Development of a next generation SNP genotyping array for wheat
High throughput genotyping arrays have provided a cost effective, reliable and interoperable system for genotyping hexaploid wheat and its related germplasm pool. Existing, highly cited arrays including our 35K Axiom Wheat Breeder’s genotyping array and the Illumina 90K iSelect array were designed b...
| Autores principales: | , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/160009 |
| _version_ | 1855540948678737920 |
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| author | Burridge, Amanda J. Winfield, Mark O. Przewieslik-Allen, Alexandra M. Edwards, Keith J. Imteaz Siddique Barral-Arca, Ruth Griffiths, Simon Shifeng Cheng Zejian Huang Cong Feng Dreisigacker, Susanne Bentley, Alison R. Brown-Guedira, Gina Barker, Gary L.A. |
| author_browse | Barker, Gary L.A. Barral-Arca, Ruth Bentley, Alison R. Brown-Guedira, Gina Burridge, Amanda J. Cong Feng Dreisigacker, Susanne Edwards, Keith J. Griffiths, Simon Imteaz Siddique Przewieslik-Allen, Alexandra M. Shifeng Cheng Winfield, Mark O. Zejian Huang |
| author_facet | Burridge, Amanda J. Winfield, Mark O. Przewieslik-Allen, Alexandra M. Edwards, Keith J. Imteaz Siddique Barral-Arca, Ruth Griffiths, Simon Shifeng Cheng Zejian Huang Cong Feng Dreisigacker, Susanne Bentley, Alison R. Brown-Guedira, Gina Barker, Gary L.A. |
| author_sort | Burridge, Amanda J. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | High throughput genotyping arrays have provided a cost effective, reliable and interoperable system for genotyping hexaploid wheat and its related germplasm pool. Existing, highly cited arrays including our 35K Axiom Wheat Breeder’s genotyping array and the Illumina 90K iSelect array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in sequencing wheat varieties and landraces has given us access to a vast pool of SNP diversity, whilst technological improvements in array design has allowed us to fit significantly more probes onto a 384-well format Axiom array than was previously possible. Here we describe a novel High Density Axiom genotyping array, the Triticum aestivum Next Generation array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins “Core Collection”. We use a novel “minimal marker” optimisation approach to select up to six SNPs in each 1.5 MB region of the wheat genome with the highest combined varietal discrimination potential. A design iteration step allowed us to test and replace skim-sequence derived SNPs which failed to convert to reliable Axiom markers, resulting in a final design, designated TaNG1.1 with 43,372 SNPs derived from a haplotype-optimised combination of novel SNPs, DArTAG-derived and legacy wheat Axiom markers. We show that this design has an even distribution of SNPs across chromosomes and sub-genomes compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous Axiom array. We also demonstrate the improved performance of TaNG1.1 for Genome Wide Association Studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available, and the marker annotations, initial genotyping results and software used to generate the optimised marker sets are freely available. |
| format | Journal Article |
| id | CGSpace160009 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1600092025-12-08T09:54:28Z Development of a next generation SNP genotyping array for wheat Burridge, Amanda J. Winfield, Mark O. Przewieslik-Allen, Alexandra M. Edwards, Keith J. Imteaz Siddique Barral-Arca, Ruth Griffiths, Simon Shifeng Cheng Zejian Huang Cong Feng Dreisigacker, Susanne Bentley, Alison R. Brown-Guedira, Gina Barker, Gary L.A. single nucleotide polymorphisms wheat genotyping genetic diversity (as resource) High throughput genotyping arrays have provided a cost effective, reliable and interoperable system for genotyping hexaploid wheat and its related germplasm pool. Existing, highly cited arrays including our 35K Axiom Wheat Breeder’s genotyping array and the Illumina 90K iSelect array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in sequencing wheat varieties and landraces has given us access to a vast pool of SNP diversity, whilst technological improvements in array design has allowed us to fit significantly more probes onto a 384-well format Axiom array than was previously possible. Here we describe a novel High Density Axiom genotyping array, the Triticum aestivum Next Generation array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins “Core Collection”. We use a novel “minimal marker” optimisation approach to select up to six SNPs in each 1.5 MB region of the wheat genome with the highest combined varietal discrimination potential. A design iteration step allowed us to test and replace skim-sequence derived SNPs which failed to convert to reliable Axiom markers, resulting in a final design, designated TaNG1.1 with 43,372 SNPs derived from a haplotype-optimised combination of novel SNPs, DArTAG-derived and legacy wheat Axiom markers. We show that this design has an even distribution of SNPs across chromosomes and sub-genomes compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous Axiom array. We also demonstrate the improved performance of TaNG1.1 for Genome Wide Association Studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available, and the marker annotations, initial genotyping results and software used to generate the optimised marker sets are freely available. 2024-08 2024-11-20T17:38:01Z 2024-11-20T17:38:01Z Journal Article https://hdl.handle.net/10568/160009 en Open Access application/pdf Wiley Burridge, A., Winfield, M., Przewieslik‐Allen, A. M., Edwards, K. J., Siddique, I., Barral-Arca, R., Griffiths, S., Cheng, S., Huang, Z., Cong, F., Dreisigacker, S., Bentley, A. R., Brown-Guedira, G., & Barker, G. (2024). Development of a next generation SNP genotyping array for wheat. Plant Biotechnology Journal, 22(8), 2235-2247. https://doi.org/10.1111/pbi.14341 |
| spellingShingle | single nucleotide polymorphisms wheat genotyping genetic diversity (as resource) Burridge, Amanda J. Winfield, Mark O. Przewieslik-Allen, Alexandra M. Edwards, Keith J. Imteaz Siddique Barral-Arca, Ruth Griffiths, Simon Shifeng Cheng Zejian Huang Cong Feng Dreisigacker, Susanne Bentley, Alison R. Brown-Guedira, Gina Barker, Gary L.A. Development of a next generation SNP genotyping array for wheat |
| title | Development of a next generation SNP genotyping array for wheat |
| title_full | Development of a next generation SNP genotyping array for wheat |
| title_fullStr | Development of a next generation SNP genotyping array for wheat |
| title_full_unstemmed | Development of a next generation SNP genotyping array for wheat |
| title_short | Development of a next generation SNP genotyping array for wheat |
| title_sort | development of a next generation snp genotyping array for wheat |
| topic | single nucleotide polymorphisms wheat genotyping genetic diversity (as resource) |
| url | https://hdl.handle.net/10568/160009 |
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