Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Abstract

BackgroundWRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown.ResultsA total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes.ConclusionsThis was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2677-3) contains supplementary material, which is available to authorized users.

Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

“…Further analysis of the proso millet transcriptome using computational prediction identified 32 PmWRKY genes involved in abiotic stress response. In plants, the WRKY genes are key transcription factors regulating various physiological processes, including plant growth, development, and stress response (Yue et al, 2016b). In addition to detecting differentially expressed genes, Yue et al (2016a) also identified 35,000 SSR and 406,000 SNP loci which can be developed as molecular markers.…”

“…Previously, inadequate molecular markers combined with the challenges of a tetraploid genome such as inconsistent meiotic processes, allelic and non-allelic combinations, and poor correlation between genotype and phenotype (Saha et al, 2016) have made it difficult to conduct genetic and genomic studies in proso millet. However, with the discovery of SNPs by GBS (Rajput et al, 2016) and the identification of differentially expressed genes and thousands of SSR and SNP loci by transcriptome analysis (Yue et al, 2016a,b), a considerable number of molecular markers are currently available for genomic research in proso millet.…”

“…With the discovery of thousands of unigenes, SSR and SNP loci by transcriptome analysis (Yue et al, 2016a,b), genetic linkage analysis, genome-wide association studies and genomic selection in proso millet are now distinct possibilities. Marker-assisted selection can also be incorporated into proso millet breeding programs once the SNPs flanking QTLs have been confirmed and validated (Rajput et al, 2016).…”

Responses of Different Panicum miliaceum L. Genotypes to Saline and Water Stress in a Marginal Mediterranean Environment

“…In Europe, it is cultivated in 61,233 ha, with an average grain yield of 1.9 Mg ha −1 [37]. This crop has many desirable agronomic traits, including a short growing season (60-90 days), and low nutrient and water requirements, as well as excellent tolerance to salt, drought, high temperature, and other extreme conditions [38]. For these reasons, proso millet can be also cultivated in marginal lands where other cereals do not fully succeed [39].…”

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

“…Morus005757 shows significant up-regulation in response to dehydration stress, salinity stress, and SA and ABA (Abscisic acid) treatments [27]. Similar results were also found in wheat, common bean [28], grape [29], pineapple [30], soybean [31], moso bamboo [32], Caragana intermedia [33], peanut [34], and broomcorn millet [35]. These observations suggest that studying the WRKY gene families may provide valuable insights into the mechanism underlying abiotic stress tolerance in plants.…”