Development of a next generation SNP genotyping array for wheat

Authors: BURRIDGE, AMANDA - University Of Bristol; WINFIELD, MARK - University Of Bristol; PRZEWIESLIK, ALLEN - University Of Bristol; EDWARDS, KEITH - University Of Bristol; SIDDIQUE, IMTEAZ - Thermo Fisher Scientific; BARRAL-ARCA, RUTH - Thermo Fisher Scientific; GRIFFITHS, SIMON - John Innes Center; CHENG, SHIFENG - Chinese Academy Of Agricultural Sciences; HUANG, ZEJIAN - Chinese Academy Of Agricultural Sciences; FENG, CONG - Chinese Academy Of Agricultural Sciences; DREISIGACKER, SUSANNE - International Maize & Wheat Improvement Center (CIMMYT); BENTLEY, ALISON - National Institute Of Agricultural Botany (NIAB); Brown-Guedira, Gina; BARKER, GARY - University Of Bristol

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2024
Publication Date: 3/23/2024
Citation: Burridge, A.J., Winfield, M., Przewieslik, A., Edwards, K.J., Siddique, I., Barral-Arca, R., Griffiths, S., Cheng, S., Huang, Z., Feng, C., Dreisigacker, S., Bentley, A.R., Brown Guedira, G.L., Barker, G.L. 2024. Development of a next generation SNP genotyping array for wheat. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.14341.
DOI: https://doi.org/10.1111/pbi.14341

Interpretive Summary: Data from evaluation of wheat lines and populations with molecular markers has many applications, including characterization and deployment of favorable genes for resistance to disease and other types of stress, and for predictive breeding of high-yielding varieties. Among the many types of molecular markers, Single Nucleotide Polymorphisms (SNP) are the most abundant and progress in DNA sequencing has given us access to a vast pool of identified SNPs in wheat. There is a need to improve upon arrays currently used for detection of large numbers of SNPs in wheat. In this study, a new Axiom ‘Triticum aestivum Next Generation’ array (TaNG) for genotyping was developed having 42,372 SNP selected to have high varietal discrimination. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome Wide Association Studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.

Technical Abstract: High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel 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 used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43'372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.