Comprehensive identification and systematical characterization of BRX gene family and the functional of GhBRXL5A in response to salt stress.

BACKGROUND: BRVIS RADIX (BRX) family is a small gene family with the highly conserved plant-specific BRX domains, which plays important roles in plant development and response to abiotic stress. Although BRX protein has been studied in other plants, the biological function of cotton BRX-like (BRXL) gene family is still elusive. RESULT: In this study, a total of 36 BRXL genes were identified in four cotton species. Whole genome or segmental duplications played the main role in the expansion of GhBRXL gene family during evolutionary process in cotton. These BRXL genes were clustered into 2 groups, α and ß, in which structural and functional conservation within same groups but divergence among different groups were found. Promoter analysis indicated that cis-elements were associated with the phytohormone regulatory networks and the response to abiotic stress. Transcriptomic analysis indicated that GhBRXL2A/2D and GhBRXL5A/5D were up/down-regulated in response to the different stress. Silencing of GhBRXL5A gene via virus-induced gene silencing (VIGS) improved salt tolerance in cotton plants. Furthermore, yeast two hybrid analysis suggested homotypic and heterotypic interactions between GhBRXL1A and GhBRXL5D. CONCLUSIONS: Overall, these results provide useful and valuable information for understanding the evolution of cotton GhBRXL genes and their functions in salt stress.

Virus-Induced Gene Silencing (VIGS): A Powerful Tool for Crop Improvement and Its Advancement towards Epigenetics.

Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technology that has evolved into an indispensable approach for analyzing the function of genes. It downregulates endogenous genes by utilizing the posttranscriptional gene silencing (PTGS) machinery of plants to prevent systemic viral infections. Based on recent advances, VIGS can now be used as a high-throughput tool that induces heritable epigenetic modifications in plants through the viral genome by transiently knocking down targeted gene expression. As a result of the progression of DNA methylation induced by VIGS, new stable genotypes with desired traits are being developed in plants. In plants, RNA-directed DNA methylation (RdDM) is a mechanism where epigenetic modifiers are guided to target loci by small RNAs, which play a major role in the silencing of the target gene. In this review, we described the molecular mechanisms of DNA and RNA-based viral vectors and the knowledge obtained through altering the genes in the studied plants that are not usually accessible to transgenic techniques. We showed how VIGS-induced gene silencing can be used to characterize transgenerational gene function(s) and altered epigenetic marks, which can improve future plant breeding programs.

Genome-Wide Identification, Characterization, and Transcriptomic Analysis of the Cyclin Gene Family in Brassica rapa.

Cyclins are involved in cell division and proliferation by activating enzymes required for the cell cycle progression. Our genome-wide analysis identified 76 cyclin genes in Brassica rapa, which were divided into nine different types (A-, B-, C-, D-, H-, L-, P-, T-, and SDS-type). Cyclin genes were unevenly scattered on all chromosomes, with a maximum of 10 on A08 and a minimum of 2 on A04. The gene structure and conserved motif analysis showed that the cyclins which belonged to the same type or subgroup have a comparable intron/exon pattern or motif. A total of 14 collinear gene pairs suggested that the B. rapa cyclin genes experienced a mass of segmental duplication. The Ka/Ks analysis revealed that the Brcyclin gene family has undergone an extensive purifying pressure. By analyzing the cis-elements in the promoters, we identified 11 cis-elements and five of them are related to the hormone response. We observed 48 potential miRNAs targeting 44 Brcyclin genes, which highlighted the involvement of miRNAs in the regulation of cyclin genes. An association analysis between the leaf size and SNPs in mutants and a transcriptome analysis of two Chinese cabbage-cabbage translocation lines also showed that the Brcyclin gene family was involved in the development of the leaves. The functional characterization of the B. rapa cyclin gene family will provide the foundation for future physiological and genetic studies in the regulation of leaf growth.

Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L.

BACKGROUND: Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies. AIM OF REVIEW: Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development. KEY SCIENTIFIC CONCEPTS OF REVIEW: Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.

Transgenerational impact of climatic changes on cotton production.

Changing climatic conditions are an increasing threat to cotton production worldwide. There is a need to develop multiple stress-tolerant cotton germplasms that can adapt to a wide range of environments. For this purpose, 30 cotton genotypes were evaluated for two years under drought (D), heat (H), and drought + heat stresses (DH) under field conditions. Results indicated that plant height, number of bolls, boll weight, seed cotton yield, fiber fineness, fiber strength, fiber length, K+, K+/Na+, relative water contents (RWC), chlorophyll a and b, carotenoids, and total soluble proteins got reduced under D and H and were lowest under DH, whereas superoxidase dismutase (SOD), H2O2, Na+, GOT%, total phenolic contents, ascorbate, and flavonoids got increased for consecutive years. Correlation studies indicated that there was a positive correlation between most of the traits, but a negative correlation with H2O2 and Na+ ions. PCA and clustering analysis indicated that MNH-786, KAHKSHAN, CEMB-33, MS-71, FH-142, NIAB-820, CRS-2007, and FH-312 consistently performed better than other genotypes for most traits under stress conditions. Identified genotypes can be utilized in the future cotton breeding program to develop high-yielding, climate change-resilient cotton.

HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress.

Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.