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Koshiishi Y, Uchiyama H, Murata-Okubo M, Tanaka K, Kameyama Y, Hirayama H, Wada K. Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae). Gene 2020; 769:145238. [PMID: 33068676 DOI: 10.1016/j.gene.2020.145238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/16/2020] [Accepted: 10/11/2020] [Indexed: 10/23/2022]
Abstract
The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC)n, (AT)n and (AG)n, were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed NA ranged from 2 to 12, with an average of 4.2. HE/HO ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.
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Affiliation(s)
- Yuichi Koshiishi
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Michiko Murata-Okubo
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuichi Kameyama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hiroki Hirayama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Kenta Wada
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan.
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Koshiishi Y, Murata-Okubo M, Fujisawa SI, Shimoi G, Hirayama H, Kameyama Y, Souma K, Wada K. Development and characterization of ten novel microsatellite loci for the emu (Dromaius novaehollandiae) and genetic diversity of Japanese farm populations. Mol Biol Rep 2020; 47:2521-2527. [PMID: 32086719 DOI: 10.1007/s11033-020-05335-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
The emu (Dromaius novaehollandiae) is a useful poultry animal farmed for fat, meat, and eggs. Genetic structure and relationships among farmed emu populations in Japan are unknown and the number of microsatellite markers for genetic analysis of the emu is insufficient. In this study, we isolated 16 microsatellites from the emu genome and developed ten new microsatellite markers. These microsatellite markers were used to characterize three farm emu populations in Japan. The number of alleles ranged from 3 to 13 and the expected (HE) and observed heterozygosity (HO) of these microsatellite loci was 0.187-0.802 and 0.179-0.647, respectively. The polymorphic information content ranged from 0.176 to 0.786. Positive inbreeding coefficient (FIS) values were detected in all tested populations, and they ranged from 0.027 to 0.540. These results suggest that farm populations of the emu in Japan resulted from inbreeding. The fixation index (FST) values ranged from 0.026 to 0.061, and phylogenetic trees and population structure analysis confirmed no definitive genetic differentiation among the three populations. Therefore, these populations are at a relatively low level of genetic differentiation at present. The microsatellite markers developed in our study can be utilized for genetic analysis and preservation of genetic resources in the emu.
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Affiliation(s)
- Yuichi Koshiishi
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Michiko Murata-Okubo
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Shin-Ichiro Fujisawa
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Gaku Shimoi
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Hiroki Hirayama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Yuichi Kameyama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Kousaku Souma
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Kenta Wada
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
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Identification and characterisation of ten microsatellite loci in the Noisy Scrub-bird Atrichornis clamosus using next-generation sequencing technology. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9865-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ledger JM, Malecki I, Groth DM. Characterisation of tetra-nucleotide microsatellite loci in the ostrich (Struthio camelus). Br Poult Sci 2012; 53:460-4. [PMID: 23130580 DOI: 10.1080/00071668.2012.715280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. Eleven polymorphic tetra-nucleotide microsatellite loci were identified in the ostrich (Struthio camelus) using a selective enrichment protocol. 2. The average number of alleles observed was 6·6 with an average heterozygosity of 0·4. 3. The population was found to be in Hardy-Weinberg equilibrium and two of the loci had a greater than 95% probability of having null alleles. 4. These microsatellite loci will add to the existing pool of markers available for the ostrich and help to facilitate analysis of population structure and pedigree determination.
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Affiliation(s)
- J M Ledger
- School of Animal Biology, University of Western Australia, Hackett Drive, Crawley, Western Australia 6009.
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Allentoft ME, Oskam C, Houston J, Hale ML, Gilbert MTP, Rasmussen M, Spencer P, Jacomb C, Willerslev E, Holdaway RN, Bunce M. Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and prospects. PLoS One 2011; 6:e16670. [PMID: 21304955 PMCID: PMC3031614 DOI: 10.1371/journal.pone.0016670] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 12/31/2010] [Indexed: 11/19/2022] Open
Abstract
We present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the ‘shotgun’ reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36–70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600–5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (MEA); (MB)
| | - Charlotte Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Jayne Houston
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M. Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Peter Spencer
- Wildlife Identification Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Christopher Jacomb
- Southern Pacific Archaeological Research, Department of Anthropology, University of Otago, Dunedin, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Palaecol Research Ltd, Christchurch, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- * E-mail: (MEA); (MB)
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Yáñez JM, González R, Angulo J, Vidal R, Santos JL, Martínez V. Characterization of new microsatellite markers derived from sequence databases for the emu (Dromaius novaehollandiae). Mol Ecol Resour 2008; 8:1442-4. [PMID: 21586070 DOI: 10.1111/j.1755-0998.2008.02315.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different populations kept in captivity. Between two and 11 alleles were found per locus, and the observed heterozygosity ranged from 0.05 to 0.85, in accordance with expectations. These markers will be useful as tools for detecting levels of genetic variation, reconstructing pedigrees (for quantitative genetic analysis) and identifying markers associated to fitness traits in emu populations.
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Affiliation(s)
- José M Yáñez
- Animal Breeding and Genomics Laboratory, Universidad de Chile, Santa Rosa 11735, Santiago, Chile, Laboratory of Molecular Ecology and Evolutionary Studies, Universidad de Santiago de Chile, Avenida Libertador Bernardo O'Higgins 3363, Santiago, Chile, Nutrition, Diabetes, and Metabolism Department, Pontificia Universidad Católica de Chile, Marcoleta 367, Santiago, Chile
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Tang B, Huang YH, Lin L, Hu XX, Feng JD, Yao P, Zhang L, Li N. Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthiocamelus) genome. Genome 2003; 46:833-40. [PMID: 14608400 DOI: 10.1139/g03-059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.
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Affiliation(s)
- Bo Tang
- The College of Animal Science and Technology, China Agricultural University, Beijing, China
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