Variations in the Structure and Evolution of Rice WRKY Genes in Indica and Japonica Genotypes and their Co-expression Network in Mediating Disease Resistance:
15 Jun 2019-Evolutionary Bioinformatics (Evol Bioinform Online)-Vol. 15, pp 1176934319857720-1176934319857720
TL;DR: Variations exist in the structure and evolution of WRKY genes among indica and japonica genotypes which have important implications in their differential roles including disease resistance.
Abstract: WRKY transcription factor (TF) family regulates many functions in plant growth and development and also during biotic and abiotic stress. In this study, 101 WRKY TF gene models in indica and japonica rice were used to conduct evolutionary analysis, gene structure analysis, and motif composition. Co-expression analysis was carried out first by selecting the differentially expressing genes that showed a significant change in response to the pathogens from Rice Oligonucleotide Array Database (ROAD). About 82 genes showed responses to infection by Magnaporthe oryzae or Xanthomonas oryzae pv. oryzae. Co-expression gene network was constructed using direct neighborhood and context associated inbuilt mode in RiceNetv2 tool. Only 41 genes showed interaction with 2299 non-WRKY genes. Variations exist in the structure and evolution of WRKY genes among indica and japonica genotypes which have important implications in their differential roles including disease resistance. WRKY genes mediate a complex networking and co-express along with other WRKY and non-WRKY genes to mediate resistance against fungal and bacterial pathogens in rice.
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TL;DR: Functional characterization of identified PgWRKYs can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions.
Abstract: Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF family are well known for their role in plant development, phytohormone signaling and developing resistance against biotic or abiotic stresses. In this study, we performed a genome-wide screening to identify and analyze the WRKY TFs in pearl millet (Pennisetum glaucum; PgWRKY), which is one of the most widely grown cereal crops in the semi-arid regions. A total number of 97 putative PgWRKY proteins were identified and classified into three major Groups (I-III) based on the presence of WRKY DNA binding domain and zinc-finger motif structures. Members of Group II have been further subdivided into five subgroups (IIa-IIe) based on the phylogenetic analysis. In-silico analysis of PgWRKYs revealed the presence of various cis-regulatory elements in their promoter region like ABRE, DRE, ERE, EIRE, Dof, AUXRR, G-box, etc., suggesting their probable involvement in growth, development and stress responses of pearl millet. Chromosomal mapping evidenced uneven distribution of identified 97 PgWRKY genes across all the seven chromosomes of pearl millet. Synteny analysis of PgWRKYs established their orthologous and paralogous relationship among the WRKY gene family of Arabidopsis thaliana, Oryza sativa and Setaria italica. Gene ontology (GO) annotation functionally categorized these PgWRKYs under cellular components, molecular functions and biological processes. Further, the differential expression pattern of PgWRKYs was noticed in different tissues (leaf, stem, root) and under both drought and salt stress conditions. The expression pattern of PgWRKY33, PgWRKY62 and PgWRKY65 indicates their probable involvement in both dehydration and salinity stress responses in pearl millet. Functional characterization of identified PgWRKYs can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions. Further, these PgWRKYs can be employed in genome editing for millet crop improvement.
44 citations
TL;DR: In this article, a novel 'SAPK10-WRKY87-ABF1' biological pathway was identified, through which they harmoniously enhanced drought and salinity tolerance.
14 citations
TL;DR: In this paper, transgenic rice plants were generated with constitutive promoters (pZmUbi::ZmG1 and p35S:: ZmG2), individually or simultaneously, with maize promoters.
Abstract: Chloroplasts are the sites for photosynthesis, and two Golden2-like factors act as transcriptional activators of chloroplast development in rice (Oryza sativa L.) and maize (Zea mays L.). Rice OsGLK1 and OsGLK2 are orthologous to maize ZmGLK1 (ZmG1) and ZmGLK2 (ZmG2), respectively. However, while rice OsGLK1 and OsGLK2 act redundantly to regulate chloroplast development in mesophyll cells, maize ZmG1 and ZmG2 are functionally specialized and expressed in different cell-specific manners. To boost rice chloroplast development and photosynthesis, we generated transgenic rice plants overexpressing ZmG1 and ZmG2, individually or simultaneously, with constitutive promoters (pZmUbi::ZmG1 and p35S::ZmG2) or maize promoters (pZmG1::ZmG1, pZmG2::ZmG2, and pZmG1::ZmG1/pZmG2::ZmG2). Both ZmG1 and ZmG2 genes were highly expressed in transgenic rice leaves. Moreover, ZmG1 and ZmG2 showed coordinated expression in pZmG1::ZmG1/pZmG2::ZmG2 plants. All GLK transgenic plants had higher chlorophyll and protein contents, Rubisco activities and photosynthetic rates per unit leaf area in flag leaves. However, the highest grain yields occurred when maize promoters were used; pZmG1::ZmG1, pZmG2::ZmG2 and pZmG1::ZmG1/pZmG2::ZmG2 transgenic plants showed increases in grain yield by 51%, 47% and 70%, respectively. In contrast, the pZmUbi::ZmG1 plant produced smaller seeds without yield increases. Transcriptome analysis indicated that maize GLKs act as master regulators promoting the expression of both photosynthesis-related and stress-responsive regulatory genes in both rice shoot and root. Thus, by promoting these important functions under the control of their own promoters, maize GLK1 and GLK2 genes together dramatically improved rice photosynthetic performance and productivity. A similar approach can potentially improve the productivity of many other crops.
14 citations
TL;DR: This study provides a new insight on the evolution of the WRKY gene family in O. rufipogon and will help further functional characterization of candidate genes toward wild rice germplasm exploration for rice genetic improvement programs.
Abstract: WRKY gene family is widespread in plants, which is of significance in determining plant development and stress response. Although WRKY transcription factors have been widely characterized in many plants, a genome-wide analysis of the WRKY gene family is still lacking in Oryza rufipogon. In this study, we identified 101 O. rufipogon WRKY (OrWRKY) transcription factors, which were further classified into eight subgroups. Phylogenetic analysis showed that OrWRKY transcription factors were supported by highly conserved motifs and gene structures. Chromosomal distribution of OrWRKYs indicated that most genes were dispersed on all twelve chromosomes, especially enriched on Chromosome 1. Syntenic analysis revealed that 69 (68.3%) genes were derived from either segmental (49) or tandem duplication events (20), suggesting a essential role of segmental duplications. We characterized a total of 39 orthologous gene pairs between O. sativa ssp. japonica WRKY (OsjWRKY) and OrWRKY. We then performed quantitative real-time polymerase chain reaction (qPCR) experiments to validate tissue-specific and differential expression of the OrWRKYs. We also investigated corresponsive expression of the OrWRKYs in response to salt stresses in leaves and roots. This study gains a new insight on the evolution of the OrWRKYs and will help further functional characterization of candidate genes towards wild rice germplasm exploration for rice genetic improvement.
14 citations
Cites background from "Variations in the Structure and Evo..."
...Except for plant development, WRKY genes also play important roles in biotic and abiotic stress responses including fungal-induced defense programs and responses to heat/cold, drought, and salt stresses (Raineri et al., 2015; Yang et al., 2018; Jimmy and Babu, 2019)....
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13 citations
References
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TL;DR: The Molecular Evolutionary Genetics Analysis (MEGA) software as discussed by the authors provides facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, including the inference of timetrees.
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