Favorable allele mining and breeding utilization of ALK in rice

ALK is the key gene of controlling rice gelatinization temperature (GT), and at least three ALK alleles are thought to be responsible for the diversity of GT among rice cultivars. But whether the sequence polymorphism of the promoter region also associated with GT is not clearly studied. In this study, we analyzed sequence variation in the promoter region of ALK and mainly two types of promoter were identified. ALK type I promoter prevails among thousands of indica and japonica rice varieties, while ALK type II promoter predominates over varieties from Aus/boro and Basmati ecotypes. Phenotypic analysis and quality characterization of CSSLs with different alleles of ALK and promoter activity assays revealed that type II promoter downregulates the expression level of ALK and subsequently, negatively affects ASV values. ALKQ1882, owning type II promoter region and TT SNP at 4329/4330 bp of ALK gene, was identified as a rare and elite ALK allele for rice quality improvement. Transcriptional detection in hybrid triploid endosperm revealed that ALK is simultaneously expressed by gene copes from both parents, the ASV of hybrid rice varieties can be estimated through the genotypes of two parents. More importantly, a new dCAPS marker was developed to discriminate the functional SNP of TT at 4329/4330 bp, which is an efficient tool for improving the grain quality with high accuracy on low testing cost.