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Vijh RK, Sharma U, Arora R, Kapoor P, Raheja M, Sharma R, Ahlawat S, Dureja V. Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids. Gene 2024; 921:148541. [PMID: 38723784 DOI: 10.1016/j.gene.2024.148541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Camels play a crucial socio-economic role in sustaining the livelihoods of millions in arid and semi-arid regions. They possess remarkable physiological attributes which enable them to thrive in extreme environments, and provide a source of meat, milk and transportation. With their unique traits, camels embody an irreplaceable source of untapped genomic knowledge. This study introduces Axiom-MaruPri, a medium-density SNP chip meticulously designed and validated for both Camelus bactrianus and Camelus dromedarius. Comprising of 182,122 SNP markers, derived from the re-sequenced data of nine Indian dromedary breeds and the double-humped Bactrian camel, this SNP chip offers 34,894 markers that display polymorphism in both species. It achieves an estimated inter-marker distance of 14 Kb, significantly enhancing the coverage of the camel genome. The medium-density chip has been successfully genotyped using 480 camel samples, achieving an impressive 99 % call rate, with 96 % of the 182,122 SNPs being highly reliable for genotyping. Phylogenetic analysis and Discriminant Analysis of Principal Components yield clear distinctions between Bactrian camels and dromedaries. Moreover, the discriminant functions substantially enhance the classification of dromedary camels into different breeds. The clustering of various camel breeds reveals an apparent correlation between geographical and genetic distances. The results affirm the efficacy of this SNP array, demonstrating high genotyping precision and clear differentiation between Bactrian and dromedary camels. With an enhanced genome coverage, accuracy and economic efficiency the Axiom_MaruPri SNP chip is poised to advance genomic breeding research in camels. It holds the potential to serve as an invaluable genetic resource for investigating population structure, genome-wide association studies and implementing genomic selection in domesticated camelid species.
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Affiliation(s)
- Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Prerna Kapoor
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Meenal Raheja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Vandana Dureja
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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O’Connor RE, Kretschmer R, Romanov MN, Griffin DK. A Bird's-Eye View of Chromosomic Evolution in the Class Aves. Cells 2024; 13:310. [PMID: 38391923 PMCID: PMC10886771 DOI: 10.3390/cells13040310] [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: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome ("chromosomic") organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The 'signature' avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.
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Affiliation(s)
- Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Campus Universitário Capão do Leão, Universidade Federal de Pelotas, Pelotas 96010-900, RS, Brazil;
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.E.O.); (M.N.R.)
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Piro M. Aspects of Molecular Genetics in Dromedary Camel. Front Genet 2021; 12:723181. [PMID: 34764978 PMCID: PMC8577052 DOI: 10.3389/fgene.2021.723181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Dromedary camels are unique in their morphological and physiological characteristics and are capable of providing milk and meat even under extreme environmental conditions. Like other species, the dromedary camel has also benefitted from the development of the molecular genetics to increase the knowledge about different aspect in camel genetics (genetic variation, molecular marker, parentage control, gene of interest, whole genome, dating…etc.). In this paper we review the different molecular genetic technics used in this particular species and future prospects. Dromedary genetic studies started in the end of the 1980s with phenotypic evaluation and the attempts to highlight the protein and biochemical diversity. In the 2000s, with the development of molecular markers such as microsatellites, genetic diversity of different types in several countries were estimated and microsatellites were also used for parentage control. In terms of genetic characterization, microsatellites revealed a defined global structure, differentiating East African and South Arabian dromedaries from North African, North Arabian, and South Asian individuals, respectively. Also, mitochondrialDNA sequence analysis of ancient DNA proved to be crucial in resolving domestication processes in dromedaries. Ancient and modern DNA revealed dynamics of domestication and cross-continental dispersion of the dromedary. Nuclear SNPs, single nucleotide polymorphisms changes that occur approximately each 1000 bps in the mammalian genome were also applied in some studies in dromedary. These markers are a very useful alternative to microsatellites and have been employed in some studies on genetic diversity and relevant phenotypic traits in livestock. Finally, thanks to the use of Next Generation Sequencing (NGS) the whole-genome assemblies of the dromedary (Camelus dromedarius) and a work to establish the organization of the dromedary genome at chromosome level were recently published.
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Affiliation(s)
- Mohammed Piro
- Veterinary Genetics Laboratory (LAGEV), Hassan II Agronomic and Veterinary Institute, Rabat, Morocco
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Bitaraf Sani M, Harofte JZ, Bitaraf A, Esmaeilkhanian S, Banabazi MH, Salim N, Teimoori A, Shafei Naderi A, Faghihi MA, Burger PA, Silawi M, Taghipour Sheshdeh A. Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran. Genes (Basel) 2020; 11:genes11060599. [PMID: 32485848 PMCID: PMC7349250 DOI: 10.3390/genes11060599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022] Open
Abstract
The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran's camels was estimated to be 89. Predicted Tajima's D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran's dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.B.); (A.S.N.)
- Correspondence: ; Tel.: +98-9133550060
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.B.); (A.S.N.)
| | - Ahmad Bitaraf
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.B.); (A.S.N.)
| | - Saeid Esmaeilkhanian
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, Iran;
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj 3146618361, Iran;
| | - Nader Salim
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, Yazd 8916713449, Iran; (N.S.); (A.T.)
| | - Abbas Teimoori
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, Yazd 8916713449, Iran; (N.S.); (A.T.)
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, Iran; (J.Z.H.); (A.B.); (A.S.N.)
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz, Iran, Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL 33136, USA;
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna,1160 Vienna, Austria;
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, Shiraz 7134767617, Iran; (M.S.); (A.T.S.)
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Sabahat S, Brauning R, Clarke SM, Nadeem A, Thomson PC, Khatkar MS. SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method. Anim Genet 2020; 51:620-623. [PMID: 32421863 DOI: 10.1111/age.12953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
Pakistani camels have been classified socio-geographically into 20 breeds, but they have not yet been subjected to substantial selective pressures and the genetic basis for these breeds is not understood. However, it should be possible to distinguish them by use of molecular data. This study investigated the genetic diversity and population structure within and between two major Pakistani camel breeds, Marecha and Lassi. As no SNP array is currently available, we first identified 63 619 SNPs using a genotyping by sequencing approach. After quality control, a panel of 36 926 SNPs was used in the analysis. Population structure was investigated with a principal coordinate analysis as well as a cluster analysis using NetView, and multilocus heterozygosity analysis to explore between- and within-breed genetic variation. In addition, between-breed variation was explored using the fixation index, FST . We also compared relationship matrices computed using the VanRaden SNP-based method and a method developed specifically for genotyping by sequencing data. Among the two camel breeds, Lassi showed a lower level of genetic diversity whereas Marecha showed a higher level. As a genotyping platform has not yet been developed for the camel, the SNPs discovered in this study will be useful in future genetic studies in camels.
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Affiliation(s)
- S Sabahat
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
| | - R Brauning
- Invermay Agricultural Centre, AgResearch, 176 Puddle Alley, Mosgiel, 9092, New Zealand
| | - S M Clarke
- Invermay Agricultural Centre, AgResearch, 176 Puddle Alley, Mosgiel, 9092, New Zealand
| | - A Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - P C Thomson
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Shaykh Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
| | - M S Khatkar
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, NSW, 2570, Australia
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Farré M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, Ma J, Graphodatsky AS, Zhang G, Larkin DM, Lewin HA. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 2020; 8:5542321. [PMID: 31367745 PMCID: PMC6669057 DOI: 10.1093/gigascience/giz090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 06/12/2019] [Accepted: 07/09/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. FINDINGS Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. CONCLUSIONS We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.
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Affiliation(s)
- Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK.,School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Qiye Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Iulia Darolti
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK.,Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Yang Zhou
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK.,The Genome Center, University of California, Davis, CA 95616, USA
| | - Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | | | - Leona G Chemnick
- San Diego Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, South Korea
| | - Oliver A Ryder
- San Diego Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Guoije Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA 95616, USA.,Department of Evolution and Ecology, College of Biological Sciences, and the Department of Reproduction and Population Health, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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