CRISPR/Cas9-mediated mutagenesis of SMXL4 alters plant height and yield-related traits in rice (cv. Samkwang)

Yurim Kim, Yeeun Jun, Jiheon Han, Sieun Choi, Hwarim Kim, Minje Lee, Song Lim Kim, Sang-Ho Kang, Eun-Jung Suh, Sang Ryeol Park & Youngjun Mo

Scientific Reports – Nature; Published: 06 March 2026

Recent climate change and frequent extreme weather events during the maturation period of rice exacerbate lodging and threaten stable production. Samkwang, a widely cultivated rice variety in Korea, is particularly vulnerable to lodging due to its tall stature. To improve lodging tolerance while preserving Samkwang’s elite genetic background, we identified an SMXL4-edited line (smxl4) with reduced culm length and stable growth from a CRISPR/Cas9-edited Samkwang population. The biological function of SMXL4, a clade Ⅳ member of the SMXL (SUPPRESSOR OF MAX2 1-LIKE) family, has not been well characterized in rice. Compared to Samkwang, the smxl4 plants showed reduced plant height, internode length, panicle length, grain number per panicle, and grain weight, while panicle number per plant increased. Transcriptome profiling of elongating internodes at booting and heading stages revealed upregulation of genes associated with cell wall remodeling and defense responses in smxl4 relative to Samkwang. These findings highlight the broad involvement of SMXL4 in rice growth and development and provide insights for breeding lodging tolerant rice cultivars.

See https://www.nature.com/articles/s41598-026-38708-z

Fig. 1. Verification of SMXL4 gene editing. (A) Schematic diagram of the gene structure and CRISPR-Cas9 meditated gene editing target sequence in SMXL4. (B) DNA sequence analysis of SMXL4 from Samkwang (WT) and smxl4. (C) Cas9-free screening of smxl4 plants (Unlabeled lanes are samples irrelevant to this study; the full-length agarose gel image is provided in Fig. S3).