WDR6K, a designed SNP array for the research and improvement of rice drought-resistance

• The chip targets enhancing drought resistance in rice. • It contains a considerable amount of upland-lowland differentiated loci. • a higher proportion of SNPs associated with known function genes of drought resistance and other green traits required Water-saving and drought-resistance rice (WDR) integrates many green characters (e.g., drought resistance, water/nutrient use efficiency, direct seeding, etc.) from upland rice into the elite paddy rice. The molecular designed breeding is a promising breeding technology for WDR based on the high-throughput genotyping. Therefore, an efficient and low-cost genotyping tool for WDR breeding, which is suitable in the foreground selection of drought resistance and other green traits, is required. In this study, we designed a SNP array named as WDR6K with special strategies in loci selection. WDR6K contains 5895 SNP/InDel loci distributes evenly across the rice genome. Compared with other rice 6K SNP arrays, WDR6K possesses a high proportion (>90.0%) of missense SNPs without apparent loss of polymorphism. Moreover, WDR6K possesses considerable amount (∼41.0%) of upland-lowland differentiated loci, by which we can identify and utilize genetic resources of upland rice. WDR6K refers to 5001 genes, including hundreds of known genes of green characters quired by WDR. These genes are related to rice drought resistance as indicate by the GO/KEGG enrichments and their greater expression responses to drought, osmotic, and oxidative stresses and abscisic acid. Furthermore, WDR6K shall be closely associated with drought resistance as it contains 922 drought resistance contributing loci, which can facilitate the foreground selection for drought resistance. Finally, developed by the liquid phase genotyping by pinpoint sequencing of captured targets technology, WDR6K is low-cost and flexible for further version updates to add markers. Therefore, WDR6K has great prospective in the molecular designed breeding of WDR.