Comparative compositions of grain of tritordeum, durum wheat and bread wheat grown in multi-environment trials

Shewry, Peter R.; Brouns, Fred; Dunn, Jack; Evans, Jessica; Burridge, Amanda J.; America, A.H.P.; Gilissen, L.J.W.J.; Proos-Huijsmans, Zsuzsan A. M.; Straaten, Jan Philip van; Jonkers, Daisy; Lazzeri, P. A.; Ward, Jane L.; Lovegrove, Alison

doi:10.1016/j.foodchem.2023.136312

Cited by 4 publications

(1 citation statement)

References 37 publications

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“…The bread wheat genome already contains significant genetic variation and much work is being done to enhance the germplasm with novel alleles from wide crosses. The previous 35k Breeders array had previously been used with wheat wild relative material in a pre-breeding context (Kumar et al, 2020; Wright et al, 2023) and for elite durum wheat cultivars (Kabbaj et al, 2017; Ganugi et al, 2021; Shewry et al, 2023). The genotype calls generated on the TaNG v1.1 array across a diverse set of wheat relative material here (Supplementary File S4) illustrate that secondary and tertiary genepool material may also be genotyped alongside T. aestivum accessions.…”

Section: Discussionmentioning

confidence: 99%

Development of a Next Generation SNP Genotyping Array for Wheat

Burridge,

Winfield,

Przewieslik-Allen

et al. 2023

Preprint

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SummaryHigh 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, theTriticum aestivumNext 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.

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Section: Discussionmentioning

confidence: 99%

Development of a Next Generation SNP Genotyping Array for Wheat

Burridge,

Winfield,

Przewieslik-Allen

et al. 2023

Preprint

Self Cite

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Variation of the ferulic acid concentration and kernel weight in CIMMYT bread wheat germplasm and selection of lines for functional food production

Tian,

Gong,

Ibba

et al. 2024

LWT

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Development of a next generation SNP genotyping array for wheat

Burridge,

Winfield,

Przewieslik‐Allen

et al. 2024

Plant Biotechnology Journal

View full text Add to dashboard Cite

SummaryHigh‐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.

show abstract

Comparative compositions of grain of tritordeum, durum wheat and bread wheat grown in multi-environment trials

Cited by 4 publications

References 37 publications

Development of a Next Generation SNP Genotyping Array for Wheat

Development of a Next Generation SNP Genotyping Array for Wheat

Variation of the ferulic acid concentration and kernel weight in CIMMYT bread wheat germplasm and selection of lines for functional food production

Development of a next generation SNP genotyping array for wheat

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