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Amano T, Yokawa H, Masuda Y, Tozaki T, Kawai M, Shirai K. Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse. Anim Sci J 2023; 94:e13884. [PMID: 37983921 DOI: 10.1111/asj.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HKD as a breed. Tajima's D analysis and runs of homozygosity analysis identified 23 selection signatures unique to HKD (P < 0.05), and following database search found 20 traits that were associated with those selection signatures; among these traits, coat color traits, face and body markings, showed the highest important value (0.50 and 0.46). Enrichment analysis of genes in the selection signatures identified six gene ontology terms (P < 0.05), and a term related to innate immunity (regulation of defense response; GO:0031347) showed the highest positive fold enrichment value (7.13). These results provide the first scientific evidence of a genetic basis for the traits of HKD.
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Affiliation(s)
- Tomoko Amano
- Laboratory of Animal Genetics, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan
| | - Haruhi Yokawa
- Laboratory of Animal Genetics, Graduate School of Dairy Science, Rakuno Gakuen University, Hokkaido, Japan
| | - Yutaka Masuda
- Laboratory of Animal Breeding, Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Kouichi Shirai
- Hokkaido Native Horse Conservation Association, Hokkaido, Japan
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Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 2023; 17:100690. [PMID: 36566708 DOI: 10.1016/j.animal.2022.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic.
| | - Héctor Marina
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Juan Jose Arranz
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Rocío Pelayo
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Jana Rychtářová
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Michal Milerski
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Luboš Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic
| | - Aroa Suárez-Vega
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
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Lashmar SF, Visser C, Okpeku M, Muchadeyi FC, Mapholi NO, van Marle-Köster E. A within- and across-country assessment of the genomic diversity and autozygosity of South African and eSwatini Nguni cattle. Trop Anim Health Prod 2022; 54:365. [DOI: 10.1007/s11250-022-03373-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
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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.
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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
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Wang H, Wang Q, Tan X, Wang J, Zhang J, Zheng M, Zhao G, Wen J. Estimation of genetic variability and identification of regions under selection based on runs of homozygosity in Beijing-You Chickens. Poult Sci 2022; 102:102342. [PMID: 36470032 PMCID: PMC9719870 DOI: 10.1016/j.psj.2022.102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic composition of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. Runs of homozygosity (ROHs) are homozygous segments of the genome where the 2 haplotypes inherited from the parents are identical. The detection of ROH can be used to describe the genetic variability and quantify the level of inbreeding in an individual. Here, we investigated the occurrence and distribution of ROHs in 40 Beijing-You Chickens from the random breeding population (BJY_C) and 40 Beijing-You Chickens from the intramuscular fat (IMF) selection population (BJY_S). Principal component analysis (PCA) and maximum likelihood (ML) analyses showed that BJY_C was completely separated from the BJY_S. The nucleotide diversity of BJY_C was higher than that of BJY_S, and the decay rate of LD of BJY_C was faster. The ROHs were identified for a total of 7,101 in BJY_C and 9,273 in BJY_S, respectively. The ROH-based inbreeding estimate (FROH) of BJY_C was 0.079, which was significantly lower than that of BJY_S (FROH = 0.114). The results were the same as the estimates of the inbreeding coefficients calculated based on homozygosity (FHOM), the correlation between uniting gametes (FUNI), and the genomic relationship matrix (FGRM). Additionally, the distribution and number of ROH islands in chromosomes of BJY_C and BJY_S were significantly different. The ROH islands of BJY_S that included genes associated with lipid metabolism and fat deposition, such as CIDEA and S1PR1, were absent in BJY_C. However, GPR161 was detected in both populations, which is a candidate gene for the formation of the unique five-finger trait in Beijing-You chickens. Our findings contributed to the understanding of the genetic diversity of random or artificially selected populations, and allowed the accurate monitoring of population inbreeding using genomic information, as well as the detection of genomic regions that affect traits under selection.
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Affiliation(s)
- Hailong Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Qiao Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Xiaodong Tan
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jin Zhang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Maiqing Zheng
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Guiping Zhao
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wen
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China.
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Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse. J Anim Sci Biotechnol 2022; 13:127. [PMID: 36336696 PMCID: PMC9639299 DOI: 10.1186/s40104-022-00781-5] [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: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. RESULTS The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. CONCLUSIONS Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
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Affiliation(s)
- Davinia Isabel Perdomo-González
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain.
| | - Nora Laseca
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
| | - Mercedes Valera
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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Assessment of Genetic Diversity, Runs of Homozygosity, and Signatures of Selection in Tropical Milking Criollo Cattle Using Pedigree and Genomic Data. Genes (Basel) 2022; 13:genes13101896. [PMID: 36292782 PMCID: PMC9602073 DOI: 10.3390/genes13101896] [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: 09/28/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree (FPed), the genomic relationship matrix (FGRM), and runs of homozygosity (FROH) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for FPED, FGRM, and FROH, respectively. Correlation between FPED and FROH was significant only for runs of homozygosity > 4 Mb, indicating the FPED of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program.
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Addo S, Jung L. An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs. Front Genet 2022; 13:909986. [DOI: 10.3389/fgene.2022.909986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
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Human impact on the recent population history of the elusive European wildcat inferred from whole genome data. BMC Genomics 2022; 23:709. [PMID: 36258177 PMCID: PMC9578205 DOI: 10.1186/s12864-022-08930-w] [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: 05/20/2022] [Accepted: 10/07/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The extent and impact of evolutionary change occurring in natural populations in response to rapid anthropogenic impact is still poorly understood on the genome-wide level. Here, we explore the genetic structure, demographic history, population differentiation, and domestic introgression based on whole genome data of the endangered European wildcat in Germany, to assess potential genomic consequences of the species' recent spread across human-dominated cultural landscapes. RESULTS Reconstruction of demographic history and introgression rates based on 47 wildcat and 37 domestic cat genomes suggested late introgression between wild and domestic cat, coinciding with the introduction of domestic cat during the Roman period, but overall relatively low rates of hybridization and introgression from domestic cats. Main population divergence found between an eastern and central German wildcat clade was found to be of rather recent origin (200 y), and thus the likely consequence of anthropogenic persecution and resulting isolation in population refugia. We found similar effective population sizes and no substantial inbreeding across populations. Interestingly, highly differentiated genes between wild cat populations involved in the tryptophan-kynurenine-serotonin pathway were revealed, which plays a role in behavioral processes such as stress susceptibility and tolerance, suggesting that differential selection acted in the populations. CONCLUSIONS We found strong evidence for substantial recent anthropogenic impact on the genetic structure of European wildcats, including recent persecution-driven population divergence, as well as potential adaptation to human-dominate environments. In contrast, the relatively low levels of domestic introgression and inbreeding found in this study indicate a substantial level of "resistance" of this elusive species towards major anthropogenic impacts, such as the omnipresence of domestic cats as well as substantial habitat fragmentation. While those findings have strong implications for ongoing conservation strategies, we demand closer inspection of selective pressures acting on this and other wildlife species in anthropogenic environments.
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Mowry BJ, Periyasamy S. Genome‐Wide Association Studies in Schizophrenia. ELS 2022:1-14. [DOI: 10.1002/9780470015902.a0025337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [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: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mirte Bosse,
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Lozada-Soto EA, Tiezzi F, Jiang J, Cole JB, VanRaden PM, Maltecca C. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. J Dairy Sci 2022; 105:8956-8971. [PMID: 36153159 DOI: 10.3168/jds.2022-22116] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022]
Abstract
Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (FPED), marker-based using a genomic relationship matrix (FGRM), and segment-based using ROH (FROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using FPED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using FGRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using FROH. In addition, the effective population size at past generations (5-100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.
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Affiliation(s)
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50144 Florence, Italy
| | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh 27607
| | | | - Paul M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh 27607
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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [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: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
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Lin R, Li J, Yang Y, Yang Y, Chen J, Zhao F, Xiao T. Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province. Animals (Basel) 2022; 12:ani12172302. [PMID: 36078022 PMCID: PMC9454422 DOI: 10.3390/ani12172302] [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: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary The aim of this study was to conduct a genome-wide comparative analysis of four indigenous Chinese duck breeds (Jinding, Liancheng white, Putian black, and Shanma ducks) from Fujian Province, to understand their genetic diversity and population structure. Population parameters showed that the four indigenous breeds were separated groups. Five genomic regions are presented as hotspots of autozygosity among these indigenous duck breeds, with candidate genes involved in muscle growth, pigmentation, and neuroregulation. Genomic information may play a vital role in the improvement of conservation strategies. Abstract The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.
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Meiring C, Schurz H, van Helden P, Hoal E, Tromp G, Kinnear C, Kleynhans L, Glanzmann B, van Schalkwyk L, Miller M, Möller M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 2022; 12:14979. [PMID: 36056068 PMCID: PMC9440078 DOI: 10.1038/s41598-022-19025-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
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Affiliation(s)
- Christina Meiring
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Louis van Schalkwyk
- Department of Agriculture, Land Reform and Rural Development, PO Box 12, Skukuza, 1350, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
| | - Michele Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Private bag X1, Merriman Avenue, Stellenbosch, 7600, South Africa
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Wu MY, Lau CJ, Ng EYX, Baveja P, Gwee CY, Sadanandan K, Ferasyi TR, Haminuddin, Ramadhan R, Menner JK, Rheindt FE. Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation. Mol Biol Evol 2022; 39:6692815. [PMID: 36124912 PMCID: PMC9486911 DOI: 10.1093/molbev/msac189] [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] [Indexed: 11/12/2022] Open
Abstract
Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world's organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.
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Affiliation(s)
- Meng Yue Wu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Clara Jesse Lau
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Elize Ying Xin Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Pratibha Baveja
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Keren Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | - Haminuddin
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | - Rezky Ramadhan
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun Biol 2022; 5:821. [PMID: 36008681 PMCID: PMC9411537 DOI: 10.1038/s42003-022-03757-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution. Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.
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Banos G, Talenti A, Chatziplis D, Sánchez-Molano E. Genomic analysis of the rare British Lop pig and identification of distinctive genomic markers. PLoS One 2022; 17:e0271053. [PMID: 35960784 PMCID: PMC9374264 DOI: 10.1371/journal.pone.0271053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Concentration of production on a few commercial pig breeds has led to the marginalization of many native, numerically small breeds, increasing their risk of endangerment. In the UK, one such rare breed is the British Lop, a lop-eared breed, of similar origin to the Welsh breed. The objective of the present study was to address the genomic status of the British Lop and its relationship with other breeds and identify a small set of genomic markers that uniquely characterize and distinguish British Lop animals. Results have shown that the British Lop is a relatively distinct population with reduced genomic diversity and effective size consistent with its status as a rare breed. Furthermore, we demonstrated the genetic closeness of the British Lop to phenotypically similar breeds such as Landrace and Welsh as well Large White, Middle White and Pietrain. Finally, a set of 75 Single Nucleotide Polymorphisms distributed across multiple chromosomes were identified and validated as markers that can consistently distinguish British Lops from other closely related breeds. Results may inform breeding and management strategies aiming to enhance diversity as well as the development of a breed purity test.
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Affiliation(s)
- Georgios Banos
- Scotland’s Rural College (SRUC), Department of Animal and Veterinary Sciences, The Roslin Institute Building, Edinburgh, United Kingdom
| | - Andrea Talenti
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Dimitrios Chatziplis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Sindos, Greece
| | - Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Berghöfer J, Khaveh N, Mundlos S, Metzger J. Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs. BMC Genomics 2022; 23:564. [PMID: 35933356 PMCID: PMC9357325 DOI: 10.1186/s12864-022-08801-4] [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: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes. RESULTS Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation. CONCLUSIONS The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.
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Affiliation(s)
- Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Stefan Mundlos
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Charité-Universitätsmedizin Berlin, BCRT, Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
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Zhang Y, Zhuo Y, Ning C, Zhou L, Liu JF. Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population. G3 (BETHESDA, MD.) 2022; 12:jkac118. [PMID: 35551391 PMCID: PMC9258530 DOI: 10.1093/g3journal/jkac118] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
With the broad application of genomic information, SNP-based measures of estimating inbreeding have been widely used in animal breeding, especially based on runs of homozygosity. Inbreeding depression is better estimated by SNP-based inbreeding coefficients than pedigree-based inbreeding in general. However, there are few comprehensive comparisons of multiple methods in pigs so far, to some extent limiting their application. In this study, to explore an appropriate strategy for estimating inbreeding depression on both growth traits and reproductive traits in a Large White pig population, we compared multiple methods for the inbreeding coefficient estimation based on both pedigree and genomic information. This pig population for analyzing the influence of inbreeding was from a pig breeding farm in the Inner Mongolia of China. There were 26,204 pigs with records of age at 100 kg (AGE) and back-fat thickness at 100 kg (BF), and 6,656 sows with reproductive records of the total number of piglets at birth (TNB), and the number of alive piglets at birth (NBA), and litter weight at birth. Inbreeding depression affected growth and reproductive traits. The results indicated that pedigree-based and SNP-based inbreeding coefficients had significant effects on AGE, TNB, and NBA, except for BF. However, only SNP-based inbreeding coefficients revealed a strong association with inbreeding depression on litter weight at birth. Runs of homozygosity-based methods showed a slight advantage over other methods in the correlation analysis of inbreeding coefficients and estimation of inbreeding depression. Furthermore, our results demonstrated that the model-based approach (RZooRoH) could avoid miscalculations of inbreeding and inbreeding depression caused by inappropriate parameters, which had a good performance on both AGE and reproductive traits. These findings might improve the extensive application of runs of homozygosity analysis in pig breeding and breed conservation.
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Affiliation(s)
- Yu Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yue Zhuo
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271000, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jian-Feng Liu
- Corresponding author: College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, China. ; Corresponding author: College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, China.
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Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs. Comput Struct Biotechnol J 2022; 20:4060-4071. [PMID: 35983229 PMCID: PMC9364102 DOI: 10.1016/j.csbj.2022.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/23/2022] Open
Abstract
Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using FST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.
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Genomic Population Structure of the Main Historical Genetic Lines of Spanish Merino Sheep. Animals (Basel) 2022; 12:ani12101327. [PMID: 35625173 PMCID: PMC9138057 DOI: 10.3390/ani12101327] [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: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Historical documentation shows that the Spanish Merino sheep was selected over many centuries due to the quality of wool, following which it was used to originate all other Merino breeds around the world, mainly by crossbreeding with local breeds. Today, the historical genetic lines that originated the Spanish Merino are still preserved in several closed herds in which they have been bred for nearly 200 years, maintaining their original genetic purity. Our study demonstrates, using a genomic approach, the exceptional genetic richness and variability of these lines, which are clearly differentiated from modern Merino breeds, and must therefore be protected to safeguard the large genetic pool they represent. Abstract According to historiographical documentation, the Romans first began to select Merino sheep in the Iberian Peninsula during the first century, with the aim of obtaining a breed appreciated for the quality of its wool. This process continued locally during the Middle Ages, when Spanish sheep were protected, and their export to foreign countries was banned. It was during the 16th century when individual Merino sheep were allowed to spread around the world to be used to improve the wool quality of local breeds. However, the wool crisis of the 1960s shifted the selection criteria of the Merino breed towards meat production at the expenses of wool. Consequently, individuals that display the genetic and phenotypic characteristics of those sheep originally bred in the kingdom of Spain in the Middle Ages are extremely difficult to find in commercial herds. In this study, we characterized the genetic basis of 403 individuals from the main historical Spanish Merino genetic lines (Granda, Hidalgo, Lopez-Montenegro, Maeso, Donoso and Egea), which were bred in isolation over the last 200 years, using a genomic approach based on genotyping data from the Axiom™ Ovine 50K SNP Genotyping Array. Our analysis included measuring population structure, genomic differentiation indexes, runs of homozygosity (ROH) patterns, and an analysis of molecular variance (AMOVA). The results showed large genetic differences between the historical lines, even though they belong to the same breed. In addition, ROH analysis showed differences due to increased inbreeding among the ancient generations compared with the modern Merino lines, confirming the breed’s ancestral and closed origin. However, our results also showed a high variability and richness within the Spanish historical Merino lines from a genetic viewpoint. This fact, together with their great ability to produce high-quality wool, suggests that ancestral Merino lines from Spain should be considered a valuable genetic population to be maintained as a resource for the improvement of wool-producing sheep breeds all around the world.
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Nguyen TN, Chen N, Cosgrove EJ, Bowman R, Fitzpatrick JW, Clark AG. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida
Scrub‐Jays
,
Aphelocoma coerulescens. Evol Appl 2022; 15:1018-1027. [PMID: 35782006 PMCID: PMC9234620 DOI: 10.1111/eva.13421] [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: 12/16/2021] [Revised: 04/04/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.
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Affiliation(s)
- Tram N. Nguyen
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Ithaca NY USA
| | - Nancy Chen
- Department of Biology University of Rochester Rochester NY USA
| | - Elissa J. Cosgrove
- Department of Molecular Biology and Genetics Cornell University Ithaca NY USA
| | - Reed Bowman
- Avian Ecology Lab, Archbold Biological Station, Venus FL USA
| | - John W. Fitzpatrick
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Ithaca NY USA
| | - Andrew. G. Clark
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Avian Ecology Lab, Archbold Biological Station, Venus FL USA
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74
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Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed. Genes (Basel) 2022; 13:genes13050866. [PMID: 35627251 PMCID: PMC9140571 DOI: 10.3390/genes13050866] [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: 03/24/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
There is a growing concern about the loss of animal genetic resources. The aim of this study was to analyze the genetic diversity and potential peculiarity of the endangered Kosovar sheep breed Balusha. For this purpose, a dataset consisting of medium-density SNP chip genotypes (39,879 SNPs) from 45 Balusha sheep was generated and compared with SNP chip genotypes from 29 individuals of a second Kosovar breed, Bardhoka. Publicly available SNP genotypes from 39 individuals of the relatively closely located sheep breeds Istrian Pramenka and Ruda were additionally included in the analyses. Analysis of heterozygosity, allelic richness and effective population size was used to assess the genetic diversity. Inbreeding was evaluated using two different methods (FIS, FROH). The standardized FST (di) and cross-population extended haplotype homozygosity (XPEHH) methods were used to detect signatures of selection. We observed the lowest heterozygosity (HO = 0.351) and effective population size (Ne5 = 25, Ne50 = 228) for the Balusha breed. The mean allelic richness levels (1.780–1.876) across all analyzed breeds were similar and also comparable with those in worldwide breeds. FROH estimates (0.023–0.077) were highest for the Balusha population, although evidence of decreased inbreeding was observed in FIS results for the Balusha breed. Two Gene Ontology (GO) TERMs were strongly enriched for Balusha, and involved genes belonging to the melanogenesis and T cell receptor signaling pathways, respectively. This could result from selection for the special coat color pattern of Balusha (black head) and resistance to certain infectious diseases. The analyzed diversity parameters highlight the urgency to preserve the local Kosovar Balusha sheep as it is clearly distinguished from other sheep of Southeastern Europe, has the lowest diversity level and may harbor valuable genetic variants, e.g., for resistance to infectious diseases.
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75
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Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam JT, Marusi M, Cassandro M, Sabbioni A, Summer A. Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci 2022; 105:5926-5945. [DOI: 10.3168/jds.2021-21125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
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76
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Morrill K, Hekman J, Li X, McClure J, Logan B, Goodman L, Gao M, Dong Y, Alonso M, Carmichael E, Snyder-Mackler N, Alonso J, Noh HJ, Johnson J, Koltookian M, Lieu C, Megquier K, Swofford R, Turner-Maier J, White ME, Weng Z, Colubri A, Genereux DP, Lord KA, Karlsson EK. Ancestry-inclusive dog genomics challenges popular breed stereotypes. Science 2022; 376:eabk0639. [PMID: 35482869 DOI: 10.1126/science.abk0639] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h2) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.
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Affiliation(s)
- Kathleen Morrill
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Hekman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xue Li
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse McClure
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brittney Logan
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Linda Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Fauna Bio Inc., Emeryville, CA 94608, USA
| | - Mingshi Gao
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Yinan Dong
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marjie Alonso
- The International Association of Animal Behavior Consultants, Cranberry Township, PA 16066, USA.,IAABC Foundation, Cranberry Township, PA 16066, USA
| | - Elena Carmichael
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Rice University, Houston, TX 77005, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85251, USA.,School for Human Evolution and Social Change, Arizona State University, Tempe, AZ 85251, USA.,School of Life Sciences, Arizona State University, Tempe, AZ 85251, USA
| | - Jacob Alonso
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hyun Ji Noh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Charlie Lieu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Darwin's Ark Foundation, Seattle, WA 98026, USA
| | - Kate Megquier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michelle E White
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhiping Weng
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Andrés Colubri
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kathryn A Lord
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Darwin's Ark Foundation, Seattle, WA 98026, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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77
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No evidence that long runs of homozygosity tend to harbor risk variants for polygenic obesity in Labrador retriever dogs. J Appl Genet 2022; 63:557-561. [PMID: 35471496 DOI: 10.1007/s13353-022-00693-0] [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: 05/21/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
Abstract
Canine polygenic obesity can be influenced by relatively recent mutations with large effects. We determined whether, as with monogenic diseases, long autozygous tracts may be disproportionately likely to harbor detrimental variants for additive polygenic obesity in Labrador retriever dogs. Both our detection of runs of homozygosity (ROH) and our preliminary association study were based on whole-genome sequencing of 28 obese and 22 healthy dogs. We detected and analyzed the distribution of 19,655 ROH. We observed 237 and 98 ROH-harboring genotypes associated with obesity and increased body mass, respectively. We found no evidence that long ROH tend to harbor genotypes linked to obesity or increased body weight, and we concluded that data on ROH overlapping GWAS signals for canine obesity are unlikely to help prioritize candidate genes for validation studies.
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78
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Bi XA, Li L, Wang Z, Wang Y, Luo X, Xu L. IHGC-GAN: influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data. Brief Bioinform 2022; 23:6554128. [PMID: 35348583 DOI: 10.1093/bib/bbac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/28/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Predicting disease progression in the initial stage to implement early intervention and treatment can effectively prevent the further deterioration of the condition. Traditional methods for medical data analysis usually fail to perform well because of their incapability for mining the correlation pattern of pathogenies. Therefore, many calculation methods have been excavated from the field of deep learning. In this study, we propose a novel method of influence hypergraph convolutional generative adversarial network (IHGC-GAN) for disease risk prediction. First, a hypergraph is constructed with genes and brain regions as nodes. Then, an influence transmission model is built to portray the associations between nodes and the transmission rule of disease information. Third, an IHGC-GAN method is constructed based on this model. This method innovatively combines the graph convolutional network (GCN) and GAN. The GCN is used as the generator in GAN to spread and update the lesion information of nodes in the brain region-gene hypergraph. Finally, the prediction accuracy of the method is improved by the mutual competition and repeated iteration between generator and discriminator. This method can not only capture the evolutionary pattern from early mild cognitive impairment (EMCI) to late MCI (LMCI) but also extract the pathogenic factors and predict the deterioration risk from EMCI to LMCI. The results on the two datasets indicate that the IHGC-GAN method has better prediction performance than the advanced methods in a variety of indicators.
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Affiliation(s)
- Xia-An Bi
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, and the College of Information Science and Engineering in Hunan Normal University, Changsha 410081, P.R. China
| | - Lou Li
- Department of Computing, School of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Zizheng Wang
- Department of Computing, School of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Yu Wang
- Department of Computing, School of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Xun Luo
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, and the College of Information Science and Engineering in Hunan Normal University, Changsha 410081, P.R. China
| | - Luyun Xu
- College of Business, Hunan Normal University, Changsha 410081, P.R. China
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79
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Liu SH, Ma XY, Hassan FU, Gao TY, Deng TX. Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo. J Dairy Sci 2022; 105:4324-4334. [PMID: 35307184 DOI: 10.3168/jds.2021-21543] [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: 11/07/2021] [Accepted: 02/07/2022] [Indexed: 11/19/2022]
Abstract
Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (FROH) ranged from 0.0201 to 0.0371. Pearson correlations between FROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.
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Affiliation(s)
- Shen-He Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xiao-Ya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Teng-Yun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ting-Xian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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80
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Kim YM, Seong HS, Kim YS, Hong JK, Sa SJ, Lee J, Lee JH, Cho KH, Chung WH, Choi JW, Cho ES. Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon. Front Genet 2022; 13:779152. [PMID: 35186025 PMCID: PMC8847790 DOI: 10.3389/fgene.2022.779152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/07/2022] [Indexed: 02/03/2023] Open
Abstract
A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.
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Affiliation(s)
- Yong-Min Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ha-Seung Seong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Young-Sin Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Joon-Ki Hong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Soo-Jin Sa
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Jun-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Kyu-Ho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, South Korea
| | - Jung-Woo Choi
- Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
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81
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Laseca N, Molina A, Ramón M, Valera M, Azcona F, Encina A, Demyda-Peyrás S. Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares. Front Vet Sci 2022; 9:754028. [PMID: 35252415 PMCID: PMC8891756 DOI: 10.3389/fvets.2022.754028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
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Affiliation(s)
- Nora Laseca
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Molina
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Manuel Ramón
- Cersyra de Valdepeñas, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha, Tomelloso, Spain
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
| | - Florencia Azcona
- IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Ana Encina
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
- Asociación Nacional de Criadores de Caballos de Pura Raza Española, Sevilla, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET LA PLATA), La Plata, Argentina
- *Correspondence: Sebastián Demyda-Peyrás
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82
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Signer-Hasler H, Henkel J, Bangerter E, Bulut Z, Drögemüller C, Leeb T, Flury C. Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection. Genet Sel Evol 2022; 54:6. [PMID: 35073837 PMCID: PMC8785455 DOI: 10.1186/s12711-022-00695-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00695-w.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland.
| | - Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association SZZV, Schützenstrasse 10, 3052, Zollikofen, Switzerland
| | - Zafer Bulut
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052, Zollikofen, Switzerland
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83
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Mukhina V, Svishcheva G, Voronkova V, Stolpovsky Y, Piskunov A. Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping. Animals (Basel) 2022; 12:ani12030221. [PMID: 35158545 PMCID: PMC8833718 DOI: 10.3390/ani12030221] [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: 11/10/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary We performed SNP genotyping of indigenous goats of Mongolia to explore their demographic history in the global context and to estimate their genetic risks. Recently, these risks have become a subject of concern due to recent climatic disasters and uncontrolled massive breeding. Various clustering methods demonstrated close genetic relations among Mongolian, Russian, Chinese, and West Asian breeds. Mongolian goats themselves exhibited low to moderate estimates of genetic differentiation. We identified genetic features highlighting the distinct origin and breeding history of Mongolian goat breeds, as well as traces of artificial selection and geographic isolation. However, none of them met formal criteria to be considered as endangered. Abstract Mongolian goats are of great interest for studying ancient migration routes and domestication, and also represent a good model of adaptability to harsh environments. Recent climatic disasters and uncontrolled massive breeding endangered the valuable genetic resources of Mongolian goats and raised the question of their conservation status. Meanwhile, Mongolian goats have never been studied on genomic scale. We used Illumina Goat SNP50 to estimate genetic risks in five Mongolian goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, Dorgon) and explored phylogenic relationships among these populations and in the context of other breeds. Various clustering methods showed that Mongolian goats grouped with other Asian breeds and were especially close to some neighboring Russian and Chinese breeds. The Buural breed showed the lowest estimates of inbreeding and exhibited the shortest genetic distances within the other Mongolian breeds, especially, to Ulgii Red and Gobi GS. These three breeds formed a single core group, being weakly differentiated from each other. Among them, Gobi GS displayed obvious signs of inbreeding probably resulted from artificial selection pressure. Dorgon and especially Erchim goats stand apart from the other Mongolian breeds according to various types of analyses, and bear unique features pointing to different breeding histories or distinct origins of these breeds. All populations showed strong decline in effective population size. However, none of them met formal criteria to be considered as endangered breeds. The SNP data obtained in this study improved the knowledge of Mongolian goat breeds and could be used in future management decisions in order to preserve their genetic diversity.
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Affiliation(s)
- Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (V.M.); (G.S.); (V.V.); (Y.S.)
- Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (V.M.); (G.S.); (V.V.); (Y.S.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Valery Voronkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (V.M.); (G.S.); (V.V.); (Y.S.)
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (V.M.); (G.S.); (V.V.); (Y.S.)
| | - Aleksei Piskunov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (V.M.); (G.S.); (V.V.); (Y.S.)
- Correspondence:
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84
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Zhang QS, Goudet J, Weir BS. Rank-invariant estimation of inbreeding coefficients. Heredity (Edinb) 2022; 128:1-10. [PMID: 34824382 PMCID: PMC8733021 DOI: 10.1038/s41437-021-00471-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 09/05/2021] [Accepted: 09/05/2021] [Indexed: 11/18/2022] Open
Abstract
The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.
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Affiliation(s)
- Qian S Zhang
- Department of Biostatistics, University of Washington, Seattle, WA, 98195-1617, USA
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, 98195-1617, USA.
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85
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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: 5] [Impact Index Per Article: 1.7] [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.
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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.
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Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol 2021; 4:1412. [PMID: 34921240 PMCID: PMC8683477 DOI: 10.1038/s42003-021-02935-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC's ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Zoller
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Bernard Wooding
- Quagga Project, Elandsberg Farms, Hermon, 7308, South Africa
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | - Dewey Maddox
- White Oak Conservation, 581705 White Oak Road, Yulee, FL, 32097, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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87
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Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle. Animals (Basel) 2021; 11:ani11123574. [PMID: 34944349 PMCID: PMC8697887 DOI: 10.3390/ani11123574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Genetic diversity of livestock is vitally important as it enables the adaptation of future populations to changing environments. Therefore, preserving a sufficiently large genetic diversity is key. However, for many local cattle populations, little is known about their genetic diversity such as inbreeding level, effective size etc. We studied the genetic diversity of two local Belgian red cattle populations (Belgian Red and Belgian White Red cattle) using state-of-the-art genomic techniques. These tools assessed diversity at the population and individual level, and allowed the positioning of these two breeds in an international context of 52 other (European) cattle breeds. Accordingly, we contribute to the general knowledge of European red cattle, and more specifically we help the breeders, breed organization and the government to manage the genetic diversity of both breeds. Abstract Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and Fst analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, Fst and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, Fst analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.
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88
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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Esdaile E, Avila F, Bellone RR. Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms. J Hered 2021; 113:238-247. [PMID: 34893836 PMCID: PMC9270868 DOI: 10.1093/jhered/esab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (Ar), expected heterozygosity (HE), observed heterozygosity (HO), unbiased heterozygosity (HU), inbreeding coefficient (FIS), and fixation index (FST). These analyses found that trotting and pacing sires were less genetically diverse than dams (HEPBonferroni = 0.029 and 6.3 × 10−5, respectively) and their offspring (ArPBonferroni = 0.034 and 6.9 × 10-6, respectively), and pacing offspring were significantly less diverse than their dams (HEPBonferroni = 2 × 10-3). Inbreeding coefficients for trotters (FIS = −0.014) and pacers (FIS = −0.012) suggest that breeding practices have maintained diversity. Moderate levels of genetic differentiation (0.066 < FST < 0.11) were found between pacing and trotting groups. Additionally, 10 of the most prolific trotting sires and their male offspring (n = 84) were genotyped on the 670K Axiom Equine HD Array. HO values higher than HE (P < 0.001), low inbreeding coefficients (mean F = −0.064), and mean FROH = 21% indicate relatively high levels of diversity in this cohort, further supporting the STR data. However, in contrast, HO values were higher for trotting sires (0.41) than their offspring (0.36). This observation warrants further monitoring of diversity over time. These data provide an updated foundation of diversity indices for further, long-term analysis in the breed.
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Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California- Davis, Davis, CA
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California- Davis, Davis, CA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California- Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
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Tsartsianidou V, Sánchez-Molano E, Kapsona VV, Basdagianni Z, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet Sel Evol 2021; 53:90. [PMID: 34856922 PMCID: PMC8641236 DOI: 10.1186/s12711-021-00682-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00682-7.
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Affiliation(s)
- Valentina Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Enrique Sánchez-Molano
- Division of Genetics and Genomics, School of Veterinary Studies, The Roslin Institute and Royal (Dick), University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Vanessa Varvara Kapsona
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zoitsa Basdagianni
- Department of Animal Production, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Alexander Campus, 57400, Sindos, Greece
| | - Georgios Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK.,Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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91
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Fabbri MC, Dadousis C, Tiezzi F, Maltecca C, Lozada-Soto E, Biffani S, Bozzi R. Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity. PLoS One 2021; 16:e0248087. [PMID: 34695128 PMCID: PMC8544844 DOI: 10.1371/journal.pone.0248087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
- * E-mail:
| | - Christos Dadousis
- Dipartimento di Scienze Medico‐Veterinarie, Università di Parma, Parma, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology (CNR), Milano, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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92
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Huo JL, Zhang LQ, Zhang X, Wu XW, Ye XH, Sun YH, Cheng WM, Yang K, Pan WR, Zeng YZ. Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line. Anim Genet 2021; 53:146-151. [PMID: 34658041 DOI: 10.1111/age.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 01/28/2023]
Abstract
Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.
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Affiliation(s)
- J L Huo
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.,Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - L Q Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X Zhang
- College of Life Science, Lvliang University, Lvliang, 033001, China
| | - X W Wu
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X H Ye
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Y H Sun
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - W M Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - K Yang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - W R Pan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Y Z Zeng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
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93
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Selli A, Ventura RV, Fonseca PAS, Buzanskas ME, Andrietta LT, Balieiro JCC, Brito LF. Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations. Animals (Basel) 2021; 11:2696. [PMID: 34573664 PMCID: PMC8472390 DOI: 10.3390/ani11092696] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.
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Affiliation(s)
- Alana Selli
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Ricardo V. Ventura
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Pablo A. S. Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Marcos E. Buzanskas
- Department of Animal Science, Federal University of Paraíba, João Pessoa 58051-900, Paraiba, Brazil;
| | - Lucas T. Andrietta
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Júlio C. C. Balieiro
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
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94
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Poyato-Bonilla J, Laseca N, Demyda-Peyrás S, Molina A, Valera M. 500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data. J Anim Breed Genet 2021; 139:84-99. [PMID: 34363624 DOI: 10.1111/jbg.12641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 01/19/2023]
Abstract
The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500 years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (FROH ) inbreeding coefficient in the case of PRE subpopulations partially related and non-related to Carthusian strain (0.68) but a lower value in the 100% Carthusian horses (0.42), due to the high weight of founders not detected by GEL analysis. GEN (PCA, AMOVA, and Admixture) and GEL analysis showed a good differentiation of subpopulations, but also a high level of introgression of the CS in the breed during past decades. A recent change in this trend was noteworthy, with a considerable reduction in CS variability and a genetic bottleneck (effective population sizes of 31.57 and 30.20 in GEL and GEN analysis, respectively, in last generation). The PRE has maintained its variability, and a considerable difference in estimated Ne by GEL (60.77) and GEN (188.0) data was observed. Using two sources of complementary information, it was found the existence of an ancient PRE strain with a unique genetic landmark, practically free from the influence of other equine populations.
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Affiliation(s)
- Julia Poyato-Bonilla
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
| | - Nora Laseca
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina.,CONICET, CCT La Plata, La Plata, Argentina
| | - Antonio Molina
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Mercedes Valera
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
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95
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Sumreddee P, Hay EH, Toghiani S, Roberts A, Aggrey SE, Rekaya R. Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. BMC Genomics 2021; 22:538. [PMID: 34256689 PMCID: PMC8278650 DOI: 10.1186/s12864-021-07872-z] [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: 10/28/2020] [Accepted: 07/05/2021] [Indexed: 12/02/2022] Open
Abstract
Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07872-z.
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Affiliation(s)
- Pattarapol Sumreddee
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA.
| | - Sajjad Toghiani
- USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Samuel E Aggrey
- Department of Poultry Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA.,Department of Statistics, The University of Georgia, Athens, GA, 30602, USA
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96
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Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW. Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi. Mol Ecol 2021; 30:6006-6020. [PMID: 34242449 DOI: 10.1111/mec.16068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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97
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Jensen A, Lillie M, Bergström K, Larsson P, Höglund J. Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish. Heredity (Edinb) 2021; 127:79-91. [PMID: 33963302 PMCID: PMC8249479 DOI: 10.1038/s41437-021-00438-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 02/03/2023] Open
Abstract
The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Mette Lillie
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden.
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Kristofer Bergström
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
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98
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Signatures of Selection and Genomic Diversity of Muskellunge ( Esox masquinongy) from Two Populations in North America. Genes (Basel) 2021; 12:genes12071021. [PMID: 34209092 PMCID: PMC8303616 DOI: 10.3390/genes12071021] [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: 05/18/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.
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99
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How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock. Genes (Basel) 2021; 12:genes12060926. [PMID: 34207101 PMCID: PMC8234567 DOI: 10.3390/genes12060926] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.
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100
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Strucken EM, Gebrehiwot NZ, Swaminathan M, Joshi S, Al Kalaldeh M, Gibson JP. Genetic diversity and effective population sizes of thirteen Indian cattle breeds. Genet Sel Evol 2021; 53:47. [PMID: 34074236 PMCID: PMC8170732 DOI: 10.1186/s12711-021-00640-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00640-3.
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Affiliation(s)
- Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
| | - Netsanet Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Sachin Joshi
- BAIF Development Research Foundation, Pune, India
| | - Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
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