Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

Abstract

BackgroundAbiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited.ResultsIn this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response.ConclusionsThese results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

Genome-Wide Identification and Functional Characterization of the Cation Proton Antiporter (CPA) Family Related to Salt Stress Response in Radish (Raphanus sativus L.)

“…R1 and R4 harbored the most RsCPA genes (Ten, 17.67%), followed by R5 and R6 (Eight, 13.37%), while R3 and R8 contained the least RsCPA genes (Two, 3.33%). Genome duplication events have facilitated the expansion of plant gene families, including whole-genome duplication (WGD)/segmental duplication, dispersed duplication (DD), tandem duplication (TD), proximal duplication (PD), and transposed duplication (TRD) [34][35][36]. The duplication types driving expansion of the RsCPA gene family was explored by Multiple Collinearity Scan toolkit (MCScanX).…”

“…In the process of plant evolution, duplicated genes could obtain new functions or segment existing functions to improve the adaptability of plants [34]. For instance, expansion of the RsHSF gene family was primarily driven by WGD or segmental duplication, which might be largely related with gene duplication [36]. It was previously reported that WGD and PDs event were mainly involved in the expansion of the CPA family in Pyrus bretschneideri [14].…”

Genome-Wide Analysis of the Heat Shock Transcription Factor Gene Family in Brassica juncea: Structure, Evolution, and Expression Profiles

“…For example, eight RsHSF genes in radish were highly expressed in leaves, roots, cortex, cambium, and xyloid. The expression pattern of 12 RsHSF genes was also changed under heat, salt, and heavy metals (Tang et al, 2019). Studies revealed the roles of HSFA1 in the osmosis, salt stress, and the oxidative stress response in Arabidopsis (Liu et al, 2011).…”

Variability of plant heat shock factors: regulation, interactions and functions.

“…Comprehensive expression profiling of HSF genes in a number of plant species revealed great variability during development and in response to a number of abiotic and biotic stresses. Diversity in HSF transcription was reported for Arabidopsis (Miller & Mittler, 2006, Swindell, Huebner & Weber, 2007, rice (Chauhan, Khurana, Agarwal & Khurana, 2011, Yang, Wang, Gao, Zhou, Zhang, Hu, Yuan, Liang & Xu, 2014, barley (Reddy, Kavi Kishor, Seiler, Kuhlmann, Eschen-Lippold, Lee, Reddy & Sreenivasulu, 2014), tomato (Fragkostefanakis et al , 2015), wheat (Agarwal & Khurana, 2019, Xue, Sadat, Drenth & McIntyre, 2014, Ye, Yang, Hu, Liu, Li, Zhang & Song, 2020, maize (Yang et al , 2014, Zhang, Li, Fu, Duan, Hu & Guo, 2020a, Brachipodium and sorghum (Nagaraju, Reddy, Kumar, Srivastava, Kishor & Rao, 2015, pepper (Guo, Lu, Zhai, Chai, Gong & Lu, 2015), radish (Tang, Xu, Wang, Cheng, Luo, Xie, Fan & Liu, 2019), physic nut (Zhang, Chen & Shi, 2020b), tea (Xu, Guo, Pang, Zhang, Kong & Liu, 2020), poplar (Liu, Hu & Zhang, 2019a) and chinese cabbage (Huang, Li, Wang, Xu, Huang, Wang, Ma & Xiong, 2015). For example soybean HSF genes were shown to respond diversely to drought or high temperatures.…”