The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat.

Area of Science:

• Plant Genetics and Breeding
• Genomics
• Molecular Markers

Background:

• Molecular marker assays are crucial for genomic selection and association studies in wheat breeding.
• Previous marker technologies like PCR-based markers and genotyping by sequencing have aided gene discovery.
• Advancements in wheat genome sequencing have enabled the development of high-density single-nucleotide polymorphism (SNP) arrays.

Purpose of the Study:

• To evaluate and compare seven types of wheat SNP arrays.
• To assess SNP number, distribution, density, gene association, heterozygosity, and application potential.
• To identify the most effective SNP array for wheat genetic improvement.

Main Methods:

• Comparative analysis of seven wheat SNP arrays.
• Evaluation of SNP characteristics including genome specificity, physical position reliability, and distribution.
• Assessment of SNP association with annotated genes and promoter regions.

Main Results:

• The Wheat 660K SNP array demonstrated the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions.
• SNPs in the Wheat 660K array were evenly distributed across the genome and located within 66,834 annotated gene or promoter intervals.
• The Wheat 660K SNP array's gene annotation coverage surpassed that of other evaluated arrays (35K, 55K, 90K, 820K).

Conclusions:

• The Wheat 660K SNP array is a reliable, cost-effective, and comprehensive tool for wheat genetic studies.
• It can effectively substitute for six other evaluated SNP arrays.
• The Wheat 660K SNP array shows significant promise for targeted genotyping and marker-assisted selection in wheat breeding programs.