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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.

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