Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of <i>SLR1</i> Using the CRISPR/Cas9 System in Rice

• Main Authors: Yu Jin Jung, Jong Hee Kim, Hyo Ju Lee, Dong Hyun Kim, Jihyeon Yu, Sangsu Bae, Yong-Gu Cho, Kwon Kyoo Kang
• Format: Article
• Language: English
• Published: MDPI AG 2020-07-01
• Series: International Journal of Molecular Sciences
• Subjects: CRISPR/Cas9; GA; DELLA/TVHYNP; Dwarf; <i>GA₂₀OX₂</i>; GA signaling
• Online Access: https://www.mdpi.com/1422-0067/21/15/5492
• ISSN: 1661-6596; 1422-0067

The rice <i>SLR1</i> gene encodes the DELLA protein, and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the <i>SLR1</i> gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, <i>GA₂₀OX₂</i> (Gibberellin oxidase) and <i>GA₃OX₂</i>, were increased in the edited mutant plants, suggesting that <i>GA₂₀OX₂</i> acts as a convert of GA₁₂ signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.