KNOX II transcription factor HOS59 functions in regulating rice grain size. (1st March 2022)

• Record Type: Journal Article
• Authors: Sheng, Minghao; Ma, Xuelian; Wang, Jiyao; Xue, Tianxi; Li, Zhongqiu; Cao, Yaxin; Yu, Xinyue; Zhang, Xinyi; Wang, Yonghong; Xu, Wenying; Su, Zhen
• Is Part Of: Plant journal. Volume 110:Number 3(2022)
• Page Start: 863
• Page End: 880
• Publication Date: 2022-03-01
• Subjects: KNOX Class II subfamily -- HOS59 -- grain size -- rice; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15709
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: Plant Knotted1‐like homeobox (KNOX) genes encode homeodomain‐containing transcription factors. In rice ( Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)–sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome‐wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP–quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP‐MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA‐mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild‐type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT‐PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size‐related genes such as OsSPL13, OsSPL18, and PGL2 . In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks. Significance Statement: We identified downstream target genes and possible interaction partners of rice ( Oryza sativa L.) HOS59 (a KNOX Class II subfamily member) through ChIP‐seq and IP‐MS analyses. Furthermore, we found that compared to wild‐type and overexpression plants, the CRISPR/Cas9‐edited mutants showed longer grains and increased glume cell length, a loose plant architecture, and drooping leaves. Our results indicate that HOS59 is a negative regulator of the downstream genes, playing essential roles in agronomic traits such as grain size and architecture.