Genome-wide analysis of RWP-RK transcription factor family reveals its roles in nitrogen response in rice (Oryza sativa

Mei Du^1,2,3*Ziwen Guo²Siyu Gong²Liangwei Xu²

• ¹Hainan University, Haikou, China
• ²Yazhouwan National Laboratory, Sanya, China
• ³Hainan Seed Innovation Research Institute, Sanya, China

The RWP-RK transcription factor family plays a pivotal role in nitrogen response and gametophyte development, yet its evolutionary relationships and functional characteristics in rice are not fully understood. In this study, 13 RWP-RK genes (14 proteins, including two alternative splicing variants of OsNLP5) were identified in rice, with uneven distribution across 8 of the 12 chromosomes. Phylogenetic analysis divided these proteins into four groups: groups 1, 2, and 3 were classified as NLP subfamily members, while group 4 was assigned to the RKD subfamily. The NLP subfamily consists of seven proteins containing both RWP-RK and PB1 domains, while the RKD subfamily comprises seven proteins with only the RWP-RK domain. Gene and protein structure analysis found that NLP genes generally have longer CDS, more exons, and larger proteins than RKD genes. Collinearity analysis suggested that the RWP-RK genes in rice and Arabidopsis share a common ancestor and have undergone gene recombination and species-specific divergence. Promoter analysis identified abundant cis-elements responsive to hormones and stresses in OsRWP-RK promoters. Expression analysis demonstrated that OsNLP genes are widely expressed in all tissues, whereas OsRKD genes are more active in reproductive organs. Additionally, the expression levels of all OsNLP genes and 3 OsRKDs (OsRKD1, OsRKD3, OsRKD5) fluctuated after nitrogen-starved seedlings were transferred to a nitrogen-containing environment. This study enhances our understanding of OsRWP-RK transcription factors and provides a foundation for future research on their regulatory roles in nitrogen response and gametophyte development in rice.