Abstract

Japonica soft rice varieties possess excellent eating quality, and their cultivation area has been steadily expanding in recent years. This study aimed to analyze japonica soft rice varieties cultivated in the Yangtze River Delta region of China at the genome level and to provide a theoretical basis for optimizing disease resistance and other important traits. Genotypic characterization and evaluation of ten major japonica soft rice varieties from the Yangtze River Delta region were conducted using a genome-wide single nucleotide polymorphism (SNP) chip. The experimental results indicated that the soft rice varieties in the Yangtze River Delta region had a relatively high japonica component and were all classified as typical japonica rice varieties. Specifically, the highest (95.6%) and lowest (91.5%) proportions of japonica genomic segments were detected in Tai’an 1 and Zhehexiang 2, respectively. Japonica soft rice varieties from Shanghai exhibited a closer genetic distance to those from Jiangsu Province than to those from Zhejiang Province. Genomic identity was highest between Tai’an 1 and Nanjing 46 (87.9%) and lowest between Tai’an 1 and Jia 67 (74.4%). Based on the results of the chip assay, a total of twenty-six functional genes controlling key traits, such as yield, quality, and resistance to biotic and abiotic stresses, were identified in the ten analyzed varieties. Among them, Zhehexiang 2 carried the broad-spectrum blast resistance genes Pi2 and Pita, which is useful for improving the blast resistance of japonica soft rice varieties. The findings of this study provide genetic resources and carrier materials for the efficient molecular improvement of japonica soft rice varieties.

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