| Summary: | The planting area of hybrid rice (<i>Oryza sativa</i> L.) has continuously decreased in recent years partially because of the low eating quality. Longke638S and Jing4155S are two elite male sterile lines, which are used for developing many hybrid varieties with large planting areas in China. Here, 21 hybrid rice varieties of an incomplete diallel cross population with Longke638S and Jing4155S as female parents were planted under field conditions for two consecutive years, aiming to investigate the physiological and transcriptomic characteristics that is required for coordinating high yield and superior eating quality. As a result, grain yield ranged from 7.15 to 9.23 t ha<sup>−1</sup> in 2019 and from 7.49 to 9.23 t ha<sup>−1</sup> in 2020, and a negative relationship was identified between yield and quality-related traits. Hybrid varieties with Longke638S as the female parent (LLY) had higher yield but lower eating quality than those with Jing4155S as the female parent (JLY). The higher yield of LLY over JLY was due to higher biomass production and N uptake as well as higher yield stability across planting years, while their lower grain quality can be mainly ascribed to lower amylose content and alkali spreading value. Male parents significantly affected yield-related traits of LLY and eating quality-related traits of JLY. Candidate genes involved in grain starch biosynthesis were differentially expressed between LLYHZ, JLYHZ, and JLY1212, such as <i>Wx</i> and <i>ALK</i>. Overall, this study examined the relationship between grain yield and eating quality and identified the physiological and molecular traits that limited grain yield or eating quality of LLY and JLY hybrid varieties.
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