ArticleJournal of advanced research2025
Reconciliation of wheat 660K and 90K SNP arrays and their utilization in dough rheological properties of bread wheat.
Article in Journal of advanced research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Comparative Genome-Wide Association Studies of Metabolites and Grain-Related Traits in Common Wheat.Plant biotechnology journal · 2026Article
- Multi-locus genome-wide association study on the rheological traits in wheat flour dough.BMC genomics · 2026Article
- Genome-Wide Linkage Mapping for Mixograph Properties in Common Wheat.Plants (Basel, Switzerland) · 2026Article
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12 authors.
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Abstract
introductionHigh-density Wheat 660K and 90K SNP arrays are powerful tools for understanding the genetic basis of wheat traits. However, their inconsistantly physical positions that were caused by different versions of Chinese Spring genome during developing arrays are confused and inconvenient for further application.
objectiveWith the repid development of wheat geonome sequencing, we aim to reconciliate Wheat 660K and 90K SNP arrays in modern cultivar and reveal the genetic basis of dough rheological properties in bread wheat.
methodsWe refined physical positions of Wheat 660K and 90K SNP arrays in the currently popular wheat cultivar AK58 genome that was released more recently. We next performed genome-wide association studies (GWAS) and linkage analysis to identify important genetic loci related to quality traits using updated and un-updated arrays, respectively.
resultsRefining results showed that 92.3% and 83% of SNPs in the Wheat 660K and 90K SNP arrays were precisely mapped to the AK58 genome, respective. GWAS results by the updated 660K and 90K arrays indicated that 26 intervals composed of 1032 significant SNPs were associated with 9 quality traits in multiple environments. The significant interval for stability time on 1D was narrowed into an 8.4-Mb region using the updated arrays, whereas the interval is 405 Mb using the un-updated arrays. Linkage analysis revealed an important QTL QST.henau-1D.2 for stability time with 1.64 Mb. Integration of GWAS and QTL results narrowed the significant interval into 6.46 Mb containing 35 annotation genes by collinearity analysis. After T-test, gene expression analysis, seven of them are potential candidate genes and thus favorable haplotypes are identified to benefit marker-assisted selection.
conclusionA reconciliation of Wheat 660K and 90K arrays promote their efficient applications. Important genetic loci and favorable haplotypes identified in this study provided valuable information for wheat quality breeding.
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