Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress
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RESEARCH ARTICLE
Open Access
Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut Cuiling Yuan†, Chunjuan Li†, Xiaodong Lu†, Xiaobo Zhao, Caixia Yan, Juan Wang, Quanxi Sun*
and Shihua Shan*
Abstract Background: Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results: We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion: Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement. Keywords: Peanut, NAC gene family, Genome-wide characterization, RNA-seq, RT-qPCR, Salt stress, Drought stress
Background Cultivated peanut (Arachis hypogaea) is an important economic oil crop species worldwide and used to provide vegetable oil and proteins for human nutrition [1]. During the growth period of peanut plants, their yield is adversely affected by several environmental factors, such * Correspondence: [email protected]; [email protected] † Cuiling Yuan, Chunjuan Li and Xiaodong Lu contributed equally to this work. Shandong Peanut Research Institute, Qingdao 266100, China
as salt and drought stresses, which prevent plants from realizing their full genetic potential [2]. Screening stressresistant varieties is an important guarantee for achieving targets crop yields [3]. and the identification and utilization of resistant genes is fundamental for the production of new varieties. Transcription factors (TFs), which play roles in activating or repressing gene expression by binding to specific cis-acting elements within the promoters of target functiona
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