Abstract
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.
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Acknowledgments
The authors would like to thank Dr. Jingde Qiu at the University of California at Riverside for editing and comments on the manuscript. This work was supported by the grants “Breeding new varieties of disease-resistant transgenic rice, Ministry of Agriculture and Rural Affairs (2016ZX08001-002)”; the National Natural Science Foundation of China (31701406).
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YPW, BT, and LZ conceived and designed experiments. LZ, SXZ, and PL identified the CSSLs and performed agronomic trait investigation. JLL and FYX performed expression analysis. LH and YM constructed plasmids and performed luciferase activity assay. HY finished phylogenetic analyses. YFY and YKW were in charge of filed management. SGL, BTM, WLC, and PQ provided advice about the experiments. YPW, BT, and LZ supervised and complemented the manuscript writing. The authors read and approved the final manuscript.
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Main conclusion
Based on the functional analysis of sequence variation in ALK promoters and the verification of favorable allele, in combination with the study of gene expression pattern in endosperm and the development of molecular markers, we proposed a strategy for improving the alkali value of hybrid rice.
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Zheng, L., Liu, P., Zhang, S. et al. Favorable allele mining and breeding utilization of ALK in rice. Mol Breeding 40, 107 (2020). https://doi.org/10.1007/s11032-020-01183-z
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DOI: https://doi.org/10.1007/s11032-020-01183-z