing species to adapt to changing climatic conditions. Although such potential has been largely studied in various short-lived organisms, to what extent we can observe similar patterns in long-lived plant species, which often dominate natural systems, is largely unexplored. We explored the potential for rapid evolution in Festuca rubra, a long-lived grass with extensive clonal growth dominating in alpine grasslands. We used a field sowing experiment simulating expected climate change in our model region. Specifically, we exposed seeds from five independent seed sources to novel climatic conditions by shifting them along a natural climatic grid and explored the genetic profiles of established seedlings after 3 years. Data on genetic profiles of plants selected under different novel conditions indicate that different climate shifts select significantly different pools of genotypes from common seed pools. Increasing soil moisture was more important than increasing temperature or the interaction of the two climatic factors in selecting pressure. This can indicate negative genetic interaction in response to the combined effects or that the effects of different climates are interactive rather than additive. The selected alleles were found in genomic regions, likely affecting the function of specific genes or their expression. Many of these were also linked to morphological traits (mainly to trait plasticity), suggesting these changes may have a consequence on plant performance. Overall, these data indicate that even long-lived plant species may experience strong selection by climate, and their populations thus have the potential to rapidly adapt to these novel conditions.
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Affiliation(s)
- Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, Czech Republic
- Department of Population Ecology, Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
| | - Maria Šurinová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, Czech Republic
- Department of Population Ecology, Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, National Research Council (IBBA-CNR), Milan, Italy
| | - Eva Níčová
- Department of Population Ecology, Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
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2
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Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [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: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
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Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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3
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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Davaasuren N, Molaee V, Erdene-Ochir TO, Nyamdavaa G, Ganzorig S, Mazzei M, Sakoda Y, Lühken G, Tumenjargal S. Phylogenetic analysis of small ruminant lentiviruses in Mongolian sheep supports an ancient east-west split for the genotype A. Vet Res Commun 2024; 48:1955-1962. [PMID: 38530579 DOI: 10.1007/s11259-024-10361-9] [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: 01/12/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024]
Abstract
The ovine maedi-visna virus (MVV) and caprine arthritis-encephalitis virus (CAEV) are small ruminant lentiviruses (SRLVs) with striking genetic and structural similarities. The presence of SRLV in Mongolian sheep and goats was serologically demonstrated more than a decade ago; however, the viral genotype remains unknown. In total, 329 blood samples were collected from two sheep breeds (i.e., Khalkha and Sumber) in Tov, Govisumber, Arkhangay, Dornogovi, Zavkhan, and Sukhbaatar provinces, Mongolia. Serological and phylogenetic analyses were performed regardless of any apparent clinical signs, although most of the animals appeared healthy. All sheep in three of the six provinces were seronegative, whereas the seroprevalence in the Tov, Govisumber, and Zavkhan provinces averaged 7.9%. Genomic DNA from seropositive animals was tested using hemi-nested polymerase chain reaction, and sub-genomic SRLV sequences were determined from nine samples. Mongolian SRLV sequences clustered within the divergent subtype A22, which was previously found only in Fertile Crescent regions, including Lebanon, Jordan, and Iran, where the first sheep-domestication (Ovis aries) occurred. According to the phylogenetic analysis, genotype A has two ancestors from the ancient Fertile Crescent: (1) Turkish strains and (2) Iranian, Jordanian, and Lebanese strains. The first ancestor spread westward, whereas the second spread eastward, ultimately reaching Mongolia.
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Affiliation(s)
- Nergui Davaasuren
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Vahid Molaee
- Institute of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Tseren-Ochir Erdene-Ochir
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Guugandaa Nyamdavaa
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia
| | - Sumiya Ganzorig
- Department of Biology, National University of Mongolia, Ulaanbaatar, 14021, Mongolia
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 20159, Pisa, Italy
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Giessen, Ludwigstrasse 21, 35390, Giessen, Germany
| | - Sharav Tumenjargal
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Zaisan, Ulaanbaatar, 17024, Mongolia.
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Liang Z, Yue X, Liu Y, Ye M, Zhong L, Luan Y, Wang Q. Genome-Wide Identification of Specific Genetic Loci Common to Sheep and Goat. Biomolecules 2024; 14:638. [PMID: 38927042 PMCID: PMC11201639 DOI: 10.3390/biom14060638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/28/2024] Open
Abstract
Sheep and goat may become carriers of some zoonotic diseases. They are important livestock and experimental model animals for human beings. The fast and accurate identification of genetic materials originating from sheep and goat can prevent and inhibit the spread of some zoonotic diseases, monitor market product quality, and maintain the stability of animal husbandry and food industries. This study proposed a methodology for identifying sheep and goat common specific sites from a genome-wide perspective. A total of 150 specific sites were selected from three data sources, including the coding sequences of single copy genes from nine species (sheep, goat, cow, pig, dog, horse, human, mouse, and chicken), the dbSNPs for these species, and human 100-way alignment data. These 150 sites exhibited low intraspecific heterogeneity in the resequencing data of 1450 samples from five species (sheep, goat, cow, pig, and chicken) and high interspecific divergence in the human 100-way alignment data after quality control. The results were proven to be reliable at the data level. Using the process proposed in this study, specific sites of other species can be screened, and genome-level species identification can be performed using the screened sites.
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Affiliation(s)
- Zuoxiang Liang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiaoyu Yue
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yangxiu Liu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Mengyan Ye
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Ling Zhong
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yue Luan
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Qin Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
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Fonseca PAS, Suárez-Vega A, Arranz JJ, Gutiérrez-Gil B. Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits. Genet Sel Evol 2024; 56:40. [PMID: 38773423 PMCID: PMC11106937 DOI: 10.1186/s12711-024-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). RESULTS In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. CONCLUSIONS The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
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Affiliation(s)
- Pablo A S Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain.
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Zhang C, Asadollahpour Nanaei H, Jafarpour Negari N, Amiri Roudbar M, Amiri Ghanatsaman Z, Niyazbekova Z, Yang X. Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats. BMC Genomics 2024; 25:477. [PMID: 38745140 PMCID: PMC11094986 DOI: 10.1186/s12864-024-10387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. RESULTS To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (- 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. CONCLUSIONS The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.
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Affiliation(s)
- Chenxi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hojjat Asadollahpour Nanaei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | | | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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8
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Somenzi E, Partel E, Barbato M, Chero Osorio AM, Colli L, Franceschi N, Mantovani R, Pilla F, Komjanc M, Achilli A, Hauffe HC, Ajmone Marsan P. Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics. Genet Sel Evol 2024; 56:32. [PMID: 38698323 PMCID: PMC11064358 DOI: 10.1186/s12711-024-00900-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. RESULTS Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. CONCLUSIONS The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.
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Affiliation(s)
- Elisa Somenzi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Erika Partel
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Mario Barbato
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Veterinary Science, Università degli Studi di Messina, Messina, Italy
| | - Ana María Chero Osorio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Sulla Biodiversità e sul DNA Antico, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Niccolò Franceschi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Matteo Komjanc
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Paolo Ajmone Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Wu M, Wang D, Li MH, Lv F. Artificial selection shapes the lower genomic diversity and higher selective pressures on the sex chromosomes of domestic animals. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1072-1075. [PMID: 38277069 DOI: 10.1007/s11427-023-2478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 01/27/2024]
Affiliation(s)
- Meiming Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dongfeng Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Science (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572024, China.
| | - Fenghua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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10
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Ma T, Liu W, Jiang D, Zhang G, Zhao X, Zhang Y, Li Z. Analysis of Toxic Effects of Fluoride on Ovine Follicular Granulosa Cells Using RNA-Seq. Antioxidants (Basel) 2024; 13:506. [PMID: 38790611 PMCID: PMC11118050 DOI: 10.3390/antiox13050506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Fluoride is abundant in the environment and is an essential trace element in living organisms. However, prolonged excessive fluoride intake can lead to fluorosis, which poses a threat to the reproductive health of animals and humans. Although previous research has mainly focused on animal models, the impact of fluoride on ovine follicular granulosa cells (GCs) has not been comprehensively elucidated. This study employed RNA-Seq technology to elucidate the toxic effects of fluoride on ovine follicular GCs and its mechanism of action. Culturing primary ovine follicular GCs in vitro and subjecting them to fluoride treatment revealed 3218 differentially expressed genes (DEGs), with 2278 upregulated and 940 downregulated. Significantly, this study unveiled fluoride's induction of endoplasmic reticulum (ER) stress in cells, triggering a cascade involving the PERK pathway factor ATF4, leading to cell death via DDIT3/CHOP activation and the subsequent upregulation of CHAC1, ATF3, ERO1α, and TRIB3. These findings provide crucial insights into the toxicity of fluoride in ovine, offering a foundation for mitigating fluoride-related losses in the farming industry.
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Affiliation(s)
- Tian Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Wanruo Liu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Didi Jiang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Guolin Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; (T.M.); (W.L.); (D.J.); (G.Z.); (X.Z.)
| | - Zongshuai Li
- Key Laboratory of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- State Key Laboratory of Grassland Agro Ecosystems, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Lanzhou University, Lanzhou 730020, China
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11
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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Liang B, Bai T, Zhao Y, Han J, He X, Pu Y, Wang C, Liu W, Ma Q, Tian K, Zheng W, Liu N, Liu J, Ma Y, Jiang L. Two mutations at KRT74 and EDAR synergistically drive the fine-wool production in Chinese sheep. J Adv Res 2024; 57:1-13. [PMID: 37137429 PMCID: PMC10918353 DOI: 10.1016/j.jare.2023.04.012] [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: 11/02/2022] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/05/2023] Open
Abstract
INTRODUCTION Fine-wool sheep are the most common breed used by the wool industry worldwide. Fine-wool sheep have over a three-fold higher follicle density and a 50% smaller fiber diameter than coarse-wool sheep. OBJECTIVES This study aims to clarify the underlying genetic basis for the denser and finer wool phenotype in fine-wool breeds. METHOD Whole-genome sequences of 140 samples, Ovine HD630K SNP array data of 385 samples, including fine, semi-fine, and coarse wool sheep, as well as skin transcriptomes of nine samples were integrated for genomic selection signature analysis. RESULTS Two loci at keratin 74 (KRT74) and ectodysplasin receptor (EDAR) were revealed. Fine-scale analysis in 250 fine/semi-fine and 198 coarse wool sheep narrowed this association to one C/A missense variant of KRT74 (OAR3:133,486,008, P = 1.02E-67) and one T/C SNP in the regulatory region upstream of EDAR (OAR3:61,927,840, P = 2.50E-43). Cellular over-expression and ovine skin section staining assays confirmed that C-KRT74 activated the KRT74 protein and specifically enlarged cell size at the Huxley's layer of the inner root sheath (P < 0.01). This structure enhancement shapes the growing hair shaft into the finer wool than the wild type. Luciferase assays validated that the C-to-T mutation upregulated EDAR mRNA expression via a newly created SOX2 binding site and potentially led to the formation of more hair placodes. CONCLUSIONS Two functional mutations driving finer and denser wool production were characterized and offered new targets for genetic breeding during wool sheep selection. This study not only provides a theoretical basis for future selection of fine wool sheep breeds but also contributes to improving the value of wool commodities.
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Affiliation(s)
- Benmeng Liang
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China
| | - Tianyou Bai
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China
| | - Yuhetian Zhao
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China
| | - Jiangang Han
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Xiaohong He
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China
| | - Yabin Pu
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China
| | - Chunxin Wang
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 75002, Ningxia, China
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China; Xinjiang Academy of Animal Science, China
| | | | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, China
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yuehui Ma
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China.
| | - Lin Jiang
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Key Laboratory of Livestock and Poultry Resources (Cattle) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, China.
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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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Li Y, Xu W, Wang J, Liu H, Liu J, Zhang L, Hou R, Shen F, Liu Y, Cai K. Giant pandas in captivity undergo short-term adaptation in nerve-related pathways. BMC ZOOL 2024; 9:4. [PMID: 38383502 PMCID: PMC10880213 DOI: 10.1186/s40850-024-00195-y] [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: 08/12/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Behaviors in captive animals, including changes in appetite, activity level, and social interaction, are often seen as adaptive responses. However, these behaviors may become progressively maladaptive, leading to stress, anxiety, depression, and other negative reactions in animals. RESULTS In this study, we investigated the whole-genome sequencing data of 39 giant panda individuals, including 11 in captivity and 28 in the wild. To eliminate the mountain range effect and focus on the factor of captivity only, we first performed a principal component analysis. We then enumerated the 21,474,180 combinations of wild giant pandas (11 chosen from 28) and calculated their distances from the 11 captive individuals. The 11 wild individuals with the closest distances were used for the subsequent analysis. The linkage disequilibrium (LD) patterns demonstrated that the population was almost eliminated. We identified 505 robust selected genomic regions harboring at least one SNP, and the absolute frequency difference was greater than 0.6 between the two populations. GO analysis revealed that genes in these regions were mainly involved in nerve-related pathways. Furthermore, we identified 22 GO terms for which the selection strength significantly differed between the two populations, and there were 10 nerve-related pathways among them. Genes in the differentially abundant regions were involved in nerve-related pathways, indicating that giant pandas in captivity underwent minor genomic selection. Additionally, we investigated the relationship between genetic variation and chromatin conformation structures. We found that nucleotide diversity (θπ) in the captive population was correlated with chromatin conformation structures, which included A/B compartments, topologically associated domains (TADs) and TAD-cliques. For each GO term, we then compared the expression level of genes regulated by the above four factors (AB index, TAD intactness, TAD clique and PEI) with the corresponding genomic background. The retained 10 GO terms were all coordinately regulated by the four factors, and three of them were associated with nerve-related pathways. CONCLUSIONS This study revealed that giant pandas in captivity undergo short-term adaptation in nerve-related pathways. Furthermore, it provides new insights into the molecular mechanism of gene expression regulation under short-term adaptation to environmental change.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Yuliang Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Kailai Cai
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China.
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China.
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Colitti B, Daif S, Choukri I, Scalas D, Jerre A, El Berbri I, Fassi Fihri O, Rosati S. Serological and Molecular Characterization of Small Ruminant Lentiviruses in Morocco. Animals (Basel) 2024; 14:550. [PMID: 38396519 PMCID: PMC10886309 DOI: 10.3390/ani14040550] [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: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Recent studies that investigated the origins of SRLV strains offered new insights into their distribution among domestic ruminants. The aim of the study was to investigate SRLV circulation in Morocco. A total of 51 farms were selected in different geographical locations and tested by screening and genotyping ELISA. Whole blood was used for DNA extraction and nested gag PCR. The sample size allowed for an estimation of prevalence lower than 20% (CI 95%). Surprisingly, a large proportion of screening-positive samples were not correctly serotyped. Sanger and NGS amplicon sequencing approaches allowed us to obtain new sequences even from difficult-to-amplify samples. The serological data support the evidence of an intrinsic difficulty of SRLV to spread, likely due to management practices. The low rate of success by genotyping ELISA led us to suppose that divergent strains might have escaped from diagnostic tools, as partially confirmed by the evidence of an A subtype carrying a mismatch in serotyping epitope. The sequence analysis revealed the circulation of novel B and recombinant A/B subtypes. This study highlights the importance of monitoring viral sequences and their evolution to develop specific diagnostic tests, particularly in countries where control measures are in place.
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Affiliation(s)
- Barbara Colitti
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095 Grugliasco, TO, Italy; (D.S.); (S.R.)
| | - Soukaina Daif
- Department of Pathology and Veterinary Public Health, Agronomic and Veterinary Institute Hassan II, BP: 6202, Rabat-Institutes, Rabat 10101, Morocco; (S.D.); (I.C.); (I.E.B.); (O.F.F.)
| | - Imane Choukri
- Department of Pathology and Veterinary Public Health, Agronomic and Veterinary Institute Hassan II, BP: 6202, Rabat-Institutes, Rabat 10101, Morocco; (S.D.); (I.C.); (I.E.B.); (O.F.F.)
| | - Daniela Scalas
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095 Grugliasco, TO, Italy; (D.S.); (S.R.)
| | - Anniken Jerre
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway;
| | - Ikhlass El Berbri
- Department of Pathology and Veterinary Public Health, Agronomic and Veterinary Institute Hassan II, BP: 6202, Rabat-Institutes, Rabat 10101, Morocco; (S.D.); (I.C.); (I.E.B.); (O.F.F.)
| | - Ouafaa Fassi Fihri
- Department of Pathology and Veterinary Public Health, Agronomic and Veterinary Institute Hassan II, BP: 6202, Rabat-Institutes, Rabat 10101, Morocco; (S.D.); (I.C.); (I.E.B.); (O.F.F.)
| | - Sergio Rosati
- Department of Veterinary Science, University of Turin, Largo Braccini 2, 10095 Grugliasco, TO, Italy; (D.S.); (S.R.)
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Vlaic BA, Vlaic A, Russo IR, Colli L, Bruford MW, Odagiu A, Orozco-terWengel P. Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data. Animals (Basel) 2024; 14:560. [PMID: 38396528 PMCID: PMC10886219 DOI: 10.3390/ani14040560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.
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Affiliation(s)
- Bogdan Alin Vlaic
- Department of Animal Breeding, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Augustin Vlaic
- Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania;
| | - Isa-Rita Russo
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti (DIANA), BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense n. 84, 29122 Piacenza, PC, Italy;
| | - Michael William Bruford
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
| | - Antonia Odagiu
- Faculty of Agriculture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Mănăștur Street 3–5, 400372 Cluj-Napoca, Romania
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK; (I.-R.R.); (M.W.B.)
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17
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Balcarcel AM, Geiger M, Sánchez-Villagra MR. Cranial form differences in goats by breed and domestic status. Sci Rep 2024; 14:917. [PMID: 38195639 PMCID: PMC10776561 DOI: 10.1038/s41598-023-50357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Domestic goats (Capra hircus) are globally represented by over 300 breeds, making them a useful model for investigating patterns of morphological change related to domestication. However, they have been little studied, likely due to their poor representation in museum collections and the difficulty in obtaining truly wild goat (Capra aegagrus, the bezoar) samples. Similar studies on other species reveal that domestication correlates with craniofacial alterations in domestics, which are non-uniform and often species-specific. Here, we use three-dimensional geometric morphometric methods (3DGMM) to describe and quantify cranial shape variation in wild (n = 21) versus domestic (n = 54) goats. We find that mean cranial shapes differ significantly between wild and domestic goats as well as between certain breeds. The detected differences are lower in magnitude than those reported for other domestic groups, possibly explained by the fewer directions of artificial selection in goat breeding, and their low global genetic diversity compared to other livestock. We also find tooth-row length reduction in the domestics, suggestive of rostral shortening-a prediction of the "domestication syndrome" (DS). The goat model thus expands the array-and combinations of-morphological changes observed under domestication, notably detecting alterations to the calvarium form which could be related to the ~ 15% brain size reduction previously reported for domestic compared to wild goats. The global success of domestic goats is due more to their ability to survive in a variety of harsh environments than to systematized human management. Nonetheless, their domestication has resulted in a clear disruption from the wild cranial form, suggesting that even low-intensity selection can lead to significant morphological changes under domestication.
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Affiliation(s)
- A M Balcarcel
- Department of Paleontology, University of Zurich, Karl-Schmid-Str. 4, 8006, Zurich, Switzerland.
| | - M Geiger
- Naturmuseum St.Gallen, Rorschacher Strasse 263, 9016, St.Gallen, Switzerland
| | - M R Sánchez-Villagra
- Department of Paleontology, University of Zurich, Karl-Schmid-Str. 4, 8006, Zurich, Switzerland
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18
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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19
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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20
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Nikmanesh A, Esmailizadeh A, Asadollahpour Nanaei H, Ezedinloo L, Asadi Fozi M. Comparison of genetic diversity and phylogenetic structure of BRCA1 gene of some domestic and wild sheep breeds in different countries. Anim Biotechnol 2023; 34:4746-4759. [PMID: 36927261 DOI: 10.1080/10495398.2023.2187410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BRCA1 gene plays an important role in DNA damage repair, cell cycle, and transcription process regulation; hence it's called gate keeper. The current research aims to perform bioinformatics analyzes of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 14 countries using the NCBI genome database. The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. The number of mutations, nucleotide diversity, and haploid diversity were also analyzed using Dnaspv5 software. The analyses showed 296 polymorphisms, which led to the creation of 45 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences among breeds were estimated as 0.259 and 0.052, respectively. The average genetic distance within the population of countries was calculated as 0.052. The amount of sequence conservation in this research was 0.313 on average, which indicates the high polymorphism of this gene and the emergence of new proteins. Tajima's D value in Tajima's neutrality test was -2.421, which was significant (p < 0.05). One of the reasons for the high genetic diversity in Iran's wild sheep population is the existence of forests and open environments, which prevent genetic drift and reduce inbreeding.
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Affiliation(s)
- Alireza Nikmanesh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Leila Ezedinloo
- Department of Environment (DOE), Natural History Museum & Genetic Resource, Bureau, Park Nature of Pardisan, Tehran, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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21
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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22
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Manunza A, Ramirez-Diaz J, Cozzi P, Lazzari B, Tosser-Klopp G, Servin B, Johansson AM, Grøva L, Berg P, Våge DI, Stella A. Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe. Sci Rep 2023; 13:20728. [PMID: 38007600 PMCID: PMC10676416 DOI: 10.1038/s41598-023-48005-8] [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: 06/22/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023] Open
Abstract
In the last decade, several studies aimed at dissecting the genetic architecture of local small ruminant breeds to discover which variations are involved in the process of adaptation to environmental conditions, a topic that has acquired priority due to climate change. Considering that traditional breeds are a reservoir of such important genetic variation, improving the current knowledge about their genetic diversity and origin is the first step forward in designing sound conservation guidelines. The genetic composition of North-Western European archetypical goat breeds is still poorly exploited. In this study we aimed to fill this gap investigating goat breeds across Ireland and Scandinavia, including also some other potential continental sources of introgression. The PCA and Admixture analyses suggest a well-defined cluster that includes Norwegian and Swedish breeds, while the crossbred Danish landrace is far apart, and there appears to be a close relationship between the Irish and Saanen goats. In addition, both graph representation of historical relationships among populations and f4-ratio statistics suggest a certain degree of gene flow between the Norse and Atlantic landraces. Furthermore, we identify signs of ancient admixture events of Scandinavian origin in the Irish and in the Icelandic goats. The time when these migrations, and consequently the introgression, of Scandinavian-like alleles occurred, can be traced back to the Viking colonisation of these two isles during the Viking Age (793-1066 CE). The demographic analysis indicates a complicated history of these traditional breeds with signatures of bottleneck, inbreeding and crossbreeding with the improved breeds. Despite these recent demographic changes and the historical genetic background shaped by centuries of human-mediated gene flow, most of them maintained their genetic identity, becoming an irreplaceable genetic resource as well as a cultural heritage.
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Affiliation(s)
- Arianna Manunza
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy.
| | - Johanna Ramirez-Diaz
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Paolo Cozzi
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | | | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007, Uppsala, Sweden
| | - Lise Grøva
- Norwegian Institute of Bioeconomy Research, Gunnars vei 6, NO-6630, Tingvoll, Norway
| | - Peer Berg
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Dag Inge Våge
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
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23
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Cinar MU, Arslan K, Sohel MMH, Bayram D, Piel LMW, White SN, Daldaban F, Aksel EG, Akyüz B. Genome-wide association study of early liveweight traits in fat-tailed Akkaraman lambs. PLoS One 2023; 18:e0291805. [PMID: 37988399 PMCID: PMC10662757 DOI: 10.1371/journal.pone.0291805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/06/2023] [Indexed: 11/23/2023] Open
Abstract
Small ruminants, especially sheep, are essential for sustainable agricultural production systems, future food/nutrition security, and poverty reduction in developing countries. Within developed countries, the ability of sheep to survive on low-quality forage intake could act as buffer against climate change. Besides sheep's importance in sustainable agricultural production, there has been less ongoing work in terms of sheep genetics in Near East, Middle East and in Africa. For lamb meat production, body weight and average daily gain (ADG) until weaning are critical economic traits that affects the profitability of the industry. The current study aims to identify single nucleotide polymorphisms (SNPs) that are significantly associated with pre-weaning growth traits in fat tail Akkaraman lambs using a genome-wide association study (GWAS). A total of 196 Akkaraman lambs were selected for analysis. After quality control, a total of 31,936 SNPs and 146 lambs were used for subsequent analyses. PLINK 1.9 beta software was used for the analyses. Based on Bonferroni-adjusted p-values, one SNP (rs427117280) on chromosome 2 (OAR2) had significant associations with weaning weight at day 90 and ADG from day 0 to day 90, which jointly explains a 0.8% and 0.9% of total genetic variation respectively. The Ovis aries natriuretic peptide C (NPPC) could be considered as a candidate gene for the defined significant associations. The results of the current study will help to increase understanding of the variation in weaning weight and ADG until weaning of Akkaraman lambs and help enhance selection for lambs with improved weaning weight and ADG. However, further investigations are required for the identification of causal variants within the identified genomic regions.
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Affiliation(s)
- Mehmet Ulas Cinar
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri, Turkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Korhan Arslan
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Md Mahmodul Hasan Sohel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Dhaka, Bangladesh
| | - Davut Bayram
- Faculty of Veterinary Medicine, Department of Animal Science, Erciyes University, Kayseri, Turkiye
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Res. 3003 ADBF, WSU Pullman, Pullman, Washington, United States of America
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Fadime Daldaban
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Esma Gamze Aksel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
| | - Bilal Akyüz
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkiye
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24
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Morell Miranda P, Soares AER, Günther T. Demographic reconstruction of the Western sheep expansion from whole-genome sequences. G3 (BETHESDA, MD.) 2023; 13:jkad199. [PMID: 37675574 DOI: 10.1093/g3journal/jkad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
As one of the earliest livestock, sheep (Ovis aries) were domesticated in the Fertile Crescent about 12,000-10,000 years ago and have a nearly worldwide distribution today. Most of our knowledge about the timing of their expansions stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (O. gmelini, previously known as O. orientalis), to explore the demographic history of sheep. On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected 4 representative breeds from Spain, Morocco, the United Kingdom, and Iran to build a comprehensive demographic model of the Western sheep expansion. We inferred a single domestication event around 11,000 years ago. The subsequent westward expansion is dated to approximately 7,000 years ago, later than the original Neolithic expansion of sheep and slightly predating the Secondary Product Revolution associated with wooly sheep. We see some signals of recent gene flow from an ancestral population into Southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with modern breed development. Our study provides insights into the complex demographic history of Western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.
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Affiliation(s)
- Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - André E R Soares
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-752 37 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
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25
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Wang D, Salehian-Dehkordi H, Suo L, Lv F. Impacts of Population Size and Domestication Process on Genetic Diversity and Genetic Load in Genus Ovis. Genes (Basel) 2023; 14:1977. [PMID: 37895326 PMCID: PMC10606048 DOI: 10.3390/genes14101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (Ne), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild Ovis species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus Ovis have no discernible impact on recent Ne, and three species within the subgenus Pachyceros tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species' dramatic decline in population sizes within the subgenus Pachyceros ~80-250 thousand years ago. European mouflon presented with the lowest Ne, lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small Ne of European mouflon could reduce harmful mutations compared to other species within the genus Ovis. We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the "cost of domestication" during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species.
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Affiliation(s)
- Dongfeng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | | | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China;
| | - Fenghua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
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Senczuk G, Di Civita M, Rillo L, Macciocchi A, Occidente M, Saralli G, D’Onofrio V, Galli T, Persichilli C, Di Giovannantonio C, Pilla F, Matassino D. The genome-wide relationships of the critically endangered Quadricorna sheep in the Mediterranean region. PLoS One 2023; 18:e0291814. [PMID: 37851594 PMCID: PMC10584175 DOI: 10.1371/journal.pone.0291814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/22/2023] [Indexed: 10/20/2023] Open
Abstract
Livestock European diffusion followed different human migration waves from the Fertile Crescent. In sheep, at least two diffusion waves have shaped the current breeds' biodiversity generating a complex genetic pattern composed by either primitive or fine-wool selected breeds. Nowadays most of the sheep European breeds derive from the second wave which is supposed to have largely replaced oldest genetic signatures, with the exception of several primitive breeds confined on the very edge of Northern Europe. Despite this, some populations also in the Mediterranean region are characterised by the presence of phenotypic traits considered ancestral such as the policeraty, large horns in the ram, short tail, and a moulting fleece. Italy is home of a large number of local breeds, albeit some are already extinct, others are listed as critically endangered, and among these there is the Quadricorna breed which is a four-horned sheep characterised by several traits considered as ancestral. In this context we genotyped 47 individuals belonging to the Quadricorna sheep breed, a relict and endangered breed, from Central and Southern Italy. In doing so we used the Illumina OvineSNP50K array in order to explore its genetic diversity and to compare it with other 41 breeds from the Mediterranean region and Middle-East, with the specific aim to reconstruct its origin. After retaining 32,862 SNPs following data filtering, the overall genomic architecture has been explored by using genetic diversity indices, Principal Component Analysis (PCA) and admixture analysis, while the genetic relationships and migration events have been inferred using a neighbor-joining tree based on Reynolds' distances and by the maximum likelihood tree as implemented in treemix. The Quadricorna breed exhibit genetic diversity indices comparable with those of most of the other analysed breeds, however, the two populations showed opposing patterns of genetic diversity suggesting different levels of genomic inbreeding and drift (FIS and FROH). In general, all the performed genome-wide analyses returned complementary results, indicating a westward longitudinal cline compatible with human migrations from the Middle-East and several additional genetic footprints which might mirror more recent historical events. Interestingly, among the Italian breeds, the original Quadricorna (QUAD_SA) first separated showing its own ancestral component. In addition, the admixture analysis does not suggest any signal of recent gene exchange with other Italian local breeds, highlighting a rather ancestral purity of this population. On the other hand, both the neighbor-joining tree and the treemix analysis seem to suggest a proximity of the Quadricorna populations to breeds of South-Eastern Mediterranean origin. Although our results do not support a robust link between the genetics of the first wave and the presence of primitive traits, the observed genetic uniqueness together with the inferred phylogeograpic reconstruction would suggest an ancient presence of the Quadricorna breed in the Italian Peninsula. Because of this singularity, urgent conservation actions are needed in order to keep the breed and all related cultural products alive.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Marika Di Civita
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Luigina Rillo
- Consortium for Experimentation, Dissemination, and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
| | - Alessandra Macciocchi
- Agenzia Regionale per lo Sviluppo e l’Innovazione dell’Agricoltura del Lazio (ARSIAL), Roma, Italy
| | - Mariaconsiglia Occidente
- Consortium for Experimentation, Dissemination, and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
| | - Giorgio Saralli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Valentina D’Onofrio
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Tiziana Galli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri (IZSLT), Roma, Italy
| | - Christian Persichilli
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | | | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Donato Matassino
- Consortium for Experimentation, Dissemination, and Application of Innovative Biotechniques, (ConSDABI), Benevento, Italy
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Selionova M, Aibazov M, Sermyagin A, Belous A, Deniskova T, Mamontova T, Zharkova E, Zinovieva N. Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats. Animals (Basel) 2023; 13:3237. [PMID: 37893961 PMCID: PMC10603756 DOI: 10.3390/ani13203237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Magomet Aibazov
- North Caucasian Agrarian Center, Zootechnicheski 15, 355017 Stavropol, Russia;
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Deniskova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Mamontova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Ekaterina Zharkova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
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Zhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 2023; 24:392. [PMID: 37434152 DOI: 10.1186/s12864-023-09479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
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Affiliation(s)
- Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
| | - Hongmei Zhang
- First Affiliated Hospital, School of Medical College, Shihezi University, Shihezi, Xinjiang, China
| | - Hugh T Blair
- Institute Veterinary, Animal & Biomedical Sciences, Massey University, Auckland, Palmerston North, New Zealand
| | - Wei Zheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chenhui Fang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Huaqian Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hangdong Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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Arenas-Báez P, Torres-Hernández G, Castillo-Hernández G, Hernández-Rodríguez M, Sánchez-Gutiérrez RA, Vargas-López S, González-Maldonado J, Domínguez-Martínez PA, Granados-Rivera LD, Maldonado-Jáquez JA. Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion. BIOLOGY 2023; 12:929. [PMID: 37508360 PMCID: PMC10376610 DOI: 10.3390/biology12070929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.
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Affiliation(s)
- Pablo Arenas-Báez
- Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, Bermejillo, Durango 35230, Mexico
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico
| | | | - Ricardo Alonso Sánchez-Gutiérrez
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Zacatecas, Calera, Zacatecas 98500, Mexico
| | | | - Juan González-Maldonado
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali 21750, Mexico
| | - Pablo Alfredo Domínguez-Martínez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Valle del Guadiana, Durango 34170, Mexico
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Genera Terán, General Terán 67400, Mexico
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental La Laguna, Matamoros 27440, Mexico
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Dou M, Li M, Zheng Z, Chen Q, Wu Y, Wang J, Shan H, Wang F, Dai X, Li Y, Yang Z, Tan G, Luo F, Chen L, Shi YS, Wu JW, Luo XJ, Asadollahpour Nanaei H, Niyazbekova Z, Zhang G, Wang W, Zhao S, Zheng W, Wang X, Jiang Y. A missense mutation in RRM1 contributes to animal tameness. SCIENCE ADVANCES 2023; 9:eadf4068. [PMID: 37352351 PMCID: PMC10289655 DOI: 10.1126/sciadv.adf4068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/18/2023] [Indexed: 06/25/2023]
Abstract
The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.
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Affiliation(s)
- Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830011, China
| | - Yongji Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Huiquan Shan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yunjia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Zhirui Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guanghui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Medical School, Nanjing University, Nanjing, Jiangsu, 210032, China
| | - Jiang Wei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xiong-Jian Luo
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1983969412, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guojie Zhang
- Centre for Evolutionary and Organismal Biology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310000, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Wenxin Zheng
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, 830011, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, Zamani P, Moradi MH, Ferdosi MH, Sargolzaei M, Gondro C. Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep. Heredity (Edinb) 2023; 130:358-367. [PMID: 37016136 PMCID: PMC10238534 DOI: 10.1038/s41437-023-00611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.
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Affiliation(s)
- Ramin Abdoli
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran.
| | - Seyed Ziaeddin Mirhoseini
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran.
| | - Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
| | - Pouya Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, 65178-33131, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arāk, 38156-8-8349, Iran
| | - Mohammad Hossein Ferdosi
- AGBU, a joint venture of NSW Department of Primary Industries and University of New England, University of New England, Armidale, NSW, 2351, Australia
| | - Mehdi Sargolzaei
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Cedric Gondro
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
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Ceccobelli S, Landi V, Senczuk G, Mastrangelo S, Sardina MT, Ben-Jemaa S, Persichilli C, Karsli T, Bâlteanu VA, Raschia MA, Poli MA, Ciappesoni G, Muchadeyi FC, Dzomba EF, Kunene NW, Lühken G, Deniskova TE, Dotsev AV, Zinovieva NA, Zsolnai A, Anton I, Kusza S, Carolino N, Santos-Silva F, Kawęcka A, Świątek M, Niżnikowski R, Špehar M, Anaya G, Granero A, Perloiro T, Cardoso P, Grande S, de Los Santos BL, Danchin-Burge C, Pasquini M, Martínez Martínez A, Delgado Bermejo JV, Lasagna E, Ciani E, Sarti FM, Pilla F. A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds. Genet Sel Evol 2023; 55:24. [PMID: 37013467 PMCID: PMC10069132 DOI: 10.1186/s12711-023-00797-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.
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Affiliation(s)
- Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy.
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari ''Aldo Moro", 70010, Valenzano, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Maria Teresa Sardina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Valentin-Adrian Bâlteanu
- Laboratory of Genomics, Biodiversity, Animal Breeding and Molecular Pathology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, 400372, Cluj-Napoca, Romania
| | - María Agustina Raschia
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Mario Andrés Poli
- Instituto de Genética "Ewald A. Favret", Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, B1686, Hurlingham, Buenos Aires, Argentina
| | - Gabriel Ciappesoni
- Instituto Nacional de Investigación Agropecuaria, 90200, Canelones, Uruguay
| | | | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, 3209, Scottsville, Pietermaritzburg, South Africa
| | | | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, 35390, Giessen, Germany
| | | | | | | | - Attila Zsolnai
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053, Herceghalom, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Nuno Carolino
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Fátima Santos-Silva
- Instituto Nacional de Investigação Agrária e Veterinária, 2005-048, Vale de Santarém, Portugal
| | - Aldona Kawęcka
- Department of Sheep and Goat Breeding, National Research Institute of Animal Production, 32-083, Kraków, Poland
| | - Marcin Świątek
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Roman Niżnikowski
- Department of Animal Breeding, Institute of Animal Sciences, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Marija Špehar
- Croatian Agency for Agriculture and Food, 10000, Zagreb, Croatia
| | - Gabriel Anaya
- MERAGEM Group, Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
| | - Antonio Granero
- Asociación Nacional de Criadores de Ganado Merino (ACME), 28028, Madrid, Spain
| | - Tiago Perloiro
- Associação Nacional de Criadores de Ovinos da Raça Merina (ANCORME), 7005-665, Évora, Portugal
| | - Pedro Cardoso
- Associação de Produtores Agropecuários (OVIBEIRA), 6000-244, Castelo Branco, Portugal
| | - Silverio Grande
- Associazione Nazionale della Pastorizia (ASSONAPA), 00187, Rome, Italy
| | | | | | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | | | | | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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Al-Shibawi JA, Al-Yaseri AJ, Al-Dhalimi HM, Al-Gharawi JK. Impact of licorice and rosemary powder in the diet on several carcass characteristics of local goats. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
A total of 12 male goats were used at the age of four months; the animals were placed in adjacent and separated enclosures. Treatments as follows: T1 (control), T2 adding 5 g/kg of rosemary leaves to powder and T3 adding 5 g/kg of licorice root powder, T4 (the mixture treatment), adding 5 g/kg of rosemary goes to powder and 5 g of licorice root powder. The results showed that the T3 and T4 treatments were significantly superior in live weight, empty body weight, hot and cold carcass weight and the dressing ratio calculated based on empty weight compared to the control treatment. Also, T4 was significantly superior compared to T1 on the total percentages of major cuts. At the same time, there was a significant decrease in the total rates of secondary cuts in treatments T2, T3 and T4 compared to the control treatment T1. The treatments T2, T3 and T4 were significantly superior to the control treatment T1 in the shoulder ratio, while the neck ratio decreased significantly in T3 and T4 compared to the control treatment T1. The control treatment was significantly superior in the ulna segmental ratio compared to T4.
Keywords: rosemary, licorice, carcass, local goats.
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Affiliation(s)
| | - Ahmed J. Al-Yaseri
- Animal Production Department, Agriculture College, Al-Muthanna University, Iraq
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Platani M, Sokefun O, Bassil E, Apidianakis Y. Genetic engineering and genome editing in plants, animals and humans: Facts and myths. Gene 2023; 856:147141. [PMID: 36574935 DOI: 10.1016/j.gene.2022.147141] [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: 03/30/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.
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Affiliation(s)
- Maria Platani
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Owolabi Sokefun
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Elias Bassil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
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36
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Cheng H, Zhang Z, Wen J, Lenstra JA, Heller R, Cai Y, Guo Y, Li M, Li R, Li W, He S, Wang J, Shao J, Song Y, Zhang L, Billah M, Wang X, Liu M, Jiang Y. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep. PLoS Genet 2023; 19:e1010615. [PMID: 36821549 PMCID: PMC9949681 DOI: 10.1371/journal.pgen.1010615] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
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Affiliation(s)
- Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jintao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuxuan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Masum Billah
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
- * E-mail: (ML); (YJ)
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- * E-mail: (ML); (YJ)
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Hu R, Jiang X, Yang H, Liu G. Selection signature analysis reveals RDH5 performed key function in vision during sheep domestication process. Arch Anim Breed 2023. [DOI: 10.5194/aab-66-81-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Abstract. As one of the most successful domesticated animals in the Neolithic age,
sheep gradually migrated all over the world with human activities. During the
domestication process, remarkable changes have taken place in morphology,
physiology, and behavior, resulting in different breeds with different
characters via artificial and natural selection. However, the genetic
background responsible for these phenotypic variations remains largely
unclear. Here, we used whole genome resequencing technology to compare and
analyze the genome differences between Asiatic mouflon wild sheep (Ovis orientalis) and Hu
sheep (Ovis aries). A total of 755 genes were positively selected in the process of
domestication and selection, and the genes related to sensory perception had
directional evolution in the autosomal region, such as OPRL1, LEF1, TAS1R3, ATF6, VSX2, MYO1A, RDH5, and some novel
genes. A missense mutation of c.T722C/p.M241T in exon 4 of RDH5 existing in sheep
were found, and the T allele was completely fixed in Hu sheep. In addition, the
mutation with the C allele reduced the retinol dehydrogenase activity encoding
by RDH5, which can impair retinoic acid metabolism and further influenced the visual
cycle. Overall, our results showed significant enrichment for positively
selected genes involved in sensory perception development during sheep
domestication; RDH5 and its variants may be related to the retinal degeneration
in sheep. We infer that the wild sheep ancestors with weaker visual sensitivity
were weeded out by humans, and the mutation was selective, swept by the dual
pressures of natural and artificial selection.
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circITGB1 Regulates Adipocyte Proliferation and Differentiation via the miR-23a/ARRB1 Pathway. Int J Mol Sci 2023; 24:ijms24031976. [PMID: 36768295 PMCID: PMC9916083 DOI: 10.3390/ijms24031976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Adipose tissues represent an important energy storage organ in animals and are the largest endocrine organ. It plays an important regulatory role in the pathogenesis of insulin resistance, cardiovascular disease, and metabolic syndrome. Adipose development is a complex biological process involving multiple key genes, signaling pathways, and non-coding RNAs, including microRNAs and circular RNAs. In this study, we characterized circITGB1 and named its host gene ITGB1, which is differentially expressed in sheep of different months based on sequencing data. We collated and analyzed the sequencing data to select miRNA-23a with strong binding to ARRB1. We found that miRNA-23a regulates the development and differentiation of sheep adipocytes by targeting ARRB1. As a competing endogenous RNA, circITGB1 overexpression effectively alleviated the inhibitory effect of miR-23a on ARRB1. Conclusively, we provide evidence that circITGB1 regulates the proliferation and differentiation of sheep adipocytes via the miR-23a/ARRB1 pathway. This study provides a scientific basis for further studies on adipose tissue development at the circRNA level.
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Asadollahpour Nanaei H, Cai Y, Alshawi A, Wen J, Hussain T, Fu WW, Xu NY, Essa A, Lenstra JA, Wang X, Jiang Y, Wang X, Jiang Y. Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate. Zool Res 2023; 44:20-29. [PMID: 36257823 PMCID: PMC9841177 DOI: 10.24272/j.issn.2095-8137.2022.242] [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] [Indexed: 01/04/2023] Open
Abstract
Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex ( C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Akil Alshawi
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Baghdad, Iraqi Ministry of Higher Education and Scientific Research, Bagdad 10090, Iraq
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore 54000, Pakistan
| | - Wei-Wei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nai-Yi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Abdulameer Essa
- Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad 10081, Iraq
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China,E-mail:
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China,
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Gaspar D, Usié A, Leão C, Guimarães S, Pires AE, Matos C, Ramos AM, Ginja C. Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds. Front Genet 2023; 14:1109490. [PMID: 36713074 PMCID: PMC9880275 DOI: 10.3389/fgene.2023.1109490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10-3 ≤ π ≤ 3.1 × 10-3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.
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Affiliation(s)
- Daniel Gaspar
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,*Correspondence: Daniel Gaspar, ; Catarina Ginja,
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Célia Leão
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Sílvia Guimarães
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ana Elisabete Pires
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | | | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal,MED—Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Catarina Ginja
- BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal,*Correspondence: Daniel Gaspar, ; Catarina Ginja,
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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Cao C, Kang Y, Zhou Q, Nanaei HA, Bo D, Liu P, Bai Y, Li R, Jiang Y, Lan X, Pan C. Whole-genome resequencing reveals the genomic diversity and signatures of selection in Romanov sheep. J Anim Sci 2023; 101:skad291. [PMID: 37680132 PMCID: PMC10516466 DOI: 10.1093/jas/skad291] [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: 05/01/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023] Open
Abstract
Romanov sheep are adapted to the extremely cold and harsh environment and display a distinctive grey color. Herein, we analyzed the population structure, genetic diversity, and selection signatures of Romanov sheep based on whole-genome sequencing data of 17 Romanov sheep, 114 individuals from other 10 European breeds. The results of PCA, ADMIXTURE, and NJ-tree showed that the Romanov sheep was closely related to other northern European breeds. A relative high level of genetic diversity, low inbreeding coefficient, and large effective population size was observed in Romanov sheep when compared with other European breeds. We then screened the genomic selection signatures of Romanov sheep using FST, XP-XLP, and XP-EHH methods. The most significant region under selection (CHR14:14.2 to 14.3 Mb) harbored a haplotype that contained MC1R gene. Furthermore, this haplotype was also found in other grey-body breeds including Gotland sheep, Grey Tronder Sheep, and German grey heath sheep, suggesting that it was associated with the unique coat color of these breeds. We also found one region (CHR10:40.8Mb- 41.0Mb) harboring PCDH9 gene which was potentially associated with cold environmental adaptation. In summary, this study identified candidate genes that were associated with the unique grey color and environmental adaptation in Romanov sheep, which provided a basis for understanding the genetic background and utilization of this breed.
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Affiliation(s)
- Chunna Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Didi Bo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiyao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Taheri S, Saedi N, Zerehdaran S, Javadmanesh A. Identification of selection signatures in Capra hircus and Capra aegagrus in Iran. Anim Sci J 2023; 94:e13864. [PMID: 37560768 DOI: 10.1111/asj.13864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 04/09/2023] [Accepted: 05/17/2023] [Indexed: 08/11/2023]
Abstract
Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.
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Affiliation(s)
- Sadegh Taheri
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Naghmeh Saedi
- Centre for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Wan X, Jing JN, Wang DF, Lv FH. Whole-genome selective scans detect genes associated with important phenotypic traits in goat ( Capra hircus). Front Genet 2023; 14:1173017. [PMID: 37144124 PMCID: PMC10151485 DOI: 10.3389/fgene.2023.1173017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. In this study, we focused on the worldwide goat breeds with outstanding traits and used whole-genome resequencing data in 361 samples from 68 breeds to detect genomic selection sweep regions. We identified 210-531 genomic regions with six phenotypic traits, respectively. Further gene annotation analysis revealed 332, 203, 164, 300, 205, and 145 candidate genes corresponding with dairy, wool, high prolificacy, poll, big ear, and white coat color traits. Some of these genes have been reported previously (e.g., KIT, KITLG, NBEA, RELL1, AHCY, and EDNRA), while we also discovered novel genes, such as STIM1, NRXN1, LEP, that may be associated with agronomic traits like poll and big ear morphology. Our study found a set of new genetic markers for genetic improvement in goats and provided novel insights into the genetic mechanisms of complex traits.
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Affiliation(s)
- Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia-Nan Jing
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Feng-Hua Lv,
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Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022; 23:827. [PMCID: PMC9748406 DOI: 10.1186/s12864-022-09033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.
Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$
±
7.61
kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.
Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
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Dutrow EV, Serpell JA, Ostrander EA. Domestic dog lineages reveal genetic drivers of behavioral diversification. Cell 2022; 185:4737-4755.e18. [PMID: 36493753 PMCID: PMC10478034 DOI: 10.1016/j.cell.2022.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022]
Abstract
Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.
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Affiliation(s)
- Emily V Dutrow
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James A Serpell
- Department of Clinical Sciences and Advanced Medicine, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Balcarcel AM, Geiger M, Clauss M, Sánchez‐Villagra MR. The mammalian brain under domestication: Discovering patterns after a century of old and new analyses. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:460-483. [PMID: 34813150 PMCID: PMC9787656 DOI: 10.1002/jez.b.23105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022]
Abstract
Comparisons of wild and domestic populations have established brain reduction as one of the most consistent patterns correlated with domestication. Over a century of scholarly work has been devoted to this subject, and yet, new data continue to foster its debate. Current arguments, both for and against the validity of brain reduction occurring in domestic taxa, have repeatedly cited a small set of reviews on this subject. The original works, their sampling, methodological details, and nuances of results that would be key to establishing validity, particularly in light of new data, have not been investigated. To facilitate and encourage a more informed discussion, we present a comprehensive review of original brain reduction literature for four mammalian clades: Artiodactyla, Perissodactyla, Carnivora, and Glires. Among these are studies that generated the most cited brain reduction values in modern domestication literature. In doing so, we provide a fairer stage for the critique of traits associated with domestication. We conclude that while brain reduction magnitudes may contain error, empirical data collectively support the reduction in brain size and cranial capacity for domestic forms.
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Affiliation(s)
- A. M. Balcarcel
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Geiger
- Palaeontological Institute and MuseumUniversity of ZurichZurichSwitzerland
| | - M. Clauss
- Vetsuisse Faculty, Clinic for Zoo Animals, Exotic Pets and WildlifeUniversity of ZurichZurichSwitzerland
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Pan Y, Wang M, Wu H, Akhatayeva Z, Lan X, Fei P, Mao C, Jiang F. Indel mutations of sheep PLAG1 gene and their associations with growth traits. Anim Biotechnol 2022; 33:1459-1465. [PMID: 33825658 DOI: 10.1080/10495398.2021.1906265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pleiomorphic adenoma gene 1 (PLAG1) is mainly expressed in embryonic development, and it is reported to take an effect on the growth performance of mice, cattle, pigs, and sheep. To explore how conservative the PLAG1 is in different sheep breeds, the effects of the two indel variants on the growth traits of the Chinese Luxi blackhead (LXBH) sheep were firstly detected. The P2-del 30 bp and P4-del 45 bp indel loci of the sheep PLAG1 gene were significantly related to 15 growth traits (P < 0.05). Genotype ID and genotype II were dominant for the P2-del 30 bp and P4-del 45 bp loci, respectively. The above findings indicated that the two indel mutations in the ovine PLAG1 gene were suggested to become the molecular markers for the selection of economic traits in sheep.
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Affiliation(s)
- Yun Pan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Min Wang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Wu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Panfeng Fei
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Cui Mao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
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Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol 2022; 70:102236. [PMID: 36368125 DOI: 10.1016/j.mib.2022.102236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
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A Label-Free Quantitative Analysis for the Search of Proteomic Differences between Goat Breeds. Animals (Basel) 2022; 12:ani12233336. [PMID: 36496858 PMCID: PMC9740416 DOI: 10.3390/ani12233336] [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: 09/28/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The intensification and standardization of livestock farming are causing a decline in the number of animal breeds in many species, such as the goat. The availability of more studies on the potentiality of goat breeds could raise awareness of their importance, conservation and productive possibilities. Label-free quantitative analysis was applied in this study to investigate the proteomic differences between the autochthon Teramana and Saanen goats that could be useful for defining peculiar features of these breeds. A total of 2093 proteins were characterized in the muscle exudate proteome of the Teramana and Saanen breeds. A total of 41 proteins clearly separated the two breeds. Eukaryotic initiation factor proteins and aldehyde-dehydrogenase 7 family-member A1 were up-regulated in the autochthon breed and associated with its resilience, whereas catalase was down-regulated and associated with lower muscular mass. This study is the most detailed report of goat muscle proteome. Several differentially regulated proteins between the two breeds were identified, providing insights into functional pathways that define this organism and its biology.
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