MianxinNo.1: a modern cultivar genome-informed SNP array based on cGPS technology for genomics-assisted breeding in cotton.

To overcome limitations in the applications of existing SNP arrays in cotton genotyping and genomic selection (GS), we developed a liquid-phase SNP array, CottonSNP10K, for genomics-assisted breeding in cotton. Based on the high-quality reference genome of modern upland cotton cultivar NDM8, CottonSNP10K achieves precise probe design, and its marker system innovatively integrates the modern breeding genetic background, incorporating not only 13 agronomic traits associated loci (including fiber quality and yield-traits and stress resistance) identified via genome-wide association studies (GWAS), but also six exogenous gene markers targeting traits such as high lint percentage, herbicide resistance and insect resistance. The chip incorporates genome-wide background SNPs to ensure comprehensive genetic coverage, resulting in a final design comprising 11,159 SNPs, including 3,981 functionally trait-associated markers with 1,743 annotated genes and 7,178 genome-wide background markers. Through rigorous applications across diverse cotton accessions, CottonSNP10K performed exceptionally technical robustness with call rates > 99% and genotype concordance rates > 99%. The array can effectively support precisely marker-assisted selection (MAS) for agronomic traits and high-resolution breeding population analysis, and markedly enhance GS predictive accuracy for agronomically important traits using prediction models that we established. This integrated approach provides a high-throughput precision tool for parent germplasm characterization and breeding line selection in cotton, enabling reliable identification of elite germplasm and advancement of genomics-assisted breeding.