Genome-wide analysis of the S-RLK gene family and functional characterization of OsNRS1 in 9311 and Nipponbare.

S-domain receptor-like kinases (S-RLKs) represent a typical RLK subfamily, which plays key roles in various biological processes in plants. However, the genome-wide evolutionary and functional differentiation of this family remains unclear in rice. In the present study, a comprehensive computational analysis was employed and identified 109 S-RLKs in 9311 genome and 103 S-RLKs in Nipponbare (Nip) genome. The S-RLKs were unevenly distributed across 12 chromosomes. Bioinformatics analysis indicate large-scale gene duplication and family expansion may be the main driving forces for the expansion of S-RLK family members. Although the S-RLKs are highly conserved between the two subspecies, it remains unknown whether these members have undergone functional differentiation during long-term evolution. Given the differences of roots and nitrogen (N) utilization in 9311 and Nip, we focused on the S-RLKs which exhibit different expressions in roots. OsNRS1 (Nitrogen-responsive Root S-domain kinase 1) was selected due to its expression in the roots of 9311 notably more than that in Nip. Phenotypic analysis showed that OsNRS1 CRISPR/Cas9 mutants in 9311 significantly inhibited the length of primary root and total root, and N accumulation, whereas OsNRS1 CRISPR/Cas9 mutants in Nip showed significant functional divergence. In-depth research revealed that these functional divergence of OsNRS1 may be caused by the sequence variation of an auxin response element AuxRR in its promoter. Collectively, this study not only provides novel insights into the evolution of the S-RLK gene family, but also identifies OsNRS1 as a potential key target for the genetic improvement of root and N utilization in rice.