Identification of the Group III WRKY Subfamily and the Functional Analysis of GhWRKY53 in Gossypium hirsutum L

Aspartyl proteases identified as candidate genes of a fiber length QTL, qFLD05, that regulates fiber length in cotton (Gossypium hirsutum L.)

KEY MESSAGE

GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.

WRKY transcription factor family in lettuce plant (Lactuca sativa): Genome-wide characterization, chromosome location, phylogeny structures, and expression patterns

WRKY transcription factors (TF) have been identified in many plant species and play critical roles in multiple stages of growth and development and under various stress conditions. As one of the most popular vegetable crops, asparagus lettuce has important medicinal and nutritional value. However, study of WRKY TFs family in asparagus lettuce is limited. With the lettuce (Lactuca sativa L.) genome publication, we identified 76 WRKY TFs and analyzed structural characteristics, phylogenetic relationships, chromosomal distribution, interaction network, and expression profiles. The 76 LsWRKY TFs were phylogenetically classified as Groups I, II (IIa-IIe), and III. Cis element analysis revealed complex regulatory relationships of LsWRKY genes in response to different biological progresses. Interaction network analysis indicated that LsWRKY TFs could interact with other proteins, such as SIB (sigma factor binding protein), WRKY TFs, and MPK. The WRKYIII subfamily genes showed different expression patterns during the progress of asparagus lettuce stem enlargement. According to qRT-PCR analysis, abiotic stresses (drought, salt, low temperature, and high temperature) and phytohormone treatment could induce specific LsWRKYIII gene expression. These results will provide systematic and comprehensive information on LsWRKY TFs and lay the foundation for further clarification of the regulatory mechanism of LsWRKY, especially LsWRKYIII TFs, involved in stress response and the progress of plant growth and development.

Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development

Gossypium hirsutum and Gossypium barbadense are the widely cultivated tetraploid cottons around the world, which evolved great differences in the fiber yield and quality due to the independent domestication process. To reveal the genetic basis of the difference, we integrated 90 samples from ten time points during the fiber developmental period for investigating the dynamics of gene expression changes associated with fiber in G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 and acc. 3-79. Globally, 44,484 genes expressed in all three cultivars account for 61.14% of the total genes. About 61.39% (N = 3,412) of the cotton transcription factors were involved in fiber development, which consisted of 58 cotton TF families. The differential analysis of intra- and interspecies showed that 3 DPA had more expression changes. To discover the genes with temporally changed expression profiles during the whole fiber development, 1,850 genes predominantly expressed in G. hirsutum and 1,050 in G. barbadense were identified, respectively. Based on the weighted gene co-expression network and time-course analysis, several candidate genes, mainly involved in the secondary cell wall synthesis and phytohormones, were identified in this study, underlying possibly the transcriptional regulation and molecular mechanisms of the fiber quality differences between G. barbadense and G. hirsutum. The quantitative real-time PCR validation of the candidate genes was consistent with the RNA-seq data. Our study provides a strong rationale for the analysis of gene function and breeding of high-quality cotton.

Different Cis-Regulatory Elements Control the Tissue-Specific Contribution of Plastid ω-3 Desaturases to Wounding and Hormone Responses

Trienoic fatty acids are essential constituents of biomembranes and precursors of jasmonates involved in plant defense responses. Two ω-3 desaturases, AtFAD7 and AtFAD8, synthetize trienoic fatty acids in the plastid. Promoter:GUS and mutagenesis analysis was used to identify cis-elements controlling AtFAD7 and AtFAD8 basal expression and their response to hormones or wounding. AtFAD7 promoter GUS activity was much higher than that of AtFAD8 in leaves, with specific AtFAD7 expression in the flower stamen and pistil and root meristem and vasculature. This specific tissue and organ expression of AtFAD7 was controlled by different cis-elements. Thus, promoter deletion and mutagenesis analysis indicated that WRKY proteins might be essential for basal expression of AtFAD7 in leaves. Two MYB target sequences present in the AtFAD7 promoter might be responsible for its expression in the flower stamen and stigma of the pistil and in the root meristem, and for the AtFAD7 wound-specific response. Two MYB target sequences detected in the distal region of the AtFAD8 gene promoter seemed to negatively control AtFAD8 expression, particularly in true leaves and flowers, suggesting that MYB transcription factors act as repressors of AtFAD8 gene basal expression, modulating the different relative abundance of both plastid ω-3 desaturases at the transcriptional level. Our data showed that the two ABA repression sequences detected in the AtFAD7 promoter were functional, suggesting an ABA-dependent mechanism involved in the different regulation of both ω-3 plastid desaturases. These results reveal the implication of different signaling pathways for the concerted regulation of trienoic fatty acid content in Arabidopsis.