Effects of Grain Shape Genes Editing on Appearance Quality of Erect-Panicle Geng/Japonica Rice

Long grain geng/japonica rice has a higher market preference due its excellent appearance quality. The dense and erect-panicle 1 (dep1) gene has been widely used in the breeding of high-yielding geng/japonica rice cultivars in China. However, this gene causes short and round grain shape thus making it less attractive in global rice markets. Therefore, breeding of high-yielding long-grain geng/japonica rice cultivars by incorporating dep1 with major-effect grain shape gene is of high priority in rice industry. Up to now, multiple grain shape genes’ effect mechanism has been clearly elaborated, however, under the background of erect-panicle geng/japonica rice, the effect of major grain shape genes on the appearance quality need to be further clarified, as detailed reports are limited. Utilizing CRISPR/Cas9 technology, a series of near-isogenic lines (NILs) (YF47(dep1)-gw8, YF47(dep1)-gs3, YF47(dep1)-gl7, YF47(dep1)-qgl3 and YF47(dep1)-tgw6) in Yanfeng 47(YF47(dep1)) background were created. Grain appearance and yield components analysis showed that: (1) All NILs’ grain length to width ratio was significantly increased compared to that of YF47(dep1), excepted YF47(dep1)-gs3, (2) The chalkiness degree was significantly reduced in all of the NILs, (3) In all of the NILs, YF47(dep1)-gw8 grains exhibited the greatest length to width ratio and the lowest chalkiness degree, (4) The composition of glume cells and filling characteristics of the endosperm were two key factors contributing grain shape and grain chalk variations, respectively, and v) Owning to a substantial increase in the thousand grain weight, the yields of YF47(dep1)-gs3 and YF47(dep1)-tgw6 were significantly higher than that of YF47(dep1), whereas YF47(dep1)-qgl3 exhibited the lowest yield because of a dramatic decrease in the effective panicle number and thousand grain weight. All the results revealed that pyramiding dep1 with major-effect grain shape alleles was an effective approach to improving the appearance quality of erect-panicle geng/japonica rice, owning to both of the appearance quality and yield improvement, GS3 and TGW6 alleles can be applied directly for breeding long-grain shape geng/japonica rice, and editing GW8 resulted in excellent appearance quality but low yield, therefore, this gene would be difficult to use directly but can be considered as the core germplasm resource. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12284-021-00517-5.