Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we develop...
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| Format: | Article |
| Language: | English |
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MDPI AG
2014-10-01
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| Series: | Diversity |
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| Online Access: | http://www.mdpi.com/1424-2818/6/4/665 |
| _version_ | 1798041733546639360 |
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| author | Gregory W. Peterson Yibo Dong Carolee Horbach Yong-Bi Fu |
| author_facet | Gregory W. Peterson Yibo Dong Carolee Horbach Yong-Bi Fu |
| author_sort | Gregory W. Peterson |
| collection | DOAJ |
| description | Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species. |
| first_indexed | 2024-04-11T22:25:38Z |
| format | Article |
| id | doaj.art-869a4c986a934403bf7d5cbf70c7aea2 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-04-11T22:25:38Z |
| publishDate | 2014-10-01 |
| publisher | MDPI AG |
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| series | Diversity |
| spelling | doaj.art-869a4c986a934403bf7d5cbf70c7aea22022-12-22T03:59:42ZengMDPI AGDiversity1424-28182014-10-016466568010.3390/d6040665d6040665Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP GenotypingGregory W. Peterson0Yibo Dong1Carolee Horbach2Yong-Bi Fu3Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, CanadaPlant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, CanadaPlant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, CanadaPlant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, CanadaGenotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.http://www.mdpi.com/1424-2818/6/4/665next generation sequencinggenotyping-by-sequencingSNP genotypingnon-model plantplant genetic diversity analysiscontig assemblygenome reduction |
| spellingShingle | Gregory W. Peterson Yibo Dong Carolee Horbach Yong-Bi Fu Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping Diversity next generation sequencing genotyping-by-sequencing SNP genotyping non-model plant plant genetic diversity analysis contig assembly genome reduction |
| title | Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping |
| title_full | Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping |
| title_fullStr | Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping |
| title_full_unstemmed | Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping |
| title_short | Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping |
| title_sort | genotyping by sequencing for plant genetic diversity analysis a lab guide for snp genotyping |
| topic | next generation sequencing genotyping-by-sequencing SNP genotyping non-model plant plant genetic diversity analysis contig assembly genome reduction |
| url | http://www.mdpi.com/1424-2818/6/4/665 |
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