The Bra1K array: an efficient and versatile 1K liquid-phase SNP chip for genetics and breeding in Chinese cabbage

The Bra1K array, a novel 1K liquid-phase SNP chip developed using Genotyping by Target Sequencing (GBTS), serves as a versatile and efficient platform for genetic research and molecular breeding in Brassica rapa. The development of cost-effective and efficient genotyping platforms is essential for advancing genetics and breeding in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Here, we present the Bra1K array, a liquid-phase SNP chip based on Genotyping by Target Sequencing (GBTS), comprising 1002 expertly selected probes. The array incorporates markers linked to key agronomic traits, including the flowering-related gene BrFLC1, clubroot-resistant genes Crr5 and CRs, Turnip mosaic virus resistance gene retr02, and orange heading gene BrCRTISO1, enabling effective foreground selection. We validated the array's utility through comprehensive applications: Phylogenetic analysis of 173 accessions revealed a clear population structure consistent with morphological diversity, and the construction of two high-density genetic maps (384 and 262 markers, respectively) enabled the precise localization of the Br-drp1 gene for dark yellow petals on chromosome A09 and the BrYL1 gene for yellow leaves on chromosome A06. Furthermore, in a marker-assisted backcrossing program, the Bra1K array guided the rapid introgression of the Crr5 gene into the elite line Y578-2. Within just two backcross cycles and one generation of selfing, we obtained homozygous, clubroot-resistant introgression lines with over 97% recovery of the recurrent parent genome. The Bra1K array is a robust, practical, and highly efficient genotyping solution that seamlessly integrates genetic exploration with molecular breeding in B. rapa.