Candidate genes identification for internode length in rice via genome-wide association studies

Through GWAS and CRISPR/Cas9, it was found that INL1 and INL2 act as candidate genes regulating rice internodes and may affect the GA pathway. Their favorable haplotypes provide valuable gene targets for dwarf breeding. The number and length of each internode of rice are the determining factors of plant height, and are important traits for lodging resistance and yield formation. Mining the genes related to the number and length of internodes is of great significance for cultivating dwarf or semi-dwarf varieties. In order to explore the genetic basis of the number and length of internodes, the length and number of internodes in rice were determined for genome-wide association analysis, covering 429 accessions with 3.16 million high-quality single nucleotide polymorphisms. GWAS identified 34 significant marker-trait associations, found four new QTLs, and screened two candidate genes Internode number and length 1 (INL1) and INL2. They are annotated as cytochrome P450 enzymes and zinc finger protein transcription factors, respectively. These two family members are widely involved in plant physiological activities. The internode length and plant height of INL1 and INL2 knockout plants were lower than that of wild type. Transcriptomic analysis revealed that the loss of INL1 and INL2 suppresses differentially modulates gibberellin (GA) metabolism, ultimately leading to a dwarf phenotype. Haplotype analysis showed that the internode length of the HapA type of the two genes was lower than that of other haplotypes. Favorable alleles of OsINL1 and OsINL2 reduce height and can be further used in rice dwarf breeding to improve rice lodging resistance.