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. ALK^Q1882, 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.

ALK是控制水稻糊化温度（GT）的关键基因，据认为至少有3个ALK等位基因负责水稻品种间GT的多样性。但是，是否与GT相关的启动子区域的序列多态性尚不清楚。在这项研究中，我们分析了ALK启动子区域的序列变异，主要鉴定了两种类型的启动子。ALK数以千计的I型启动子各行其道籼稻和粳稻水稻品种，而ALK在从澳大利亚/硼和巴斯马蒂品种生态型II型启动子占主导地位。具有不同等位基因的CSSL的表型分析和质量表征ALK和启动子活性测定表明II型启动子下调了ALK的表达水平，随后对ASV值产生了负面影响。ALK ^Q1882在ALK基因的4329/4330 bp处具有II型启动子区域和TT SNP ，被认为是提高水稻品质的稀有和优良的ALK等位基因。杂交三倍体胚乳中的转录检测表明ALK通过两个亲本的基因应对同时表达，可以通过两个亲本的基因型估计杂交水稻品种的ASV。更重要的是，开发了一种新的dCAPS标记以区分4329/4330 bp TT的功能性SNP，这是一种以较低的测试成本高精度地提高谷物质量的有效工具。