Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Abstract

Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1–8 and 1–10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

CaIAA2‐CaARF9 module mediates the trade‐off between pepper growth and immunity

“…Auxin response factors (ARFs), the key elements in auxin signalling (Guilfoyle and Hagen, 2007 ; Li et al ., 2023 ; Simonini et al ., 2017 ), have been frequently found to play roles in both plant growth and immune responses to various pathogens, defence responses to abiotic stresses, and the trade‐off between plant growth and defence responses (Gilroy and Breen, 2022 ) in different plant species including potato (Kalsi et al ., 2022 ), tomato (Bouzroud et al ., 2018 ; El Mamoun et al ., 2023 ), wheat (Gidhi et al ., 2020 ), rice (Gu et al ., 2023 ; Qin et al ., 2020 ; Zhang et al ., 2020a ) and in sugarcane (Lin et al ., 2023 ). Among them, the potato StARF16 negatively regulates the expression of JA‐responsive StNPR1 upon necrotrophic pathogen infection (Kalsi et al ., 2022 ), while several tomato SlARF genes are activated in response to a variety of abiotic stresses (flooding, salt and drought) and biotic stress exposure to flagellin, yellow curl leave virus YCV and various bacteria agents, including Pseudomonas putida , Pseudomonas fluorescens , Pseudomonas syringae DC3000 and Agrobacterium tumefaciens (Bouzroud et al ., 2018 ).…”

“…Genome‐wide screening revealed the elevated expression of wheat TaARF1 and TaARF23 during leaf rust infection by Puccinia triticina (Gidhi et al ., 2020 ) and the differential expression of 10 sugarcane SpapARFs triggered by SA treatment and bacterial infection induced by Acidovorax avenae subsp. Avenae (Aaa) and Xanthomonas albilineans (Xa) (Lin et al ., 2023 ). In rice, OsARFs 11, 12 and 16, which interact with OsIAA10, differentially regulate plant resistance to rice dwarf virus (RDV) (Qin et al ., 2020 ).…”