The panicle architecture and grain size of rice affect not only grain yield but also grain quality, especially grain appearance. The erect-panicle (EP) trait controlled by the qpe9-1/dep1 allele has been widely used in high-yielding japonica rice breeding, but usually accompanied with moderate appearance of milled rice. The null gs9 allele shows a good potential for improving grain shape and appearance. However, GS9 and qPE9-1/DEP1 loci are tightly linked, and their interaction is unclear, which obviously restricts their utilization in modern rice breeding. In the present study, comparative analyses of protein and mRNA levels revealed that GS9 and qPE9-1 function independently. Three near-isogenic lines (NILs) carrying various allelic combinations of these two loci, NIL (gs9/qpe9-1), NIL (GS9/qPE9-1) and NIL (gs9/qPE9-1), in the EP japonica cultivar 2661 (GS9/qpe9-1) background were developed for genetic interaction analysis. GS9 and qPE9-1 had additive effects on determining grain size, and the null gs9 allele could decrease grain chalkiness and improve grain appearance without affecting plant and panicle architecture in EP japonica cultivars. Additionally, introgression lines (ILs) developed in another released EP japonica cultivar Wuyujing 27 (WYJ27) background showed the same additive effect and the feasibility of utilizing the gs9 allele to improve grain appearance quality in high-yielding EP cultivars. This study provides an effective strategy for rice breeders to improve rice grain appearance in EP japonica and related cultivars.

水稻的穗结构和颗粒大小不仅影响粮食产量，而且影响粮食质量，特别是粮食外观。由qpe9-1/dep1等位基因控制的直穗（EP）性状已广泛用于高产粳稻育种，但通常伴随着精米的中等外观。无效的gs9等位基因显示出改善谷物形状和外观的良好潜力。然而，GS9和qPE9-1/DEP1基因座联系紧密，相互作用不明确，明显限制了它们在现代水稻育种中的应用。在本研究中，蛋白质和 mRNA 水平的比较分析表明GS9和qPE9-1独立运作。在 EP japonica品种 2661 中，三个近等基因系 (NIL) 携带这两个基因座的各种等位基因组合，NIL ( gs9/qpe9-1 )、NIL ( GS9/qPE9-1 ) 和 NIL ( gs9/qPE9-1 ) ( GS9/qpe9-1 ) 背景被开发用于遗传相互作用分析。GS9和qPE9-1对确定籽粒大小具有相加作用，无效的gs9等位基因可以降低籽粒垩白度并改善籽粒外观，而不会影响 EP粳稻品种的植株和穗结构。此外，在另一个已发布的 EP japonica 中开发的基因渗入系 (ILs)品种武玉井 27 (WYJ27) 背景显示出相同的累加效应和利用gs9等位基因改善高产 EP 品种籽粒外观质量的可行性。本研究为水稻育种者提供了一种有效的策略，以改善 EP japonica和相关品种的稻米外观。