Figure 1.

SD8 knockouts showed reduced plant height and flag-leaf angle without yield penalty.

(A) Identification of a putative open reading frame on chromosome 8 (LOC_08g45030) associated with plant height based on re-analysis of SNPs in the 3000 rice genomes dataset (Alexandrov et al., 2015).

(B) Gross phenotypes of SD8 KO lines in the Nipponbare (NIP) background obtained using CRISPR-Cas9 gene editing. Top panel: mutation sites in the two knockout lines (sd8-1 and sd8-2). Bottom panels: height, flag-leaf angle, and panicle morphology in NIP, sd8-1, and sd8-2 plants.

(C and D) Comparison of plant height (C) and flag-leaf angle (D) between NIP, sd8-1, and sd8-2 plants.

(E) Representative NIP and sd8-1 plants grown under different planting densities. Seeds from NIP and sd8-1 were grown at high (5 × 20 cm) and low (10 × 20 cm) planting densities.

(F) Grain yield of NIP and sd8-1 plants grown at high and low planting densities. ns, not significant. ∗p < 0.01 (Student’s t-test).

(G) Glucuronidase staining in roots of 7-day-old seedlings, internodes at the early heading stage, glumes at the early heading stage, and glumes at the late heading stage. Scale bars: 1 mm.

(H) Gas chromatography–mass spectroscopy analysis of endogenous free IAA concentrations in NIP, sd8-1, and sd8-2 seedlings.

(I) Relative expression levels of OsIAA1/3/9/20 and OsPIN1a/1b/2 in aerial tissues of 3-week-old NIP, sd8-1, and sd8-2 seedlings.

(J) Time course analysis of IAA efflux and net influx in the primary root meristem of 7-day-old NIP and sd8-1 seedlings as measured continuously for 5 min by the scanning ion-selective electrode technique. IAA influx was measured in the presence of 10 μM exogenous IAA. Columns represent the mean net influx rates averaged over the entire 5-min observation window (±SE, n = 6–10 plants). ∗p < 0.05 (one-way analysis of variance).

(K) SD8 functionality assays for auxin acquisition in the IAA-sensitive yeast strain yap1-1. The growth status is shown for yap1-1 cells expressing empty vectors (pYES2 and pDR196) and SD8 on SD-U medium without uracil supplemented with 2, 3, 4, or 6 μM IAA. Serial dilutions (1:10) of yeast cells were spotted onto SD-U solid medium containing 2% galactose or glucose, then incubated at 30°C for 4 to 6 days.

(L) Gross phenotypes of SD8 KO lines in the Jingeng818 and Longgeng31 backgrounds.

(M–O) Quantitative analysis of plant height and flag-leaf angle in wild-type and SD8 KO lines in the Jingeng818 and Longgeng31 backgrounds.

(P and Q) Tajima’s D and nucleotide diversity (π) values for a ∼2-Mb genomic region flanking SD8 in the 3000 rice genomes dataset.

(R) A model for loss of SD8 function with and without SD1 in which plant height is reduced but yield is increased under high-density planting.