1
|
Amano T, Yokawa H, Masuda Y, Tozaki T, Kawai M, Shirai K. Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse. Anim Sci J 2023; 94:e13884. [PMID: 37983921 DOI: 10.1111/asj.13884] [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: 07/13/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HKD as a breed. Tajima's D analysis and runs of homozygosity analysis identified 23 selection signatures unique to HKD (P < 0.05), and following database search found 20 traits that were associated with those selection signatures; among these traits, coat color traits, face and body markings, showed the highest important value (0.50 and 0.46). Enrichment analysis of genes in the selection signatures identified six gene ontology terms (P < 0.05), and a term related to innate immunity (regulation of defense response; GO:0031347) showed the highest positive fold enrichment value (7.13). These results provide the first scientific evidence of a genetic basis for the traits of HKD.
Collapse
Affiliation(s)
- Tomoko Amano
- Laboratory of Animal Genetics, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan
| | - Haruhi Yokawa
- Laboratory of Animal Genetics, Graduate School of Dairy Science, Rakuno Gakuen University, Hokkaido, Japan
| | - Yutaka Masuda
- Laboratory of Animal Breeding, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Kouichi Shirai
- Hokkaido Native Horse Conservation Association, Hokkaido, Japan
| |
Collapse
|
2
|
Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
Collapse
Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| |
Collapse
|
3
|
Huricha, Kawai M, Inose Y, Yamada F, Ninomiya S. Maternal effect on first-year growth of Hokkaido native foals kept outdoors all year round. Anim Sci J 2022; 93:e13694. [PMID: 35146838 DOI: 10.1111/asj.13694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 11/28/2022]
Abstract
In this study, we investigated maternal effects on the growth of Hokkaido native horses kept outdoors throughout the year. We used the data on body weight (BW), height at withers (HW), heart girth (HG), and cannon circumference (CC) of 517 foals during the first year of life to (1) examine the growth patterns by comparing six linear mixed models and (2) analyze the maternal effect on BW, HW, HG, and CC for each month by estimating variance components. The segmented polynomial third-order regression equation was selected as the best model for all the traits. The estimated proportion of variance components for the effects of the dam were 0.25-0.38 for BW, 0.19-0.28 for HW, 0.19-0.34 for HG, and 0.10-0.21 for CC. A higher effect of the dam compared with that of the sire was observed on BW and HG at all months of age and HW at 0-2 months of age. Therefore, the dam contributed to foal growth not only through half of its heredity but also through the maternal effect derived mainly from its milk. These results provide valuable information for the breeding of Hokkaido native foals.
Collapse
Affiliation(s)
- Huricha
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
| | - Masahito Kawai
- Shizunai Livestock Farm, Field Science Center for Northern Biosphere, Hokkaido University, Shinhidaka, Japan
| | - Yoshihisa Inose
- Shizunai Livestock Farm, Field Science Center for Northern Biosphere, Hokkaido University, Shinhidaka, Japan
| | - Fumihiro Yamada
- Shizunai Livestock Farm, Field Science Center for Northern Biosphere, Hokkaido University, Shinhidaka, Japan
| | - Shigeru Ninomiya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| |
Collapse
|
4
|
Genetic diversity and genetic differentiation of Megalobrama populations inferred by mitochondrial markers. Genes Genomics 2021; 43:1119-1132. [PMID: 34342875 DOI: 10.1007/s13258-021-01126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Megalobrama is economically one of the most important freshwater fish genera in China. However, phylogenetic relationships among M. amblycephala, M. skolkovii, M. hoffmanni and M. pellegrini remain unresolved. OBJECTIVE To explore the genetic diversity and phylogenetic relationship of Megalobrama populations belonging to all four species. METHODS The concatenated sequences of mitochondrial cytochrome b (Cytb) and control region (CR) were used to analyze the genetic variation, genetic differentiation and population expansion of 15 Megalobrama populations. RESULTS The study showed that haplotype diversity and nucleotide diversity of M. hoffmanni and M. skolkovii were high, and that M. hoffmanni was the most genetically divergent of the four species. Haplotype network analysis revealed that M. hoffmanni and M. amblycephala formed a monophyletic group each, while M. skolkovii and M. pellegrini clustered together. There was a high genetic differentiation among the four Megalobrama species, and genetic distance among populations was not affected by geographical distance. Additionally, the results indicated that there was gene flow between the Liangzi Lake (LZL) population and Jinsha River Reservoir (JS) population. Also, Zhaoqing (ZQ) population of M. hoffmanni might have experienced a population expansion. CONCLUSION Our study verifies genetic diversity and differentiation of Megalobrama populations, and these findings will represent a significant contribution to the conservation and utilization of germplasm resources of Megalobrama.
Collapse
|
5
|
Amano T, Tozaki T, Takasu M, Onogi A, Yamada F, Kawai M, Ueda J. Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses. Anim Sci J 2019; 91:e13318. [PMID: 31755177 DOI: 10.1111/asj.13318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/06/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.
Collapse
Affiliation(s)
- Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumihiro Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Junji Ueda
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
| |
Collapse
|
6
|
Ablondi M, Summer A, Vasini M, Simoni M, Sabbioni A. Genetic parameters estimation in an Italian horse native breed to support the conversion from agricultural uses to riding purposes. J Anim Breed Genet 2019; 137:200-210. [PMID: 31310049 DOI: 10.1111/jbg.12425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 11/29/2022]
Abstract
Horses are nowadays mainly used for sport and leisure purposes, and several local breeds, traditionally used in agriculture, are exposed to the risk of extinction. The long-term survival of local horse breeds depends on strategies to both monitor their genetic diversity and to find their sustainable role in the equine market. Thus, several local horse breeds need to adapt their breeding objective to allow a modernization process. The Bardigiano is an example of such horse breeds; we, therefore, studied the existing evaluation protocol from a genetic standpoint to assess the protocol's suitability to convert the Bardigiano from an agricultural to a riding horse. To this end, we estimated genetic parameters for four conformation measurements, ten grading traits and 23 linear traits. For conformation measurements, the heritabilities ranged from 0.31 for cannon bone circumference to 0.63 for height at withers. For conformation and attitude grading traits, the highest heritability (0.34) was estimated for development and the lowest (0.09) for gaits. The heritabilities for linear traits ranged from 0.05 for the leg straightness to 0.32 for the coat colour. Genetic correlations between linear traits and corresponding grading traits varied considerably, ranging from -0.42 to 0.98. This study showed that the current evaluation protocol in the Bardigiano horse is appropriate for genetic evaluation. Genetic parameters estimation can, in turn, be used to develop novel breeding values to help this conversion. Our study paves the way to optimize the Bardigiano horse breeding programme, and it may help several other local horse breeds experiencing similar issues.
Collapse
Affiliation(s)
- Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Andrea Summer
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Matteo Vasini
- Libro Genealogico Cavallo Bardigiano, Associazione Regionale Allevatori dell'Emilia-Romagna, Parma, Italy
| | - Marica Simoni
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| |
Collapse
|
7
|
Ablondi M, Vasini M, Beretti V, Superchi P, Sabbioni A. Exploring genetic diversity in an Italian horse native breed to develop strategies for preservation and management. J Anim Breed Genet 2018; 135:450-459. [PMID: 30136312 DOI: 10.1111/jbg.12357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/06/2018] [Accepted: 07/24/2018] [Indexed: 11/27/2022]
Abstract
Genetic diversity is a key factor for both adaptation and response to selection. The loss of genetic diversity causes a decrease in individual fitness, and it has a dramatically negative effect on population lifespan in the long term. This study aimed at exploring the genetic diversity at pedigree level of the Bardigiano horse breed, which is a native breed from Italy shaped for living in rural areas. In 1977, the Bardigiano studbook was founded to preserve the breed and for improving its use for riding and draft purposes. Pedigree data contained 9,469 horses, of which 3,416 were alive. Demographic and genetic parameters were estimated on subpopulations to evaluate potential genetic diversity differences among breeding and nonbreeding animals, and animals showing different breeding values (EBVs) for an index combining 18 conformation traits. Throughout the studied period, inbreeding steadily increased, reaching in the last birth year cohort a mean value equal to 0.10. The rate of inbreeding per generation, assuming a mean generation interval of 8.74 years, was equal to 1.64%. Moreover, significant differences on both average relatedness and inbreeding among horses with high and low EBVs were shown. Our study unravelled the state of genetic diversity in the Bardigiano breed, highlighting that breeding strategies for optimizing the contribution of breeding animals in the coming generations are needed to ensure long-term survival of the Bardigiano horse breed.
Collapse
Affiliation(s)
- Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Matteo Vasini
- Libro Genealogico Cavallo Bardigiano, Associazione Regionale Allevatori dell'Emilia-Romagna, Parma, Italy
| | - Valentino Beretti
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Paola Superchi
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, Università di Parma, Parma, Italy
| |
Collapse
|
8
|
Amano T, Onogi A, Yamada F, Kawai M, Shirai K, Ueda J. Genome-wide association mapping and examination of possible maternal effect for the pace trait of horses. Anim Genet 2018; 49:461-463. [DOI: 10.1111/age.12711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2018] [Indexed: 11/28/2022]
Affiliation(s)
- T. Amano
- Laboratory of Animal Genetics; Department of Sustainable Agriculture; College of Agriculture, Food and Environment Sciences; Rakuno Gakuen University; Hokkaido 069-0836 Japan
| | - A. Onogi
- Department of Agricultural and Environmental Biology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Tokyo 113-8657 Japan
| | - F. Yamada
- Field Science Center for Northern Biosphere; Hokkaido University; Hokkaido 056-0141 Japan
| | - M. Kawai
- Field Science Center for Northern Biosphere; Hokkaido University; Hokkaido 056-0141 Japan
| | - K. Shirai
- Hokkaido Native Horse Preservation Association; Hokkaido 063-0804 Japan
| | - J. Ueda
- Laboratory of Animal Genetics; Department of Sustainable Agriculture; College of Agriculture, Food and Environment Sciences; Rakuno Gakuen University; Hokkaido 069-0836 Japan
| |
Collapse
|