Indica–japonica hybrid rice (I–JR) typically has greater grain yield than that of Indica hybrid rice (IR) under prolific shading, but it is not known how shading impacts on physiological characteristics underpinning grain quality. Here, we conducted a two-year field experiment in the mid-reaches of the Yangtze River region using I–JR (genotypes Yongyou 1540 and Yongyou 538) and IR (genotypes Y-liangyou 900 and Quanyouhuazhan). We found that shading reduced grain appearance and quality, particularly milling and heading rates, and chalkiness. Shading disrupted carbon and nitrogen metabolism, impacting traits influencing the human perception of the taste of the grain, such that amylose decreased by 5.9% (I–JR) and 12.9% (IR); grain protein significantly increased, with lesser effects in I–JR than IR under shading. Shading also reduced peak, hot, and final viscosities, and breakdown value. I–JR had improved rice quality compared with that of IR due to the greater propensity of the former to photosynthesize under shading, leading to the improved functioning of carbon and nitrogen metabolism.

Superior yields of super hybrid rice have demonstrably contributed to contemporary food security. Despite this, the extent to which intensive nitrogen fertilizer requirements of such crops have impacted on soil health and microbial communities primarily remains unchartered territory, evoking questions of sustainability. Here, we examine how four management treatments (zero fertilizer, CK; farm practice, FP; high-yield and high-efficiency, HYHE; and super-high-yield management, SHY) influenced the grain yields, soil biodiversity and community strata underpinning soil health of an elite super hybrid rice variety (Y-liangyou 900). We show that SHY treatments increased yields, altered soil physicochemical properties, and fostered greater biodiversity and soil bacteria and fungi abundance, while FP, HYHE and SHY treatments transformed community bacteria and fungi strata. Environmental regulators of bacterial and fungal communities differed widely, with bacterial communities most closely associated with soil organic carbon (SOC) and NH₄⁺-N, and with fungal communities more related to available phosphorus. We show that alpha diversity of bacteria and fungi and community composition of fungi were positively correlated with yield, but bacterial community composition was negatively correlated with yield. Our work clearly exemplifies the nexus between appropriate farm and landscape management in enabling soil health and driving consistently high yields, of which both are required for sustainable food security.