1
|
Zhang Z, Zhao W, Wang Z, Pan Y, Wang Q, Zhang Z. Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs. Anim Genet 2024. [PMID: 39129705 DOI: 10.1111/age.13465] [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: 05/26/2024] [Revised: 05/26/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024]
Abstract
The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.
Collapse
Affiliation(s)
- Zhenyang Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Wei Zhao
- SciGene Biotechnology Co. Ltd, Hefei, China
| | - Zhen Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Qishan Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
2
|
Sarviaho K, Uimari P, Martikainen K. Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population. J Dairy Sci 2024; 107:4822-4832. [PMID: 38490540 DOI: 10.3168/jds.2024-24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits (e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G) overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.
Collapse
Affiliation(s)
- Katri Sarviaho
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland.
| | - Pekka Uimari
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Katja Martikainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
3
|
Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [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: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
Collapse
Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| |
Collapse
|
4
|
González-Cano R, González-Martínez A, Ramón M, González Serrano M, Moreno Millán M, Rubio de Juan A, Rodero Serrano E. Exploring the Effects of Robertsonian Translocation 1/29 (Rob (1;29)) on Genetic Diversity in Minor Breeds of Spanish Berrenda Cattle via Genome-Wide Analysis. Animals (Basel) 2024; 14:793. [PMID: 38473178 DOI: 10.3390/ani14050793] [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: 01/24/2024] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Most of the previous studies on the genetic variability in Spanish "Berrenda" breeds have been carried out using DNA microsatellites. The present work aimed to estimate the genetic diversity, population structure, and potential genetic differences among individuals of both Berrenda breeds and groups based on the presence of the Robertsonian chromosomal translocation, rob (1;29). A total of 373 samples from animals belonging to the two breeds, including 169 cases diagnosed as rob (1;29)-positive, were genotyped using an SNP50K chip. The genetic diversity at the breed level did not show significant differences, but it was significantly lower in those subpopulations containing the rob (1;29). Runs of homozygosity identified a region of homozygosity on chromosome 6, where the KIT (KIT proto-oncogene, receptor tyrosine kinase) gene, which determines the typical spotted coat pattern in both breeds, is located. The four subpopulations considered showed minor genetic differences. The regions of the genome that most determined the differences between the breeds were observed on chromosomes 4, 6, 18, and 22. The presence of this Robertsonian translocation did not result in sub-structuring within each of the breeds considered. To improve the reproductive performance of Berrenda breeds, it would be necessary to implement strategies considering the involvement of potential breeding stock carrying rob (1;29).
Collapse
Affiliation(s)
- Rafael González-Cano
- Ministry of Agriculture, Fisheries and Food, Paseo Infanta Isabel 1, 28014 Madrid, Spain
- Regional Center of Animal Breeding and Reproduction (CERSYRA-IRIAF), Avenida del Vino 10, 13300 Ciudad Real, Spain
| | - Ana González-Martínez
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Manuel Ramón
- Department of Animal Breeding and Genetics, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28040 Madrid, Spain
| | - Miriam González Serrano
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Miguel Moreno Millán
- Department of Genetic, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| | - Alejandro Rubio de Juan
- Regional Center of Animal Breeding and Reproduction (CERSYRA-IRIAF), Avenida del Vino 10, 13300 Ciudad Real, Spain
| | - Evangelina Rodero Serrano
- Department of Animal Production, Faculty of Veterinary Sciences, University of Cordoba, 14071 Córdoba, Spain
| |
Collapse
|
5
|
Illa SK, Mumtaz S, Nath S, Mukherjee S, Mukherjee A. Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle. J Appl Genet 2024; 65:167-180. [PMID: 38110827 DOI: 10.1007/s13353-023-00816-1] [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: 02/10/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.
Collapse
Affiliation(s)
- Satish Kumar Illa
- Livestock Research Station, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Shabahat Mumtaz
- Animal Husbandry Department, Kolkata, West Bengal State, India
| | - Sapna Nath
- College of Veterinary Science, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Sabyasachi Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
| | - Anupama Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
| |
Collapse
|
6
|
Falchi L, Cesarani A, Criscione A, Hidalgo J, Garcia A, Mastrangelo S, Macciotta NPP. Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle. J Anim Sci 2024; 102:skae147. [PMID: 38798158 PMCID: PMC11197001 DOI: 10.1093/jas/skae147] [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: 01/24/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024] Open
Abstract
Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs). The present study aimed to test the effect of chip density in detecting ROHom and ROHet in the Italian Simmental cattle breed. A sample of 897 animals were genotyped at low density (50k SNP; 397 individuals), medium density (140k SNP; 348 individuals), or high density (800k SNP; 152 individuals). The number of ROHom and ROHet per animal (nROHom and nROHet, respectively) and their average length were calculated. ROHom or ROHet shared by more than one animal and the number of times a particular SNP was inside a run were also computed (SNPROHom and SNPROHet). As the chip density increased, the nROHom increased, whereas their average length decreased. In contrast, the nROHet decreased and the average length increased as the chip density increased. The most repeated ROHom harbored no genes, whereas in the most repeated ROHet four genes (SNRPN, SNURF, UBE3A, and ATP10A) previously associated with reproductive traits were found. Across the 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, and 37 SNP (located on BTA21) exceeded the 99th percentile in the distribution of the SNPROHom and SNPROHet, respectively. The genomic region on BTA6 mapped the SLIT2, PACRGL, and KCNIP4 genes, whereas 19 and 18 genes were mapped on BTA16 and BTA21, respectively. Interestingly, most of genes found through the ROHet analysis were previously reported to be related to health, reproduction, and fitness traits. The results of the present study confirm that the detection of ROHom is more reliable when the chip density increases, whereas the ROHet trend seems to be the opposite. Genes and quantitative trait loci (QTL) mapped in the highlighted regions confirm that ROHet can be due to balancing selection, thus related to fitness traits, health, and reproduction, whereas ROHom are mainly involved in production traits. The results of the present study strengthened the usefulness of these parameters in analyzing the genomes of livestock and their biological meaning.
Collapse
Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari 07100, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, USA
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania 95123, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens 30602, USA
| | - Andre Garcia
- American Angus Association, Angus Genetics Inc., Saint Joseph, MO, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari, e Forestali, Università degli Studi di Palermo, Palermo 90128, Italy
| | | |
Collapse
|
7
|
Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
Collapse
Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| |
Collapse
|
8
|
Menor-Flores M, Vega-Rodríguez MA, Molina F. Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients. Comput Biol Med 2023; 164:107296. [PMID: 37566933 DOI: 10.1016/j.compbiomed.2023.107296] [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: 04/09/2023] [Revised: 06/24/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
In population medical genetics, the study of autosomal recessive disorders in highly endogamous populations is a major topic where calculating the inbreeding and relationship coefficients on mating networks is crucial. However, a challenge arises when dealing with large and complex mating networks, making their traversal difficult during the calculation process. For this calculation, we propose using Iterative Level-0 (IL0) as a new and faster algorithm that traverses mating networks more efficiently. The purpose of this work is to explain in detail the IL0 algorithm and prove its superiority by comparing it with two algorithms based on the best-known algorithms in the area: Depth First Search (DFS) and Breadth First Search (BFS). A Cytoscape application has been developed to calculate the inbreeding and relationship coefficients of individuals composing any mating network. In this application, the IL0 proposal together with DFS-based and BFS-based algorithms have been implemented. Any user can access this freely available Cytoscape application (https://apps.cytoscape.org/apps/inbreeding) that allows the comparison between the IL0 proposal and the best-known algorithms (based on DFS and BFS). In addition, a diverse set of mating networks has been collected in terms of complexity (number of edges) and species (humans, primates, and dogs) for the experiments. The runtime obtained by the IL0, DFS-based, and BFS-based algorithms when calculating the inbreeding and relationship coefficients proved the improvement of IL0. In fact, a speedup study reflected that the IL0 algorithm is 7.60 to 127.50 times faster than DFS-based and BFS-based algorithms. Moreover, a scalability study found that the growth of the IL0 runtime has a linear dependence on the number of edges of the mating network, while the DFS-based and BFS-based runtimes have a quadratic dependence. Therefore, the IL0 algorithm can solve the problem of calculating the inbreeding and relationship coefficients many times faster (up to 127.50) than the two algorithms based on the famous DFS and BFS. Furthermore, our results demonstrate that IL0 scales much better as the complexity of mating networks increases.
Collapse
Affiliation(s)
- Manuel Menor-Flores
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura(1), Campus Universitario s/n, 10003 Cáceres, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura (1), Avda. de Elvas s/n, 06006 Badajoz, Spain.
| |
Collapse
|
9
|
Hewett AM, Stoffel MA, Peters L, Johnston SE, Pemberton JM. Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus). Heredity (Edinb) 2023; 130:242-250. [PMID: 36801920 PMCID: PMC10076382 DOI: 10.1038/s41437-023-00602-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (Ne) is large or selection is particularly strong. In populations having undergone a population bottleneck, genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role.
Collapse
Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Martin A Stoffel
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Lucy Peters
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| |
Collapse
|
10
|
Visser C, Lashmar SF, Reding J, Berry DP, van Marle-Köster E. Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds. Front Genet 2023; 14:1136078. [PMID: 37007942 PMCID: PMC10063850 DOI: 10.3389/fgene.2023.1136078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.
Collapse
Affiliation(s)
- Carina Visser
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Carina Visser,
| | - Simon Frederick Lashmar
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Jason Reding
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Donagh P. Berry
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Animal and Grassland Research and Innovation Centre, Teagasc, Co. Cork, Ireland
| | - Esté van Marle-Köster
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
11
|
Shi H, Li T, Su M, Wang H, Li Q, Lang X, Ma Y. Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep. BMC Genomics 2023; 24:50. [PMID: 36707771 PMCID: PMC9883975 DOI: 10.1186/s12864-023-09146-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The detection of selective traits in different populations can not only reveal current mechanisms of artificial selection for breeding, but also provide new insights into phenotypic variation in new varieties and the search for genes associated with important traits. Panou sheep is a cultivated breed of Tibetan sheep in China with stable genetic performance, consistent appearance and fast growth and development after decades of artificial selection and cultivation. Due to long-term adaptation to the high altitude, cold and hypoxic environment in the plateau area, they may have formed a unique gene pool that is different from other Tibetan sheep breeds. To explore the genetic resources of Panou sheep, we used next-generation sequencing technology for the first time to investigate the genome-wide population structure, genetic diversity, and candidate signatures of positive selection in Panou sheep. RESULTS Comparative genomic analysis with the closely related species Oula sheep (a native breed of Tibetan sheep in China) was used to screen the population selection signal of Panou sheep. Principal component analysis and neighbor joining tree showed that Panou sheep and Oula sheep had differences in population differentiation. Furthermore, analyses of population structure, they came from the same ancestor, and when K = 2, the two populations could be distinguished. Panou sheep exhibit genetic diversity comparable to Oula sheep, as shown by observed heterozygosity, expected heterozygosity and runs of homozygosity. Genome-wide scanning using the Fst and π ratio methods revealed a list of potentially selected related genes in Panou sheep compared to Oula sheep, including histone deacetylase 9 (HDAC9), protein tyrosine kinase 2 (PTK2), microphthalmia-related transcription factor (MITF), vesicular amine transporter 1 (VAT1), trichohyalin-like 1 (TCHHL1), amine oxidase, copper containing 3 (AOC3), interferon-inducible protein 35 (IFI35). CONCLUSIONS The results suggest that traits related to growth and development and plateau adaptation may be selection targets for the domestication and breeding improvement of Tibetan sheep. This study provides the fundamental footprints for Panou sheep breeding and management.
Collapse
Affiliation(s)
- Huibin Shi
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| | - Taotao Li
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| | - Manchun Su
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| | - Huihui Wang
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| | - Qiao Li
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| | - Xia Lang
- grid.464277.40000 0004 0646 9133Institute of Animal & Pasture Science and Green Agriculture, Gansu Academy of Agricultural Science, Lanzhou, 730070 China
| | - Youji Ma
- grid.411734.40000 0004 1798 5176College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070 China
| |
Collapse
|
12
|
Comparison of Marker Effects and Breeding Values at Two Levels at THI for Milk Yield and Quality Traits in Brazilian Holstein Cows. Genes (Basel) 2022; 14:genes14010017. [PMID: 36672758 PMCID: PMC9858941 DOI: 10.3390/genes14010017] [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: 10/26/2022] [Revised: 11/26/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Genomic tools can help in the selection of animals genetically resistant to heat stress, especially the genome-wide association studies (GWAS). The objective of this study was to compare the variance explained by SNPs and direct genomic breeding values (DGVs) at two levels of a temperature and humidity index (THI). Records of milk yield (MY), somatic cell score (SCS), and percentages of casein (CAS), saturated fatty acids (SFA), and unsaturated fatty acids (UFA) in milk from 1157 Holstein cows were used. Traditional breeding values (EBV) were determined in a previous study and used as pseudo-phenotypes. Two levels of THI (heat comfort zone and heat stress zone) were used as environments and were treated as "traits" in a bi-trait model. The GWAS was performed using the genomic best linear unbiased prediction (GBLUP) method. Considering the top 50 SNPs, a total of 36 SNPs were not common between environments, eight of which were located in gene regions related to the evaluated traits. Even for those SNPs that had differences in their explained variances between the two environments, the differences were very small. The animals showed virtually no rank order, with rank correlation values of 0.90, 0.88, 1.00, 0.88, and 0.97 for MY, CAS, SCS, SFA, and UFA, respectively. The small difference between the environments studied can be attributed to the small difference in the pseudo-phenotypes used between the environments, on-farm acclimation, the polygenic nature of the traits, and the THI values studied near the threshold between comfort and heat stress. It is recommended that future studies be conducted with a larger number of animals and at more extreme THI levels.
Collapse
|
13
|
Ballan M, Schiavo G, Bovo S, Schiavitto M, Negrini R, Frabetti A, Fornasini D, Fontanesi L. Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds. Anim Genet 2022; 53:849-862. [PMID: 36073189 PMCID: PMC9826494 DOI: 10.1111/age.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.
Collapse
Affiliation(s)
- Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Michele Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Contrada Giancola SncVolturara AppulaItaly
| | | | | | | | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| |
Collapse
|
14
|
Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
Collapse
|
15
|
Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China. PLoS One 2022; 17:e0271718. [PMID: 36006904 PMCID: PMC9409551 DOI: 10.1371/journal.pone.0271718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous segments from the common ancestor of parents. Evaluating ROH pattern can help to understand inbreeding level and genetic basis of important traits. In this study, three representative cattle populations including Leiqiong cattle (LQC), Lufeng cattle (LFC) and Hainan cattle (HNC) were genotyped using the Illumina BovineHD SNPs array (770K) to assess ROH pattern at genome wide level. Totally, we identified 26,537 ROH with an average of 153 ROH per individual. The sizes of ROH ranged from 0.5 to 53.26Mb, and the average length was 1.03Mb. The average of FROH ranged from 0.10 (LQC) to 0.15 (HNC). Moreover, we identified 34 ROH islands (with frequency > 0.5) across genome. Based on these regions, we observed several breed-specific candidate genes related to adaptive traits. Several common genes related to immunity (TMEM173, MZB1 and SIL1), and heat stress (DNAJC18) were identified in all three populations. Three genes related to immunity (UGP2), development (PURA) and reproduction (VPS54) were detected in both HNC and LQC. Notably, we identified several breed-specific genes related to sperm development (BRDT and SPAG6) and heat stress (TAF7) in HNC, and immunity (CDC23 and NME5) and development (WNT87) in LFC. Our findings provided valuable insights into understanding the genomic homozygosity pattern and promoting the conservation of genetic resources of Chinese indigenous cattle.
Collapse
|
16
|
Toro-Ospina AM, Herrera Rios AC, Pimenta Schettini G, Vallejo Aristizabal VH, Bizarria dos Santos W, Zapata CA, Ortiz Morea EG. Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia). Genes (Basel) 2022; 13:genes13071232. [PMID: 35886015 PMCID: PMC9318017 DOI: 10.3390/genes13071232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.
Collapse
Affiliation(s)
- Alejandra M. Toro-Ospina
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Correspondence:
| | - Ana C. Herrera Rios
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia
| | - Gustavo Pimenta Schettini
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA;
| | - Viviana H. Vallejo Aristizabal
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil;
| | - Cesar A. Zapata
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Edna Gicela Ortiz Morea
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| |
Collapse
|
17
|
Mulim HA, Brito LF, Pinto LFB, Ferraz JBS, Grigoletto L, Silva MR, Pedrosa VB. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics 2022; 23:209. [PMID: 35291953 PMCID: PMC8925140 DOI: 10.1186/s12864-022-08384-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023] Open
Abstract
Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08384-0.
Collapse
Affiliation(s)
| | - Luiz F Brito
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA
| | | | - José Bento Sterman Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Lais Grigoletto
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA.,Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Bahia, Brazil. .,Department of Animal Science, State University of Ponta Grossa, Av. General Carlos Cavalcanti, 4748 - Uvaranas, Ponta Grossa, PR, 84030-900, Brazil.
| |
Collapse
|
18
|
Ablondi M, Sabbioni A, Stocco G, Cipolat-Gotet C, Dadousis C, van Kaam JT, Finocchiaro R, Summer A. Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection. Front Vet Sci 2022; 8:773985. [PMID: 35097040 PMCID: PMC8792952 DOI: 10.3389/fvets.2021.773985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.
Collapse
Affiliation(s)
- Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Giorgia Stocco
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Claudio Cipolat-Gotet
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
- *Correspondence: Claudio Cipolat-Gotet
| | - Christos Dadousis
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| | - Jan-Thijs van Kaam
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Raffaella Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, Cremona, Italy
| | - Andrea Summer
- Dipartimento di Scienze Medico-Veterinarie, University of Parma, Parma, Italy
| |
Collapse
|
19
|
Schiavo G, Bovo S, Ribani A, Moscatelli G, Bonacini M, Prandi M, Mancin E, Mantovani R, Dall'Olio S, Fontanesi L. Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. J Dairy Sci 2021; 105:2408-2425. [PMID: 34955250 DOI: 10.3168/jds.2021-20915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.
Collapse
Affiliation(s)
- Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy.
| |
Collapse
|
20
|
Bertolini F, Moscatelli G, Schiavo G, Bovo S, Ribani A, Ballan M, Bonacini M, Prandi M, Dall'Olio S, Fontanesi L. Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours. J Anim Breed Genet 2021; 139:307-319. [PMID: 34841617 PMCID: PMC9300179 DOI: 10.1111/jbg.12659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/01/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed-specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well-known Protected Designation of Origin Parmigiano-Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome-wide information in comparative FST analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% FST values, a total of 64 markers were detected in the single-marker analysis. The top FST value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window-based analyses, which included 0.5-Mb or 1-Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle.
Collapse
Affiliation(s)
- Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giulia Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anisa Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Reggio Emilia, Italy
| | - Stefania Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| |
Collapse
|
21
|
Buaban S, Lengnudum K, Boonkum W, Phakdeedindan P. Genome-wide association study on milk production and somatic cell score for Thai dairy cattle using weighted single-step approach with random regression test-day model. J Dairy Sci 2021; 105:468-494. [PMID: 34756438 DOI: 10.3168/jds.2020-19826] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 08/24/2021] [Indexed: 12/26/2022]
Abstract
Genome-wide association studies are a powerful tool to identify genomic regions and variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. The objectives of this study were to identify genomic regions as well as genes and pathways associated with the first-lactation milk, fat, protein, and total solid yields; fat, protein, and total solid percentage; and somatic cell score (SCS) in a Thai dairy cattle population. Effects of SNPs were estimated by a weighted single-step GWAS, which back-solved the genomic breeding values predicted using single-step genomic BLUP (ssGBLUP) fitting a single-trait random regression test-day model. Genomic regions that explained at least 0.5% of the total genetic variance were selected for further analyses of candidate genes. Despite the small number of genotyped animals, genomic predictions led to an improvement in the accuracy over the traditional BLUP. Genomic predictions using weighted ssGBLUP were slightly better than the ssGBLUP. The genomic regions associated with milk production traits contained 210 candidate genes on 19 chromosomes [Bos taurus autosome (BTA) 1 to 7, 9, 11 to 16, 20 to 21, 26 to 27 and 29], whereas 21 candidate genes on 3 chromosomes (BTA 11, 16, and 21) were associated with SCS. Many genomic regions explained a small fraction of the genetic variance, indicating polygenic inheritance of the studied traits. Several candidate genes coincided with previous reports for milk production traits in Holstein cattle, especially a large region of genes on BTA14. We identified 141 and 5 novel genes related to milk production and SCS, respectively. These novel genes were also found to be functionally related to heat tolerance (e.g., SLC45A2, IRAG1, and LOC101902172), longevity (e.g., SYT10 and LOC101903327), and fertility (e.g., PAG1). These findings may be attributed to indirect selection in our population. Identified biological networks including intracellular cell transportation and protein catabolism implicate milk production, whereas the immunological pathways such as lymphocyte activation are closely related to SCS. Further studies are required to validate our findings before exploiting them in genomic selection.
Collapse
Affiliation(s)
- S Buaban
- Bureau of Animal Husbandry and Genetic Improvement, Department of Livestock Development, Pathum Thani 12000, Thailand
| | - K Lengnudum
- Bureau of Biotechnology in Livestock Production, Department of Livestock Development, Pathum Thani 12000, Thailand
| | - W Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - P Phakdeedindan
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
22
|
Liu D, Chen Z, Zhao W, Guo L, Sun H, Zhu K, Liu G, Shen X, Zhao X, Wang Q, Ma P, Pan Y. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC Genomics 2021; 22:747. [PMID: 34654366 PMCID: PMC8520274 DOI: 10.1186/s12864-021-08042-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08042-x.
Collapse
Affiliation(s)
- Dengying Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Zhenliang Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Wei Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Longyu Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Xiuping Shen
- Shanghai Agricultural Development Promotion Center, 200335, Shanghai, PR China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China.
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China.
| |
Collapse
|
23
|
Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle. BMC Genomics 2021; 22:678. [PMID: 34548021 PMCID: PMC8454143 DOI: 10.1186/s12864-021-07992-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. RESULTS We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. CONCLUSIONS Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.
Collapse
|
24
|
Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia. Life (Basel) 2021; 11:life11080861. [PMID: 34440604 PMCID: PMC8400874 DOI: 10.3390/life11080861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.
Collapse
|
25
|
Bovo S, Schiavo G, Kazemi H, Moscatelli G, Ribani A, Ballan M, Bonacini M, Prandi M, Dall'Olio S, Fontanesi L. Exploiting within-breed variability in the autochthonous Reggiana breed identified several candidate genes affecting pigmentation-related traits, stature and udder defects in cattle. Anim Genet 2021; 52:579-597. [PMID: 34182594 PMCID: PMC8519023 DOI: 10.1111/age.13109] [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] [Accepted: 06/11/2021] [Indexed: 01/13/2023]
Abstract
Autochthonous cattle breeds constitute important reservoirs of genetic diversity. Reggiana is an Italian local cattle breed reared in the north of Italy for the production of a mono‐breed Parmigiano–Reggiano cheese. Reggiana cattle usually have a classical solid red coat colour and pale muzzle. As part of the strategies designed for the sustainable conservation of this genetic resource, we investigated at the genome‐wise level the within‐breed detected variability of three pigmentation‐related traits (intensity of red coat colour, based on three classes – light/diluted, normal and dark; spotted patterns/piebaldism that sometime emerge in the breed; muzzle colour – pink/pale, grey and black), stature, presence/absence and number of supernumerary teats and teat length. A total of 1776 Reggiana cattle (about two‐thirds of the extant breed population) were genotyped with the GeneSeek GGP Bovine 150k SNP array and single‐marker and haplotype‐based GWASs were carried out. The results indicated that two main groups of genetic factors affect the intensity of red coat colour: darkening genes (including EDN3 and a few other genes) and diluting genes (including PMEL and a few other genes). Muzzle colour was mainly determined by MC1R gene markers. Piebaldism was mainly associated with KIT gene markers. Stature was associated with BTA6 markers upstream of the NCAPG–LCORL genes. Teat defects were associated with TBX3/TBX5, MCC and LGR5 genes. Overall, the identified genomic regions not only can be directly used in selection plans in the Reggiana breed, but also contribute to clarifying the genetic mechanisms involved in determining exterior traits in cattle.
Collapse
Affiliation(s)
- S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - H Kazemi
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - G Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Ballan
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, Reggio Emilia, 42124, Italy
| | - M Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, Reggio Emilia, 42124, Italy
| | - S Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Science, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| |
Collapse
|
26
|
Terán E, Azcona F, Ramón M, Molina A, Dorado J, Hidalgo M, Ross P, Goszczynski D, Demyda-Peyrás S. Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach. Mol Reprod Dev 2021; 88:416-426. [PMID: 34009693 DOI: 10.1002/mrd.23475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022]
Abstract
The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm2 ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P2 /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.
Collapse
Affiliation(s)
- Ester Terán
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina.,Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Florencia Azcona
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Manuel Ramón
- CERSYRA-Centro Regional de Selección y Reproducción Animal de Castilla-La Mancha, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Valdepeñas, España
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
| | - Jesús Dorado
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Manuel Hidalgo
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Pablo Ross
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Daniel Goszczynski
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| |
Collapse
|
27
|
Schiavo G, Bovo S, Muñoz M, Ribani A, Alves E, Araújo JP, Bozzi R, Čandek-Potokar M, Charneca R, Fernandez AI, Gallo M, García F, Karolyi D, Kušec G, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. Anim Genet 2021; 52:155-170. [PMID: 33544919 DOI: 10.1111/age.13045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.
Collapse
Affiliation(s)
- G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - A Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - E Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J P Araújo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, Ponte de Lima, 4990-706, Portugal
| | - R Bozzi
- DAGRI - Animal Science Division, Università di Firenze, Via delle Cascine 5, Firenze, 50144, Italy
| | - M Čandek-Potokar
- Kmetijski Inštitut Slovenije, Hacquetova 17, Ljubljana, SI-1000, Slovenia
| | - R Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Polo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - A I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Rome, 00198, Italy
| | - F García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - D Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, Zagreb, 10000, Croatia
| | - G Kušec
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, Osijek, 31000, Croatia
| | - J M Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Polo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - M-J Mercat
- IFIP Institut du porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex, 35651, France
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - R Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona, 08140, Spain
| | - Č Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - V Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania
| | - J Riquet
- GenPhySE, Université de Toulouse, INRA, Chemin de Borde-Rouge 24, Auzeville Tolosane, Castanet Tolosan, 31326, France
| | - R Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - G Usai
- Agris Sardegna, Loc. Bonassai, Sassari, 07100, Italy
| | - V J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| | - C Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, Wolpertshausen, 74549, Germany
| | - C Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, Bologna, 40127, Italy
| |
Collapse
|
28
|
Noce A, Qanbari S, González-Prendes R, Brenmoehl J, Luigi-Sierra MG, Theerkorn M, Fiege MA, Pilz H, Bota A, Vidu L, Horwath C, Haraszthy L, Penchev P, Ilieva Y, Peeva T, Lüpcke W, Krawczynski R, Wimmers K, Thiele M, Hoeflich A. Genetic Diversity of Bubalus bubalis in Germany and Global Relations of Its Genetic Background. Front Genet 2021; 11:610353. [PMID: 33552127 PMCID: PMC7863760 DOI: 10.3389/fgene.2020.610353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022] Open
Abstract
This is the first study to explore the genetic diversity and population structure of domestic water buffalo (Bubalus bubalis) in Germany and their potential relations to herds in other parts of Europe or worldwide. To this end, animals from different herds in Germany, Bulgaria, Romania, and Hungary were genotyped and compared to genotypes from other populations with worldwide distribution and open to the public. The pilot study analyzed population structure, phylogenetic tree, and inbreeding events in our samples. In buffalos from Germany, a mixed genetic make-up with contributions from Bulgaria (Murrah breed), Romania, and Italy was found. All in all, a high degree of genetic diversity was identified in European buffalos, and a novel genotype was described in Hungarian buffalos by this study. We demonstrate that European buffalos stand out from other buffalo populations worldwide, supporting the idea that buffalos have not completely disappeared from the European continent during the late Pleistocene. The high genetic diversity in European buffalos seems to be an excellent prerequisite for the establishment of local breeds characterized by unique traits and features. This study may also be considered as an initial step on the way to genome characterization for the sustainable development of the buffalo economy in Germany and other parts of Europe in the future.
Collapse
Affiliation(s)
- Antonia Noce
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Saber Qanbari
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Rayner González-Prendes
- Animal Breeding and Genomics Group, Wageningen University & Research, Wageningen, Netherland
| | - Julia Brenmoehl
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - María Gracia Luigi-Sierra
- Department of Animal Genetics, Center for Research in Agricultural Genomics, Campus Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | | | - Heike Pilz
- Wiesenburger Land eG, Wiesenburg, Germany
| | - Adrian Bota
- Research and Development Station for Buffalos Şercaia, Şercaia, Romania
| | - Livia Vidu
- University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | | | | | - Pencho Penchev
- Bulgarian National Association for Development of Buffalo Breeding, Shumen, Bulgaria
| | - Yordanka Ilieva
- Bulgarian National Association for Development of Buffalo Breeding, Shumen, Bulgaria
| | - Tzonka Peeva
- Bulgarian National Association for Development of Buffalo Breeding, Shumen, Bulgaria
| | - Wolfgang Lüpcke
- Higher School in Agribusiness and Development of Regions, Agricultural University Plovdiv, Tarnovo, Bulgaria
| | | | - Klaus Wimmers
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | | | | |
Collapse
|
29
|
Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
Collapse
Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
| |
Collapse
|
30
|
Moscarelli A, Sardina MT, Cassandro M, Ciani E, Pilla F, Senczuk G, Portolano B, Mastrangelo S. Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations. Anim Genet 2020; 52:21-31. [PMID: 33174276 DOI: 10.1111/age.13019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The FST -outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual-purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.
Collapse
Affiliation(s)
- A Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - M Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, 35020, Italy
| | - E Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, Bari, 70124, Italy
| | - F Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - G Senczuk
- Dipartimento Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, 86100, Italy
| | - B Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| | - S Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, 90128, Italy
| |
Collapse
|
31
|
Schiavo G, Bovo S, Bertolini F, Dall'Olio S, Nanni Costa L, Tinarelli S, Gallo M, Fontanesi L. Runs of homozygosity islands in Italian cosmopolitan and autochthonous pig breeds identify selection signatures in the porcine genome. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
32
|
Cendron F, Perini F, Mastrangelo S, Tolone M, Criscione A, Bordonaro S, Iaffaldano N, Castellini C, Marzoni M, Buccioni A, Soglia D, Schiavone A, Cerolini S, Lasagna E, Cassandro M. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals (Basel) 2020; 10:E1441. [PMID: 32824706 PMCID: PMC7460279 DOI: 10.3390/ani10081441] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/06/2023] Open
Abstract
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.
Collapse
Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
| | - Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Marco Tolone
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Andrea Criscione
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Salvatore Bordonaro
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Nicolaia Iaffaldano
- Department of Agricultural, Environment and Food, University of Molise, Via De Sanctis s/n, 86100 Campobasso, Italy;
| | - Cesare Castellini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Margherita Marzoni
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy;
| | - Arianna Buccioni
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, Via di San Bonaventura, 50145 Firenze, Italy;
| | - Dominga Soglia
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Achille Schiavone
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Silvia Cerolini
- Department of Veterinary Science, University of Milano, Via Trentacoste, 2, 20134 Milano, Italy;
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
| |
Collapse
|
33
|
Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle. Animals (Basel) 2020; 10:ani10081425. [PMID: 32824035 PMCID: PMC7460448 DOI: 10.3390/ani10081425] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.
Collapse
|
34
|
Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations. Animals (Basel) 2020; 10:ani10061040. [PMID: 32560248 PMCID: PMC7341319 DOI: 10.3390/ani10061040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits. Abstract Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.
Collapse
|
35
|
Mastrangelo S, Ben Jemaa S, Ciani E, Sottile G, Moscarelli A, Boussaha M, Montedoro M, Pilla F, Cassandro M. Genome-wide detection of signatures of selection in three Valdostana cattle populations. J Anim Breed Genet 2020; 137:609-621. [PMID: 32219904 DOI: 10.1111/jbg.12476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/15/2022]
Abstract
The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST ) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.
Collapse
Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, Bari, Italy
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, Palermo, Italy
| | - Angelo Moscarelli
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, GABI, Université Paris Saclay, Jouy-en-Josas, France
| | - Marina Montedoro
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Rivolta d'Adda, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, Legnaro, Italy
| |
Collapse
|
36
|
Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino. Animals (Basel) 2020; 10:ani10030524. [PMID: 32245132 PMCID: PMC7143548 DOI: 10.3390/ani10030524] [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: 01/26/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Runs of homozygosity (ROH) are commonly used to estimate inbreeding coefficients and identify selection signatures in livestock population. The present study determined ROH patterns, estimated the inbreeding levels, and identified the genome regions with high ROH frequency (ROH hotspots) in Chinese Merino. Our results showed that the genome of Chinese Merino harbored lower ROH abundance. Moreover, the inbreeding levels were relatively low. Thirteen ROH hotspots consisting of 190 genes were identified. The ROH hotspots overlapped the selective signatures might be associated with body size, horn traits, immune traits and environment adaption. These findings could contribute to an optimum breeding program by identifying the candidate genes related to economically traits in Chinese Merino. Abstract In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.
Collapse
|
37
|
Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, Khansefid M. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis. BMC Genet 2020; 21:16. [PMID: 32041535 PMCID: PMC7011551 DOI: 10.1186/s12863-020-0824-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Background Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
Collapse
Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.
| | - Mohammad Hossein Fallahi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Jalil Sarghale
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Rostam Abdollahi-Arpanahi
- Departments of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, 33916-53755, Iran
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| |
Collapse
|
38
|
Toro Ospina AM, Silva Faria RA, Vercesi Filho AE, Cyrillo JNDSG, Zerlotti Mercadante ME, Curi RA, Vasconcelos Silva JA. Genome‐wide identification of runs of homozygosity islands in the Gyr breed (
Bos indicus
). Reprod Domest Anim 2020; 55:333-342. [DOI: 10.1111/rda.13639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/29/2019] [Indexed: 01/19/2023]
|
39
|
Comparative selection signature analyses identify genomic footprints in Reggiana cattle, the traditional breed of the Parmigiano-Reggiano cheese production system. Animal 2020; 14:921-932. [PMID: 31928542 DOI: 10.1017/s1751731119003318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Reggiana is an autochthonous cattle breed reared mainly in the province of Reggio Emilia, located in the North of Italy. Reggiana cattle (originally a triple-purpose population largely diffused in the North of Italy) are characterised by a typical solid red coat colour. About 2500 cows of this breed are currently registered to its herd book. Reggiana is now considered a dual-purpose breed even if it is almost completely dedicated to the production of a mono-breed branded Protected Designation of Origin Parmigiano-Reggiano cheese, which is the main driver of the sustainable conservation of this local genetic resource. In this study, we provided the first overview of genomic footprints that characterise Reggiana and define the diversity of this local cattle breed. A total of 168 Reggiana sires (all bulls born over 35 years for which semen was available) and other 3321 sires from 3 cosmopolitan breeds (Brown, Holstein and Simmental) were genotyped with the Illumina BovineSNP50 panel. ADMIXTURE analysis suggested that Reggiana breed might have been influenced, at least in part, by the other three breeds included in this study. Selection signatures in the Reggiana genome were identified using three statistical approaches based on allele frequency differences among populations or on properties of haplotypes segregating in the populations (fixation index (FST); integrated haplotype score; cross-population extended haplotype homozygosity). We identified several regions under peculiar selection in the Reggiana breed, particularly on bovine chromosome (BTA) 6 in the KIT gene region, that is known to be involved in coat colour pattern distribution, and within the region of the LAP3, NCAPG and LCORL genes, that are associated with stature, conformation and carcass traits. Another already known region that includes the PLAG1 gene (BTA14), associated with conformation traits, showed a selection signature in the Reggiana cattle. On BTA18, a signal of selection included the MC1R gene that causes the red coat colour in cattle. Other selection sweeps were in regions, with high density of quantitative trait loci for milk production traits (on BTA20) and in several other large regions that might have contributed to shape and define the Reggiana genome (on BTA17 and BTA29). All these results, overall, indicate that the Reggiana genome might still contain several signs of its multipurpose and non-specialised utilisation, as already described for other local cattle populations, in addition to footprints derived by its ancestral origin and by its adaptation to the specialised Parmigiano-Reggiano cheese production system.
Collapse
|
40
|
Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
Collapse
Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| |
Collapse
|
41
|
Oliveira HR, Lourenco DAL, Masuda Y, Misztal I, Tsuruta S, Jamrozik J, Brito LF, Silva FF, Cant JP, Schenkel FS. Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle. J Dairy Sci 2019; 102:9995-10011. [PMID: 31477296 DOI: 10.3168/jds.2019-16821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/08/2019] [Indexed: 11/19/2022]
Abstract
Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression.
Collapse
Affiliation(s)
- H R Oliveira
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - Y Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - J Jamrozik
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - L F Brito
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F F Silva
- Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - J P Cant
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
42
|
Mastrangelo S, Bahbahani H, Moioli B, Ahbara A, Al Abri M, Almathen F, da Silva A, Belabdi I, Portolano B, Mwacharo JM, Hanotte O, Pilla F, Ciani E. Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia. PLoS One 2019; 14:e0209632. [PMID: 31199810 PMCID: PMC6568386 DOI: 10.1371/journal.pone.0209632] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/28/2019] [Indexed: 01/24/2023] Open
Abstract
Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.
Collapse
Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Monterotondo, Italy
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Oman
| | - Faisal Almathen
- Department of Public Health and Animal Welfare, College of Veterinary Medicine, King Faisal University, Alhufuf, Al-Ahsa, Saudi Arabia
| | - Anne da Silva
- Université de Limoges, INRA, PEREINE EA7500, USC1061 GAMAA, Limoges, France
| | - Ibrahim Belabdi
- Science Veterinary Institute, University of Blida, Blida, Algeria
- Laboratory of Biotechnology related to Animal Reproduction (LBRA), University of Blida, Blida, Algeria
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- * E-mail:
| |
Collapse
|