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In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing
BACKGROUND: Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. He...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137276/ https://www.ncbi.nlm.nih.gov/pubmed/32280361 http://dx.doi.org/10.1186/s13007-020-00588-3 |
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author | Singh, Narinder Raupp, John Koo, Dal-Hoe Friebe, Bernd Gill, Bikram Poland, Jesse |
author_facet | Singh, Narinder Raupp, John Koo, Dal-Hoe Friebe, Bernd Gill, Bikram Poland, Jesse |
author_sort | Singh, Narinder |
collection | PubMed |
description | BACKGROUND: Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps. RESULTS: Using GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines. CONCLUSION: We envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species. |
format | Online Article Text |
id | pubmed-7137276 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-71372762020-04-11 In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing Singh, Narinder Raupp, John Koo, Dal-Hoe Friebe, Bernd Gill, Bikram Poland, Jesse Plant Methods Methodology BACKGROUND: Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps. RESULTS: Using GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines. CONCLUSION: We envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species. BioMed Central 2020-04-06 /pmc/articles/PMC7137276/ /pubmed/32280361 http://dx.doi.org/10.1186/s13007-020-00588-3 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Methodology Singh, Narinder Raupp, John Koo, Dal-Hoe Friebe, Bernd Gill, Bikram Poland, Jesse In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title | In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title_full | In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title_fullStr | In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title_full_unstemmed | In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title_short | In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
title_sort | in-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137276/ https://www.ncbi.nlm.nih.gov/pubmed/32280361 http://dx.doi.org/10.1186/s13007-020-00588-3 |
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