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Recuerda M, Campagna L. How structural variants shape avian phenotypes: Lessons from model systems. Mol Ecol 2024; 33:e17364. [PMID: 38651830 DOI: 10.1111/mec.17364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.
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Affiliation(s)
- María Recuerda
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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Cendron F, Cassandro M, Penasa M. Genome-wide investigation to assess copy number variants in the Italian local chicken population. J Anim Sci Biotechnol 2024; 15:2. [PMID: 38167097 PMCID: PMC10763469 DOI: 10.1186/s40104-023-00965-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome. RESULTS Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. CONCLUSIONS The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy.
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy
- Federazione Delle Associazioni Nazionali Di Razza E Specie, Via XXIV Maggio 43, 00187, Rome, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, 35020, Legnaro, PD, Italy
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Wang Q, Song X, Bi Y, Zhu H, Wu X, Guo Z, Liu M, Pan C. Detection distribution of CNVs of SNX29 in three goat breeds and their associations with growth traits. Front Vet Sci 2023; 10:1132833. [PMID: 37706075 PMCID: PMC10495836 DOI: 10.3389/fvets.2023.1132833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/17/2023] [Indexed: 09/15/2023] Open
Abstract
As a member of the SNX family, the goat sorting nexin 29 (SNX29) is initially identified as a myogenesis gene. Therefore, this study aimed to examine the polymorphism in the SNX29 gene and its association with growth traits. In this study, we used an online platform to predict the structures of the SNX29 protein and used quantitative real-time PCR to detect potential copy number variation (CNV) in Shaanbei white cashmere (SBWC) goats (n = 541), Guizhou black (GB) goats (n = 48), and Nubian (NB) goats (n = 39). The results showed that goat SNX29 protein belonged to non-secretory protein. Then, five CNVs were detected, and their association with growth traits was analyzed. In SBWC goats, CNV1, CNV3, CNV4, and CNV5 were associated with chest width and body length (P < 0.05). Among them, the CNV1 individuals with gain and loss genotypes were superior to those individuals with a median genotype, but CNV4 and CNV5 of individuals with the median genotype were superior to those with the loss and gain genotypes. In addition, individuals with the gain genotype had superior growth traits in CNV3. In brief, this study suggests that the CNV of SNX29 can be used as a molecular marker in goat breeding.
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Affiliation(s)
- Qian Wang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, China
- Life Science Research Center, Yulin University, Yulin, Shaanxi, China
| | - Yi Bi
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, China
- Life Science Research Center, Yulin University, Yulin, Shaanxi, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Zhengang Guo
- Animal Husbandry and Veterinary Science Institute of Bijie City, Bijie, Guizhou, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Chuanying Pan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
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4
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Cigarroa-Vázquez FA, Granados-Rivera LD, Portillo-Salgado R, Ventura-Ríos J, Esponda-Hernández W, Hernández-Marín JA, Cruz-Tamayo AA, Bautista-Martinez Y. Fatty Acids Profile and Healthy Lipids Indices of Native Mexican Guajolote Meat Treated to Two Heat Treatments. Foods 2022; 11:foods11101509. [PMID: 35627079 PMCID: PMC9141284 DOI: 10.3390/foods11101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The native guajolote meat is an important dietary source of proteins of high biological value for the rural population of Mexico. However, many of its quality characteristics are still unknown. Therefore, the fatty acids (FAs) profile and nutritional indices of breast and leg meat of native guajolote subjected to two heat treatments (boiled and baked) were evaluated. The heat treatments increased the concentration of saturated (SFA) and monounsaturated FA (MUFA) in the meat; in contrast, the concentration of polyunsaturated FA (PUFA) decreased. Likewise, the dietary FA index and the atherogenic index increased in guajolote meat from the effect of the heat treatments, while the essential and hypercholesterolemic FA indices decreased. Based on the results obtained, heat treatments increase the content of SFA and MUFA in breast and leg meat of native guajolote. Baking is less favorable for both types of muscle. Abstract Meat is a complex food with a structured nutritional composition that makes it an essential component of the human diet. In particular, the meat of native guajolote that is traditionally raised in natural conditions is an important dietary source of proteins of high biological value for the rural population of Mexico. The study aimed to evaluate fatty acids (FAs) profile and nutritional indices of breast and leg meat of native guajolote subjected to two heat treatments. For the study, a total of sixty muscle samples (30 breast meat and 30 leg meat) from adult male native guajolotes were used. The FA profile and nutritional indices were evaluated in raw meat (control) and meat subjected to two heat treatments (boiled and baked). The heat treatments, independently of the type of muscle, increased (p ≤ 0.05) the concentration of saturated (SFA) and monounsaturated FA (MUFA); in contrast, polyunsaturated FA (PUFA) decreased. Likewise, the dietary FA index, which has a negative hypercholesterolemic effect, and the atherogenic index increased in guajolote meat from the effect of the heat treatments, while the essential and undesirable hypercholesterolemic FA indices decreased. In conclusion, heat treatments increase the content of SFA and MUFAs in breast and leg meat of native guajolote. Boiling or baking the meat deteriorates PUFAs but increases the nutritional indices. The present investigation would provide valuable information for the guajolote meat product processing.
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Affiliation(s)
- Francisco A. Cigarroa-Vázquez
- School of Agricultural Studies Mezcalapa, Autonomous University of Chiapas, Copainalá 29620, Mexico; (F.A.C.-V.); (W.E.-H.)
| | - Lorenzo Danilo Granados-Rivera
- Experimental Field—General Teran, National Institute of Forestry, Agricultural and Livestock Research, General Teran 67400, Mexico
- Correspondence: (L.D.G.-R.); (Y.B.-M.)
| | | | - Joel Ventura-Ríos
- School of Veterinary Medicine and Animal Husbandry, Autonomous Agrarian University Antonio Narro, Saltillo 25315, Mexico;
| | - William Esponda-Hernández
- School of Agricultural Studies Mezcalapa, Autonomous University of Chiapas, Copainalá 29620, Mexico; (F.A.C.-V.); (W.E.-H.)
| | | | - Alvar A. Cruz-Tamayo
- Faculty of Agricultural Sciences, Autonomous University of Campeche, Escarcega 24350, Mexico;
| | - Yuridia Bautista-Martinez
- School of Veterinary Medicine and Animal Husbandry, Autonomous University of Tamaulipas, Ciudad Victoria 87000, Mexico
- Correspondence: (L.D.G.-R.); (Y.B.-M.)
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6
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Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds. Animals (Basel) 2022; 12:ani12020217. [PMID: 35049839 PMCID: PMC8773107 DOI: 10.3390/ani12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
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7
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Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey ( Meleagris gallopavo) Breeds. Genes (Basel) 2021; 12:genes12091342. [PMID: 34573324 PMCID: PMC8470100 DOI: 10.3390/genes12091342] [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: 07/26/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/10/2023] Open
Abstract
Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright's F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d'Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species.
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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9
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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021; 44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.
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10
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Castillo A, Gariglio M, Franzoni A, Soglia D, Sartore S, Buccioni A, Mannelli F, Cassandro M, Cendron F, Castellini C, Mancinelli AC, Iaffaldano N, Iorio MD, Marzoni M, Salvucci S, Cerolini S, Zaniboni L, Schiavone A. Overview of Native Chicken Breeds in Italy: Conservation Status and Rearing Systems in Use. Animals (Basel) 2021; 11:ani11020490. [PMID: 33673395 PMCID: PMC7917728 DOI: 10.3390/ani11020490] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The ongoing loss of domestic animal breeds around the world is occurring at an alarming rate. Thus, the registration and preservation of native breeds is of great importance. The aim of this study, which forms part of a conservation program, was to provide an overview of the conservation statuses of native Italian poultry breeds being reared by local breeders in Italy. The data collected by means of a census questionnaire demonstrate the low population sizes of these breeds in Italy and highlight the need for campaigns aimed at publicizing and promoting the benefits of native breeds with the goal of increasing population sizes. Identifying strategies to facilitate breeders’ access to pure breed birds is also essential, and would require collaborative efforts of university research centers, public entities, and breeders. Abstract The most reared species of farm animal around the world is the chicken. However, the intensification of livestock systems has led to a gradual increase in the concentration of a limited number of breeds, resulting in substantial erosion to the genetic pool. The initial step of an ‘animal conservation program’ entails establishing the actual conservation statuses of the breeds concerned in a defined area; in this case, in Italy. To this end, a survey of breeds was performed by means of a census questionnaire divided into two parts. The first part collected information on breeds, breeders, housing facilities, and management aspects, the results of which are presented here. The second part of the questionnaire regarded chicken products and their markets, and these data will be reported in a second paper. The breed status of six chicken breeds was shown to be exceptionally worrying, with total numbers ranging from just 18 to 186 birds. Population sizes exceeding 1000 birds was identified for just four breeds, the maximum being 3400. Some improvements in status were noted in relation to breeds which had been the subject of conservation efforts in the past. The two most common breeds reported are the Bionda Piemontese, a double-purpose breed, and the Livorno egg-laying hen. Collo Nudo Italiano, Millefiori Piemontese, Pollo Trentino, and Tirolese chicken breeds and the Castano Precoce turkey breed were not listed by breeders at all. The most reported turkey breeds are the Bronzato Comune and the Ermellinato di Rovigo. The population sizes of native Italian poultry breeds were shown to be generally poor. Italian poultry farmers and the population at large are largely ignorant about indigenous poultry breeds. Thus, promoting the virtues of Italian breeds would help their conservation by encouraging breeders to rear these birds and consumers to buy their products. The identification of strategies to facilitate access to pure breed birds is essential, and will require the collaboration of university research centers, public entities, and breeders. The results presented in this paper constitute the initial part of a more complex conservation program.
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Affiliation(s)
- Annelisse Castillo
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
| | - Marta Gariglio
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
| | - Alessandro Franzoni
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
| | - Dominga Soglia
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
| | - Stefano Sartore
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
| | - Arianna Buccioni
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Via delle Cascine 5, 50144 Firenze, Italy; (A.B.); (F.M.)
| | - Federica Mannelli
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Via delle Cascine 5, 50144 Firenze, Italy; (A.B.); (F.M.)
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (M.C.); (F.C.)
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (M.C.); (F.C.)
| | - Cesare Castellini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (C.C.); (A.C.M.)
| | - Alice Cartoni Mancinelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (C.C.); (A.C.M.)
| | - Nicolaia Iaffaldano
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via Francesco De Sanctis, 86100 Campobasso, Italy; (N.I.); (M.D.I.)
| | - Michele Di Iorio
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via Francesco De Sanctis, 86100 Campobasso, Italy; (N.I.); (M.D.I.)
| | - Margherita Marzoni
- Dipartimento di Scienze Veterinarie, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.M.); (S.S.)
| | - Sonia Salvucci
- Dipartimento di Scienze Veterinarie, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.M.); (S.S.)
| | - Silvia Cerolini
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (S.C.); (L.Z.)
| | - Luisa Zaniboni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (S.C.); (L.Z.)
| | - Achille Schiavone
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (A.C.); (M.G.); (A.F.); (D.S.); (S.S.)
- Correspondence: ; Tel.: +39-011-6709208
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Copy Number Variants in Four Italian Turkey Breeds. Animals (Basel) 2021; 11:ani11020391. [PMID: 33546454 PMCID: PMC7913726 DOI: 10.3390/ani11020391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Hybrid Turkey selection is focusing on meat production traits characterized by high genetic heritability; the strong directional selection is well known to produce a constant loss in genetic diversity. Genetic characterization is one of the essential activities in the management of populations at risk of extinction. In addition, the genetic structure at the population level and the relationships between individuals are nowadays analysable at the genomic level. In this paper, the genome of 4 different Italian turkey breeds included in the Autochthonous Italian Poultry Breeds Register are analysed in order to obtain a genome-wide Copy Number Variant scan to ameliorate the existing knowledge of the genomic structure of Italian local turkey breeds. Differences have been described at genomic level for physiological, reproductive, and behavioral traits. The analyzed breeds are clearly distinguishable at the genomic level, and their relationships are clearly linked to their geographical origin and to the history of the rural structure of their developing regions. Genome information based on Copy Number Variant (CNV) detection has generated important information in this study concerning the uniqueness of the Italian local turkey breeds. Abstract Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions.
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Strillacci MG, Marelli SP, Martinez-Velazquez G. Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection. Animals (Basel) 2020; 10:ani10081318. [PMID: 32751760 PMCID: PMC7460020 DOI: 10.3390/ani10081318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary In this study we investigate the genomic differentiation of traditional Mexican turkey breeds and commercial hybrid strains. The analysis aimed to identify the effects of different types of selection on the birds’ genome structure. Mexican turkeys are characterized by an adaptive selection to their specific original environment; on the other hand, commercial hybrid strains are directionally selected to maximize productive traits and to reduce production costs. The Mexican turkeys were grouped in two geographic subpopulations, while high genomic homogeneity was found in hybrid birds. Traditional breeds and commercial strains are clearly differentiated from a genetic point of view. Inbreeding coefficients were here calculated with different approaches. A clear effect of selection for productive traits was recorded. Abstract The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and FROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (FST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and FROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, University of Milan, Via Festa del Perdono, 7, 20122 Milano, Italy;
- Correspondence: ; Tel.: +39-025-033-4582
| | - Stefano Paolo Marelli
- Department of Veterinary Medicine, University of Milan, Via Festa del Perdono, 7, 20122 Milano, Italy;
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Morinha F, Magalhães P, Blanco G. Standard guidelines for the publication of telomere qPCR results in evolutionary ecology. Mol Ecol Resour 2020; 20. [PMID: 32133733 DOI: 10.1111/1755-0998.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
Telomere length has been used as a proxy of fitness, aging and lifespan in vertebrates. In the last decade, dozens of articles reporting on telomere dynamics in the fields of ecology and evolution have been published for a wide range of taxa. With this growing interest, it is necessary to ensure the accuracy and reproducibility of telomere length measurement techniques. Real-time quantitative PCR (qPCR) is routinely applied to measure relative telomere length. However, this technique is highly sensitive to several methodological variables and the optimization of qPCR telomere assays remains highly variable between studies. Therefore, standardized guidelines are required to enable the optimization of robust protocols, and to help in judging the validity of the presented results. This review provides an overview of preanalytical and analytical factors that can lead to qPCR inconsistencies and biases, including: (a) sample type, collection and storage; (b) DNA extraction, storage and quality; (c) qPCR primers, laboratory reagents, and assay conditions; and (d) data analysis. We propose a minimum level of information for publication of qPCR telomere assays in evolutionary ecology considering the methodological pitfalls and sources of error. This review highlights the complexity of the optimization and validation of qPCR for telomere measurement per se, demonstrating the importance of transparency and clarity of reporting methodological details required for reliable, reproducible and comparable qPCR telomere assays. We encourage efforts to implement standardized protocols that ensure the rigour and quality of telomere dynamics studies.
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Affiliation(s)
- Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Paula Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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