1
|
Medeiros BB, Barcelos KMC, Andrade MO, Cristina da Paz Carvalho M, Miranda VR, de Oliveira Maia K, Reinhardt S, Patterson Rosa L. The Weight of Genetic Drift: A Pedigree-Based Evaluation of the Breton Horse Population in Brazil. Vet Med Int 2024; 2024:4714077. [PMID: 39220466 PMCID: PMC11364472 DOI: 10.1155/2024/4714077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/05/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
The genetic diversity of Breton horses in Brazil is a critical concern, mainly due to the small population size and low number of births per year. Given that the inbreeding was overlooked by breeders for multiple generations, we estimated the genetic diversity of this population utilizing pedigree-based measures of population diversity. A total of 1394 six-generation pedigrees representing the full population of registered Breton horses in Brazil defined a total population (TP, N = 2679), with horses born between 2000 and 2022, reproductively active and alive, as reported by the breed association, representing the reference population (RP, N = 731). Using the R package PurgeR, we estimated inbreeding coefficient (F ped ), maternal inbreeding coefficient (F da m ), paternal inbreeding coefficient (F sire ), individual reproductive values, number of equivalents to complete generations (t), and unbiased ancestral inbreeding coefficient (Fa). We established the equivalent complete generations (ECG), effective population size (Ne), total number of founders (Nf), effective number of founders (Nfe), total number of ancestors (Na), effective number of ancestors (Nae), founder genomes (Ng), and the inbreeding coefficient estimated with effective population size (Ne) and generation numbers (t) (F Ne:t ), as well as Nfe/Nae and Nfe/Ng ratios for the RP. The RP inbreeding levels have stabilized, although they are still significantly rising by generation (t), and the Nfe/Ng ratio strongly suggests genetic drift. Pedigree-based analysis demonstrates that only five stallions have sired 52.83% of the RP individuals, which along with the Nae value of 36.73 implies that the observed inbreeding can be arising from patrilines. Our results suggest that observed inbreeding is due to Popular Sire Effect, highlighting the importance of monitoring breeding schemes and genetic diversity to maintain health.
Collapse
Affiliation(s)
- Bruno B. Medeiros
- Department of Agriculture and IndustrySul Ross State University, Alpine, TX, USA
| | - Kate M. C. Barcelos
- Escola de Veterinária e ZootecniaUniversidade Federal de Goias, Campus Samambaia, Goiânia, Brazil
| | - Millena Oliveira Andrade
- Escola de Veterinária e ZootecniaUniversidade Federal de Goias, Campus Samambaia, Goiânia, Brazil
| | | | - Victoria Rocha Miranda
- Escola de Veterinária e ZootecniaUniversidade Federal de Goias, Campus Samambaia, Goiânia, Brazil
| | - Kalebe de Oliveira Maia
- Escola de Veterinária e ZootecniaUniversidade Federal de Goias, Campus Samambaia, Goiânia, Brazil
| | - Susana Reinhardt
- Superintendência do Serviço de Registro Genealógico da Raça BretãAssociação Brasileira de Criadores do Cavalo Bretāo, Sao Paulo, Brazil
| | - Laura Patterson Rosa
- Department of Veterinary Clinical SciencesCollege of Veterinary MedicineLong Island University, New York, NY, USA
| |
Collapse
|
2
|
Giontella A, Silvestrelli M, Cocciolone A, Pieramati C, Sarti FM. Breeding Value Estimation Based on Morphological Evaluation of the Maremmano Horse Population through Factor Analysis. Animals (Basel) 2024; 14:2232. [PMID: 39123761 PMCID: PMC11310958 DOI: 10.3390/ani14152232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/22/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Morphological scoring is a common evaluation method for domestic animals. The National Association of Maremmano Breeders (ANAM) has provided a dataset containing the records of 600 horses, four metric measurements (cm) and 24 traits with a continuous evaluation scale, each one with 15 classes. Moreover, a body condition score (BCS) with five classes is included. In this study, factor analysis was conducted to create a small number of informative factors (3) obtained from these traits, and a new BLUP-AM-MT index was established. The New Estimated Breeding Value (NEBV1) of each horse was computed by adding the genetic indexes of the three factors, with each one multiplied using a coefficient indicated by ANAM. The practical feasibility of the NEBV1 was evaluated through Spearman correlations between the rankings of the NEBV1 and the rankings of the BLUP-AM-MT, estimated through the four biometric measures and the morphological score (MS) assigned to each horse by the ANAM judges. The factorial analysis was used to estimate three factors: the "Trunk Dimension", "Legs" and "Length". As the explained variance was only 32%, the model was rotated, and the heritability of the three factors were 0.51, 0.05 and 0.41, respectively. After rotation, the estimated correlations between the new NEBV1 and the biometric measures were improved. These results should encourage breeders to adopt a breeding value index that takes into consideration the factors derived from all the variables observed in the morphological evaluation of the Maremmano. In this way, breeders can use it to select the best animals for breeding.
Collapse
Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, Via S. Costanzo 4, 06126 Perugia, Italy; (M.S.); (C.P.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, Via S. Costanzo 4, 06126 Perugia, Italy; (M.S.); (C.P.)
| | - Alessandro Cocciolone
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (A.C.); (F.M.S.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, Via S. Costanzo 4, 06126 Perugia, Italy; (M.S.); (C.P.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (A.C.); (F.M.S.)
| |
Collapse
|
3
|
Klecel W, Kloch M, Wojciechowska M, Gajewska M, Martyniuk E. Population structure and genetic diversity of Polish Arabian horses based on pedigree data. Animal 2024; 18:101148. [PMID: 38642411 DOI: 10.1016/j.animal.2024.101148] [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: 12/22/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/22/2024] Open
Abstract
With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the dataset of 12 254 individuals (total population). We traced their genealogy to assess inbreeding coefficients (F), founder effects, and genetic variability measures such as the effective number of founders (fe), ancestors (fa), or founder genome equivalents (fge). The results indicated a good pedigree quality with an average of 28.1 maximum traced generations, revealing high pedigree completeness for initial generations with a decline beyond the seventh generation. The genetic diversity parameters showed a considerable bottleneck effect, with an effective number of founders at 73, which reflects a substantial loss of genetic diversity over time. Despite the vast total number of founders (852), only a few have had a lasting impact on the current population, signaling the need for revised breeding strategies to maintain diversity. The study identified a slight but consistent rise in inbreeding over the last century, with a marginal recent decline, and a significant difference in the contribution of various founders. The average F was 5.8%, with 99.6% of the reference population being inbred. The analysis of effective population size (Ne) highlighted potential risks for genetic diversity, urging for revision of breeding goals to consider a wider array of founder lineages. The study indicated that stallions belonging to RP can be attributed to 15 distinct sirelines, whereas mares to 45 unique damlines, more than considered in the current breeding program (8 and 15, respectively). Conclusively, the study underlines the need for ongoing monitoring and strategic breeding to maintain and enhance the genetic diversity of Polish Arabians, considering the breed's historical significance and contemporary genetic challenges.
Collapse
Affiliation(s)
- W Klecel
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-787 Warsaw, Poland.
| | - M Kloch
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-787 Warsaw, Poland
| | - M Wojciechowska
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-787 Warsaw, Poland
| | - M Gajewska
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-787 Warsaw, Poland
| | - E Martyniuk
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-787 Warsaw, Poland
| |
Collapse
|
4
|
Xing J, Xie L, Qi X, Liu G, Akhtar MF, Li X, Bou G, Bai D, Zhao Y, Dugarjaviin M, Zhang X. Integrated analysis of transcriptome and proteome for exploring mechanism of promoting proliferation of equine satellite cells associated with leucine. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101118. [PMID: 37633218 DOI: 10.1016/j.cbd.2023.101118] [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: 05/10/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/28/2023]
Abstract
The proliferation and differentiation of skeletal muscle satellite cells (SCs) are necessary for the development of mature skeletal muscle. Leucine (Leu) is both an essential amino acid (EAA) and a branched-chain amino acid (BCAA), which has attracted worldwide attention due to its ability to repair and become new fibers. We separated the equine SCs into the control group (CON) and the Leu-supplemented group (LEU), which the cells were cultured in Leu-deprived and Leu-supplemented media respectively. We combined the transcriptome (RNA-Seq) and quantitative proteome (TMT) profiling analyses on proliferation of equine SCs associated with Leu. 1839 up-regulated and 631 down-regulated genes made up the 2470 differentially expressed genes (DEGs), and the 253 differentially abundant proteins (DEPs) included 118 up-regulated and 135 down-regulated proteins. 110 overlapping genes were verified based on the mRNA and protein translation relationship. Moreover, by comparing overlapped pathways through enrichment analysis, we found 13 genes not only appeared among 110 key DEGs/DEPs but also enriched in the KEGG overlapping signaling pathway, including CCL26, STAT2, PCK2, ASNS, GPT2, SHMT2, PHGDH, PGAM2, PSAT1, FTL, HMOX1, STEAP1 and STEAP2. To our knowledge, this is the first report in the world to systematically show how Leu regulated the growth of equine SCs. Leu deficiency inhibits the proliferation of equine SCs and development of fresh muscle fibers was proved in this paper. The main genes in charge of the Leu-induced proliferation of horse SCs have been found. These genes will make it easier to understand the mechanism at work and offer new information for enhancing the performance of sport horses and alleviating the equine muscle damage during exercise in the future.
Collapse
Affiliation(s)
- Jingya Xing
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; College of animal science, Qingdao Agricultural University, Qingdao 266000, China
| | - Lan Xie
- College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng 252059, Shandong Province, China
| | - Xingzhen Qi
- College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng 252059, Shandong Province, China
| | - Guiqin Liu
- College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng 252059, Shandong Province, China
| | - Muhammad Faheem Akhtar
- College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng 252059, Shandong Province, China
| | - Xinyu Li
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Gerelchimeg Bou
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Dongyi Bai
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yiping Zhao
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Manglai Dugarjaviin
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xinzhuang Zhang
- Key Laboratory of Equus Germplasm Innovation (Co-const ruction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
| |
Collapse
|
5
|
Giontella A, Cardinali I, Sarti FM, Silvestrelli M, Lancioni H. Y-Chromosome Haplotype Report among Eight Italian Horse Breeds. Genes (Basel) 2023; 14:1602. [PMID: 37628653 PMCID: PMC10454838 DOI: 10.3390/genes14081602] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies.
Collapse
Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (A.G.); (M.S.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy;
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy; (A.G.); (M.S.)
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| |
Collapse
|
6
|
Capomaccio S, Ablondi M, Colombi D, Sartori C, Giontella A, Cappelli K, Mancin E, Asti V, Mantovani R, Sabbioni A, Silvestrelli M. Exploring the Italian equine gene pool via high-throughput genotyping. Front Genet 2023; 14:1099896. [PMID: 36755577 PMCID: PMC9900106 DOI: 10.3389/fgene.2023.1099896] [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: 11/16/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.
Collapse
Affiliation(s)
- Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Daniele Colombi
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Vittoria Asti
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| |
Collapse
|
7
|
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
|
8
|
Klein R, Oláh J, Mihók S, Posta J. Pedigree-Based Description of Three Traditional Hungarian Horse Breeds. Animals (Basel) 2022; 12:ani12162071. [PMID: 36009663 PMCID: PMC9405318 DOI: 10.3390/ani12162071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The most important purpose of animal conservation programs is to maintain genetic variability. The Furioso-North Star, the Gidran, and the Nonius are indigenous Hungarian horse breeds from the Mezőhegyes Stud. In the last century, the role of the horses was changed, the technical innovations and motorization replaced them, so the population size and the genetic variability of these breeds were reduced. Nowadays these breeds are endangered. The aims of this study were to give information about the current breeding population and support breeder associations during their gene conservation work. The pedigree quality, generation intervals, probability of gene origin, and inbreeding were evaluated. We found that breeds had a large bottleneck effect during breeding history. The level of inbreeding was measured with different methods, such as Ballou’s, Wright’s, and Kalinowski’s coefficient. Most of the current inbreeding coefficient was the result of previously fixed alleles for each breed. Effective population size was also estimated, and the status of the breeds was found to be not critical according to FAO criteria. Abstract The Mezőhegyes Stud was founded in 1784 where three different horse breeds were developed: the Furioso-North Star, the Gidran, and the Nonius. These breeds were based on the same mare population, but each breed had different utilization purposes. Our aim was to analyze the pedigree information of these three indigenous breeds. The genealogical information was traced back from the actual breeding population back to the founder animals, and the final database contained more than 47,000 horses. The reference populations were defined as the registered breeding animals in 2019. The complete generation equivalent was 16.45 for the Gidran breed, 15.18 for Furioso-North Star, and 12.64 for Nonius, respectively. Due to the utilization of English Thoroughbred during the breeding history, the average maximum generations were close to 36 generations for each breed. The average relatedness was approximately 4%. The average Wright’s inbreeding coefficient was the highest for the Nonius breed (5.59%). Kalinowski’s decomposition of inbreeding showed that inbreeding is originated mainly from the past; the current fixation of alleles was higher for the Nonius horse breed. There was a reasonable bottleneck effect for each breed. The estimated effective population sizes suggest that there is no problem with the maintaining of Mezőhegyes horse breeds.
Collapse
Affiliation(s)
- Renáta Klein
- Department of Animal Husbandry, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, H-4032 Debrecen, Hungary
| | - János Oláh
- Farm and Regional Research Institute of Debrecen, University of Debrecen, H-4032 Debrecen, Hungary
| | - Sándor Mihók
- Department of Animal Husbandry, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
| | - János Posta
- Department of Animal Husbandry, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary
- Correspondence:
| |
Collapse
|
9
|
Criscione A, Mastrangelo S, D'Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S. Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern. J Anim Breed Genet 2022; 139:540-555. [PMID: 35445758 PMCID: PMC9541879 DOI: 10.1111/jbg.12680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022]
Abstract
Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome‐wide single‐nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model‐based clustering and Neighbour‐Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the Arab as well as between Sanfratellano, Siciliano and Maremmano. The highest expected heterozygosity (He) and contemporary effective population size (cNe) were reported in Siciliano (He = 0.323, cNe = 397), and the lowest were reported in Purosangue Orientale Siciliano (He = 0.277, cNe = 10). The analysis of the runs of homozygosity and the relative derived inbreeding revealed high internal homogeneity in Purosangue Orientale Siciliano and Arab horses, intermediate values in Maremmano and Sanfratellano and high heterogeneity in the Siciliano population. The genome‐wide SNP analysis showed the selective pressure on Purosangue Orientale Siciliano towards traits related to endurance performance. Our results underline the importance of planning adequate conservation and exploitation programmes to reduce the level of inbreeding and, therefore, the loss of genetic diversity.
Collapse
Affiliation(s)
- Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | | | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Alessandro Zumbo
- Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| |
Collapse
|
10
|
Ivanković A, Bittante G, Konjačić M, Kelava Ugarković N, Pećina M, Ramljak J. Evaluation of the Conservation Status of the Croatian Posavina Horse Breed Based on Pedigree and Microsatellite Data. Animals (Basel) 2021; 11:ani11072130. [PMID: 34359258 PMCID: PMC8300408 DOI: 10.3390/ani11072130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Conservation of local horse breeds as part of animal genetic resources is of national and global importance. Monitoring of local breeds is often fragmentary, i.e., it involves analysis of pedigrees, phenotype, and genetic structure. Using the Croatian Posavina horse as an example, we analyzed the status of the population with regard to available pedigree information, phenotype measures of stallions and mares, and genetic structure based on microsatellites. The generation interval is about eight years, indicating relatively early involvement of animals in reproduction for economic use of the breed. The depth of the pedigree is relatively modest due to a relatively short period of systematic breeding work (two decades). The number of active sire-lines and mare-lines is favorable and forms a good basis for the preservation of the breed. Regarding conformation, the Croatian Posavina horse kept the recognizability of the small-sized horse breed in the coldblooded type, in which there are clear traces of the earlier controlled introduction of the Arabian and other breeds. Its genetic diversity component has been preserved. The above results are a guide for further implementation of effective programs for the conservation of endangered local horse breeds. Abstract The Croatian Posavina horse (CPH) is native Croatian breed under a conservation program and under various programs of economic use (ecosystem services, agrotourism, and meat production). The aim of this study was to analyze the status of the CPH population through an analysis of their pedigree (28,483 records), phenotype (292 licensed stallions, 255 mares), and genetic structure (292 licensed stallions). The average generation interval was 8.20 years, and the number of complete generations was 1.66. The effective number of founders and ancestors was 138 and 107, respectively, with a ratio of 1.29, and the genetic conservation index was 4.46. As for the morphometric characteristics, the average withers height of the stallions was 142.79 cm, the chest circumference was 194.28 cm, and the cannon bone circumference was 22.34. In mares, the withers height, chest, and cannon bone circumference were lower (139.71 cm, 190.30 cm, and 20.94 cm, respectively). Genetic microsatellite analysis of the 29 sire-lines showed high genetic diversity, expressed as the mean allele number (7.7), allele richness (4.0), and expected heterozygosity (0.740). There was no evidence of high inbreeding or a genetic bottleneck. The genetic and phenotypic data indicate that the CPH is an important and diverse reservoir of genetic diversity and can be conserved because of its special characteristics (adaptability).
Collapse
Affiliation(s)
- Ante Ivanković
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (M.K.); (N.K.U.); (M.P.); (J.R.)
- Correspondence: ; Tel.: +385-1-2393-991
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Via dell’Università 16, 35020 Legnaro, Italy;
| | - Miljenko Konjačić
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (M.K.); (N.K.U.); (M.P.); (J.R.)
| | - Nikolina Kelava Ugarković
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (M.K.); (N.K.U.); (M.P.); (J.R.)
| | - Mateja Pećina
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (M.K.); (N.K.U.); (M.P.); (J.R.)
| | - Jelena Ramljak
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia; (M.K.); (N.K.U.); (M.P.); (J.R.)
| |
Collapse
|
11
|
Faria RAS, Vicente APA, Ospina AMT, Silva JAIIV. Pedigree analysis of the racing line Quarter Horse: Genetic diversity and most influential ancestors. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
12
|
Próchniak T, Kasperek K, Knaga S, Rozempolska-Rucińska I, Batkowska J, Drabik K, Ziȩba G. Pedigree Analysis of Warmblood Horses Participating in Competitions for Young Horses. Front Genet 2021; 12:658403. [PMID: 33936176 PMCID: PMC8082513 DOI: 10.3389/fgene.2021.658403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022] Open
Abstract
The aim of the study was to characterize the population structure and assess the genetic diversity of warmblood horses used in the show jumping discipline. Pedigree data of 1,048 horses participating in the Polish Championships for Young Horses were analyzed. The pedigree of these animals included 12 863 individuals. The study consisted in analysis of the pedigree structure of the horses and characterization of the homozygosity and genetic diversity in the population. It was found that pedigree completeness and depth were sufficient for reliable assessment of the genetic diversity in the analyzed population. Although the average inbreeding coefficient exhibited at an acceptable level (approx. 1.01%), the increasing percentage of inbred animals seems disturbing. The results have shown that modern sport horses are derived from a small number of high-quality sires whose offspring were intensively used for breeding—bottleneck effect. In consequence, a greater part of the genetic variation reduction was observed in the non-founder generations. Given the changes in the studied population, the level of inbreeding in modern sport horses should be monitored, and pedigree data should be effectively used in selection for mating.
Collapse
Affiliation(s)
- Tomasz Próchniak
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Kornel Kasperek
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Sebastian Knaga
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Iwona Rozempolska-Rucińska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Justyna Batkowska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Kamil Drabik
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Grzegorz Ziȩba
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| |
Collapse
|
13
|
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Rodriguez de la Borbolla y Ruiberriz de Torres A, Navas González FJ. Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses. Animals (Basel) 2021; 11:ani11020269. [PMID: 33494478 PMCID: PMC7912545 DOI: 10.3390/ani11020269] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The demographic and genetic diversity structure and the contributions of Spanish (PRE) and Arabian Purebred (PRá) horses to the process of conformation of the Hispano-Arabian (Há) horse breed were evaluated. Genetic diversity parameters (inbreeding coefficient, genetic conservation index, coancestry coefficient, non-random mating degree, relatedness coefficient, maximum, complete, and equivalent generations, and number of offspring) were evaluated using a discriminant canonical analysis to determine the partial contributions of each founder breed to the development of Há horse breed. The calculation of Nei genetic distances suggests the overlapping could be estimated in 29.55% of the gene pool of the Há having a PRE origin while 70.45% of the gene pool of the breed may derive from a PRá origin. Although a progressive loss of founder representation may have occurred, breeding strategies implemented considering mating between animals with the highest genetic conservation indices (GCI) may compensate for its effects. Abstract Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).
Collapse
Affiliation(s)
- Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Amy Katherine McLean
- Department of Animal Science, University of California Davis, Davis, CA 95617, USA;
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain;
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
- Correspondence: ; Tel.: +34-957-21-87-06
| |
Collapse
|
14
|
Yahagi Rodrigues L, da Silva Faria RA, de Vasconcelos Silva JAI. Analysis of the Pedigree and Ancestors of the Cutting Population of the Quarter Horse Breed. J Equine Vet Sci 2021; 99:103385. [PMID: 33781431 DOI: 10.1016/j.jevs.2021.103385] [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: 11/18/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/30/2022]
Abstract
The aim of this study was to evaluate the genetic diversity and to identify the most influential ancestors in the population of Brazilian Quarter Horses participating in cutting competitions. Data from 1,590 elite horses born between 1970 and 2015, which participated in cutting competitions between 1981 and 2018, were evaluated based on the pedigree file that contained 5,832 animals born since 1834. Evaluation of the quality of the pedigree data showed a mean number of known equivalent generations of 5.4 ± 1.5 and a mean generation interval of 11.7 ± 8.8 years. The inbreeding coefficient (1.98 ± 7.13%), relatedness coefficient (2.18 ± 0.01%), and individual increase in inbreeding (0.43 ± 0.01%) were low. The effective population size (Ne) was 136 animals. The probability of gene origin indicated effective numbers of founders, ancestors, and founder genomes of 255, 37, and 23 animals, respectively. The number of founders and ancestors was 1,852 and 899 animals, respectively, with 10, 50, and 100 ancestors explaining 39.2%, 67.9%, and 91.6%, respectively, of the genetic diversity of the population. The five most influential ancestors were Doc Bar, Peppy San Badger, Freckles Playboy, Poco Lena, and High Brow Cat, accumulating 30.7% of the marginal genetic contributions of the population. Few ancestors were responsible for the genetic diversity, resulting in the narrowing of the initial genetic base. Breeders depend on a small group of ancestors, which could be corrected by increasing the number of breeding animals and by directed mating using ancestors of different origins.
Collapse
Affiliation(s)
- Larissa Yahagi Rodrigues
- Universidade Estadual Paulista (Unesp), Faculdade de Medicina Veterinária e Zootecnia, Botucatu, São Paulo, Brazil.
| | - Ricardo António da Silva Faria
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil; Escola Profissional Agrícola Quinta da Lageosa, Belmonte, Portugal
| | | |
Collapse
|
15
|
A Genetic Window on Sardinian Native Horse Breeds through Uniparental Molecular Systems. Animals (Basel) 2020; 10:ani10091544. [PMID: 32882901 PMCID: PMC7552234 DOI: 10.3390/ani10091544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The horse is a mammalian species showing a high variation among maternal lineages but a limited variability in the paternal inheritance. The female phylogenetic history is commonly investigated by analyzing the maternally transmitted mitochondrial DNA (mtDNA), while the male perspective is provided by the paternally inherited portion of the Y chromosome (NRY). Here we explored the variation of both non-recombining genetic systems in three horse breeds present in Sardinia: Giara, Sarcidano, and Sardinian Anglo-Arab. The analysis of 34 stallions revealed three differentially distributed NRY types: (i) the first and most ancestral one is typical of Sarcidano; (ii) the second is well represented in Giara and seems to derive from Neapolitan/Oriental stallions; (iii) the third confirms the Thoroughbred influence in the Sardinian Anglo-Arab breed. By extending the analysis to 178 mtDNAs, we observed a common maternal origin for Giara and Sarcidano. Contrarily, the outlier behavior of the Sardinian Anglo-Arab is due to its higher mitochondrial variability, testifying for multiple maternal lineages in its current population. Our preliminary findings highlight the importance of a parallel molecular screening of NRYs and mtDNAs to reconstruct both paternal and maternal phylogenetic histories and to fully evaluate the extent of autochthonous genetic resources in the island. Abstract Sardinia, an island located to the west of Italy in the Mediterranean Sea, boasts three native horse breeds: Giara, Sarcidano, and Sardinian Anglo-Arab. Here, we have investigated for the first time three loci of the non-recombining region of the Y chromosome (NRY) in 34 stallions from these breeds and performed a phylogenetic analysis of the maternal relationships among 178 previously published mitochondrial control regions. We found that the current NRY diversity of Sardinian horse breeds is linked to three haplotypes (HT), all identified within Sarcidano. Each breed showed a typical HT: HT1 (ancestral) was the most represented in Sarcidano, HT2 (Neapolitan/Oriental wave) in Giara, and HT3 (Thoroughbred wave) in Sardinian Anglo-Arab. The specificity of each haplotype suggests the influence of independent breeding strategies and the effect of genetic drift in each Sardinian population. The female counterpart, extended to 178 horses, showed a low genetic variability and a common maternal origin for Giara and Sarcidano. The higher variability of the Sardinian Anglo-Arab indicates multiple mare lineages in its current population. Further genetic analyses will be crucial to understand the paternal history of male horses, preserve the endangered mares’ and stallions’ lineages, and improve the enhancement of autochthonous genetic resources on this island.
Collapse
|
16
|
Perdomo-González DI, Sánchez-Guerrero MJ, Molina A, Valera M. Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation. Animals (Basel) 2020; 10:E1360. [PMID: 32781594 PMCID: PMC7459874 DOI: 10.3390/ani10081360] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals' breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.
Collapse
Affiliation(s)
- Davinia I. Perdomo-González
- Departamento de Ciencias Agro-forestales, ETSIA, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.J.S.-G.); (M.V.)
| | - María J. Sánchez-Guerrero
- Departamento de Ciencias Agro-forestales, ETSIA, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.J.S.-G.); (M.V.)
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Gregor J. Mendel, Planta baja, Carretera Madrid-Cádiz km 396ª, 14071 Córdoba, Spain;
| | - Mercedes Valera
- Departamento de Ciencias Agro-forestales, ETSIA, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.J.S.-G.); (M.V.)
| |
Collapse
|
17
|
Giontella A, Sarti FM, Cardinali I, Giovannini S, Cherchi R, Lancioni H, Silvestrelli M, Pieramati C. Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse. Animals (Basel) 2020; 10:ani10061018. [PMID: 32545354 PMCID: PMC7341272 DOI: 10.3390/ani10061018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.
Collapse
Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S. Costanzo 4, 06123 Perugia, Italy; (M.S.); (C.P.)
- Correspondence:
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.M.S.); (S.G.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.M.S.); (S.G.)
| | - Raffaele Cherchi
- AGRIS, Servizio Ricerca Qualità e Valorizzazione delle Produzioni Equine, piazza D. Borgia, 4, 07014 Ozieri, Sassari, Italy;
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S. Costanzo 4, 06123 Perugia, Italy; (M.S.); (C.P.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S. Costanzo 4, 06123 Perugia, Italy; (M.S.); (C.P.)
| |
Collapse
|
18
|
Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020; 10:ani10061005. [PMID: 32521830 PMCID: PMC7341496 DOI: 10.3390/ani10061005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Abstract Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
Collapse
|
19
|
Lancioni H, Cardinali I, Giontella A, Antognoni MT, Miglio A. Mitochondrial DNA variation in the Italian Heavy Draught Horse. PeerJ 2020; 8:e8996. [PMID: 32461825 PMCID: PMC7233276 DOI: 10.7717/peerj.8996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook. Methodology To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds. Results Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.
Collapse
Affiliation(s)
- Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | | | - Arianna Miglio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| |
Collapse
|
20
|
Giontella A, Cardinali I, Lancioni H, Giovannini S, Pieramati C, Silvestrelli M, Sarti FM. Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records. Animals (Basel) 2020; 10:E839. [PMID: 32408648 PMCID: PMC7278429 DOI: 10.3390/ani10050839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/30/2020] [Accepted: 05/09/2020] [Indexed: 11/16/2022] Open
Abstract
* Correspondence: andrea [...].
Collapse
Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via - Elce di Sotto, 8, 06123 Perugia, Italy; (I.C.); (H.L.)
| | - Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (S.G.); (F.M.S.)
| |
Collapse
|
21
|
Giontella A, Sarti FM, Biggio GP, Giovannini S, Cherchi R, Pieramati C, Silvestrelli M. Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse. Animals (Basel) 2020; 10:E791. [PMID: 32370302 PMCID: PMC7277675 DOI: 10.3390/ani10050791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an "ideal type" that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.
Collapse
Affiliation(s)
- Andrea Giontella
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.M.S.); (S.G.)
| | - Giovanni Paolo Biggio
- AGRIS, Servizio Ricerca Qualità e Valorizzazione delle Produzioni Equine, piazza D. Borgia, 4, Ozieri, 07014 Sassari, Italy; (G.P.B.); (R.C.)
| | - Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.M.S.); (S.G.)
| | - Raffaele Cherchi
- AGRIS, Servizio Ricerca Qualità e Valorizzazione delle Produzioni Equine, piazza D. Borgia, 4, Ozieri, 07014 Sassari, Italy; (G.P.B.); (R.C.)
| | - Camillo Pieramati
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine—Sportive Horse Research Center, University of Perugia, via S.Costanzo 4, 06123 Perugia, Italy; (C.P.); (M.S.)
| |
Collapse
|
22
|
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
|