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Sugita A, Shigeta M, Tamura N, Okazaki H, Kutsukake N, Terai Y. Development of Genetic Markers for Sex and Individual Identification of the Japanese Giant Flying Squirrel ( Petaurista leucogenys) by an Efficient Method Using High-Throughput DNA Sequencing. Zoolog Sci 2023; 40:24-31. [PMID: 36744707 DOI: 10.2108/zs220045] [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: 05/05/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022]
Abstract
DNA markers that detect differences in the number of microsatellite repeats can be highly effective for genotyping individuals that lack differences in external morphology. However, isolation of sequences with different microsatellite repeat numbers between individuals has been a time-consuming process in the development of DNA markers. Individual identification of Japanese giant flying squirrels (Petaurista leucogenys) has been challenging because this species is arboreal and nocturnal and exhibits little to no morphological variation between individuals. In this study, we developed DNA markers for sex and individual identification of this species by an efficient method using high-throughput DNA sequence data. Paired-end 5 Gb (2 × 250 bp) and 15 Gb (2 × 150 bp) genome sequences were determined from a female and a male Japanese giant flying squirrel, respectively. We searched SRY and XIST genes located on Y and X chromosomes, respectively, from high-throughput sequence data and designed primers to amplify these genes. Using these primer sets, we succeeded to identify the sex of individuals. In addition, we selected 12 loci containing microsatellites with different numbers of repeats between two individuals from the same data set, and designed primers to amplify these sequences. Twenty individuals from nine different locations were discriminated using these primer sets. Furthermore, both sex and microsatellite markers were amplified from DNA extracted non-invasively from single fecal pellet samples. Based on our results for flying squirrels, we expect our efficient method for developing non-invasive high-resolution individual- and sex-specific genotyping to be applicable to a diversity of mammalian species.
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Affiliation(s)
- Aki Sugita
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan,
| | - Mayumi Shigeta
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Hachioji City, Tokyo 193-0843, Japan
| | - Noriko Tamura
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Hachioji City, Tokyo 193-0843, Japan
| | - Hiroyuki Okazaki
- Chuo University Junior and Senior High School, Koganei City, Tokyo 184-8575, Japan
| | - Nobuyuki Kutsukake
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Hayama, Kanagawa 240-0193, Japan
| | - Yohey Terai
- SOKENDAI (The Graduate University for Advanced Studies), Department of Evolutionary Studies of Biosystems, Hayama, Kanagawa 240-0193, Japan, .,SOKENDAI (The Graduate University for Advanced Studies), Research Center for Integrative Evolutionary Science, Hayama, Kanagawa 240-0193, Japan
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Brekke TD, Supriya S, Denver MG, Thom A, Steele KA, Mulley JF. A high-density genetic map and molecular sex-typing assay for gerbils. Mamm Genome 2019; 30:63-70. [PMID: 30972478 PMCID: PMC6491409 DOI: 10.1007/s00335-019-09799-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
We constructed a high-density genetic map for Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus: 10047.
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Affiliation(s)
- Thomas D Brekke
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Sushmita Supriya
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Megan G Denver
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Angharad Thom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Katherine A Steele
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK.
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Turkia T, Selonen V, Brommer JE. Large-scale spatial synchrony in red squirrel ( Sciurus vulgaris) sex ratios. J Mammal 2016. [DOI: 10.1093/jmammal/gyw004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Lurz PWW, Hayssen V, Geissler K, Bertolino S. Callosciurus erythraeus(Rodentia: Sciuridae). ACTA ACUST UNITED AC 2013. [DOI: 10.1644/902.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Gorrell JC, Boutin S, Raveh S, Neuhaus P, Côté SD, Coltman DW. Sexing the Sciuridae: a simple and accurate set of molecular methods to determine sex in tree squirrels, ground squirrels and marmots. Mol Ecol Resour 2012; 12:806-9. [PMID: 22726203 DOI: 10.1111/j.1755-0998.2012.03165.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We determined the sequence of the male-specific minor histocompatibility complex antigen (Smcy) from the Y chromosome of seven squirrel species (Sciuridae, Rodentia). Based on conserved regions inside the Smcy intron sequence, we designed PCR primers for sex determination in these species that can be co-amplified with nuclear loci as controls. PCR co-amplification yields two products for males and one for females that are easily visualized as bands by agarose gel electrophoresis. Our method provides simple and reliable sex determination across a wide range of squirrel species.
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Affiliation(s)
- Jamieson C Gorrell
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9.
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