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The Green Revolution gene sd1 has been used extensively in modern rice breeding, especially in indica cultivars. However, elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified, and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources. Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice. Two new sd1 alleles were identified in indica rice. In 295 japonica accessions from northeast Asia, except for the weak functional allele SD1-EQ, sd1-r was the major allele, reducing plant height in comparison with SD1-EQ. Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search, genealogical analysis, and dCaps markers. Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan, and sd1-j is commonly used in east China and Kyushu in Japan. Dongnong- and Xiushui-series cultivars carrying sd1-r and sd1-j, respectively, are essential branches of the backbone parents of Chinese japonica rice, Akihikari and Ce21, with the largest number of descendants and derived generations. In semi-dwarf japonica rice breeding, sd1-d was introgressed into Daohuaxiang 2 (DHX2). Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280, respectively, after withstanding typhoon-induced strong winds and heavy rains in 2020, and are anticipated to become useful intermediate materials for future genetic research and breeding. This work will facilitate the introduction, parental selection, and marker-assisted breeding, and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.

The early-matured japonica (Geng) rice variety, Suijing18 (SJ18), carries multiple elite traits including durable blast resistance, good grain quality, and high yield. Using PacBio SMRT technology, we produced over 25 Gb of long-read sequencing raw data from SJ18 with a coverage of 62×. Using Illumina paired-end whole-genome shotgun sequencing technology, we generated 59 Gb of short-read sequencing data from SJ18 (23.6 Gb from a 200 bp library with a coverage of 59× and 35.4 Gb from an 800 bp library with a coverage of 88×). With these data, we assembled a single SJ18 genome and then generated a set of annotation data. These data sets can be used to test new programs for variation deep mining, and will provide new insights into the genome structure, function, and evolution of SJ18, and will provide essential support for biological research in general.