Maize factors ZmUBP15, ZmUBP16 and ZmUBP19 play important roles for plants to tolerance the cadmium stress and salt stress

Genome-wide identification and expression analysis of Ubiquitin-specific protease gene family in maize (Zea mays L.)

BACKGROUND

Ubiquitin-specific proteases (UBPs) are a large family of deubiquitinating enzymes (DUBs). They are widespread in plants and are critical for plant growth, development, and response to external stresses. However, there are few studies on the functional characteristics of the UBP gene family in the important staple crop, maize (Zea mays L.).

RESULTS

In this study, we performed a bioinformatic analysis of the entire maize genome and identified 45 UBP genes. Phylogenetic analysis indicated that 45 ZmUBP genes can be divided into 15 subfamilies. Analysis of evolutionary patterns and divergence levels indicated that ZmUBP genes were present before the isolation of dicotyledons, were highly conserved and subjected to purifying selection during evolution. Most ZmUBP genes exhibited different expression levels in different tissues and developmental stages. Based on transcriptome data and promoter element analysis, we selected eight ZmUBP genes whose promoters contained a large number of plant hormones and stress response elements and were up-regulated under different abiotic stresses for RT-qPCR analysis, results showed that these genes responded to abiotic stresses and phytohormones to varying degrees, indicating that they play important roles in plant growth and stress response.

CONCLUSIONS

In this study, the structure, location and evolutionary relationship of maize UBP gene family members were analyzed for the first time, and the ZmUBP genes that may be involved in stress response and plant growth were identified by combining promoter element analysis, transcriptome data and RT-qPCR analysis. This study informs research on the involvement of maize deubiquitination in stress response.

Comparative time-course transcriptome analysis of two contrasting alfalfa (Medicago sativa L.) genotypes reveals tolerance mechanisms to salt stress

Salt stress is a major abiotic stress affecting plant growth and crop yield. For the successful cultivation of alfalfa (Medicago sativa L.), a key legume forage, in saline-affected areas, it's essential to explore genetic modifications to improve salt-tolerance.Transcriptome assay of two comparative alfalfa genotypes, Adina and Zhaodong, following a 4 h and 8 h's 300 mM NaCl treatment was conducted in this study in order to investigate the molecular mechanism in alfalfa under salt stress conditions. Results showed that we obtained 875,023,571 transcripts and 662,765,594 unigenes were abtained from the sequenced libraries, and 520,091 assembled unigenes were annotated in at least one database. Among them, we identified 1,636 differentially expression genes (DEGs) in Adina, of which 1,426 were up-regulated and 210 down-regulated, and 1,295 DEGs in Zhaodong, of which 565 were up-regulated and 730 down-regulated. GO annotations and KEGG pathway enrichments of the DEGs based on RNA-seq data indicated that DEGs were involved in (1) ion and membrane homeostasis, including ABC transporter, CLC, NCX, and NHX; (2) Ca²⁺ sensing and transduction, including BK channel, EF-hand domain, and calmodulin binding protein; (3) phytohormone signaling and regulation, including TPR, FBP, LRR, and PP2C; (4) transcription factors, including zinc finger proteins, YABBY, and SBP-box; (5) antioxidation process, including GST, PYROX, and ALDH; (6) post-translational modification, including UCH, ubiquitin family, GT, MT and SOT. The functional roles of DEGs could explain the variations in salt tolerance performance observed between the two alfalfa genotypes Adina and Zhaodong. Our study widens the understanding of the sophisticated molecular response and tolerance mechanism to salt stress, providing novel insights on candidate genes and pathways for genetic modification involved in salt stress adaptation in alfalfa.

WGCNA Analysis Revealed the Hub Genes Related to Soil Cadmium Stress in Maize Kernel (Zea mays L.)

Soil contamination by heavy metals has become a prevalent topic due to their widespread release from industry, agriculture, and other human activities. Great progress has been made in elucidating the uptake and translocation of cadmium (Cd) accumulation in rice. However, there is still little known about corresponding progress in maize. In the current study, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) of maize immature kernel related to Cd stress. In total, 55, 92, 22, and 542 DEGs responsive to high cadmium concentration soil were identified between XNY22-CHS-8 vs. XNY22-YA-8, XNY22-CHS-24 vs. XNY22-YA-24, XNY27-CHS-8 vs. XNY27-YA-8, and XNY27-CHS-24 vs. XNY27-YA-24, respectively. The weighted gene co-expression network analysis (WGCNA) categorized the 9599 Cd stress-responsive hub genes into 37 different gene network modules. Combining the hub genes and DEGs, we obtained 71 candidate genes. Gene Ontology (GO) enrichment analysis of genes in the greenyellow module in XNY27-YA-24 and connectivity genes of these 71 candidate hub genes showed that the responses to metal ion, inorganic substance, abiotic stimulus, hydrogen peroxide, oxidative stress, stimulus, and other processes were enrichment. Moreover, five candidate genes that were responsive to Cd stress in maize kernel were detected. These results provided the putative key genes and pathways to response to Cd stress in maize kernel, and a useful dataset for unraveling the underlying mechanism of Cd accumulation in maize kernel.

ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17

Background

The auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize.

Results

In this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5.

Conclusions

Taken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.

Cadmium in Cereal Crops: Uptake and Transport Mechanisms and Minimizing Strategies

Cadmium (Cd) contamination in soils and accumulation in cereal grains have posed food security risks and serious health concerns worldwide. Understanding the Cd transport process and its management for minimizing Cd accumulation in cereals may help to improve crop growth and grain quality. In this review, we summarize Cd uptake, translocation, and accumulation mechanisms in cereal crops and discuss efficient measures to reduce Cd uptake as well as potential remediation strategies, including the applications of plant growth regulators, microbes, nanoparticles, and cropping systems and developing low-Cd grain cultivars by CRISPR/Cas9. In addition, miRNAs modulate Cd translocation, and accumulation in crops through the regulation of their target genes was revealed. Combined use of multiple remediation methods may successfully decrease Cd concentrations in cereals. The findings in this review provide some insights into innovative and applicable approaches for reducing Cd accumulation in cereal grains and sustainable management of Cd-contaminated paddy fields.

Fruit economic characteristics and yields of 40 superior Camellia oleifera Abel plants in the low-hot valley area of Guizhou Province, China

In this study, we assessed 26 economic characteristics and yields of the mature fruit of 40 superior Camellia oleifera Abel plants grown at the C. oleifera germplasm resource nursery in the low-hot valley area of Southwest Zuizhou, China, using principal component analysis (PCA). Correlations among the characteristics and the variability of the plants in these characteristics were also analyzed. Out of the 26 characteristics, 16 primary economic characteristics were selected for comprehensive assessment, based on the results of which the plants were ordered to obtain excellent C. oleifera germplasms. The data were subjected to PCA, and the 16 characteristics were integrated into 6 independent comprehensive indices, which included PV1 (single-fruit weight), PV2 (pericarp thickness), PV3 (seed rate), PV4 (total unsaturated fatty acids), PV5 (iodine value) and PV6 (dry seed rate). Then, the sum of the products of the contribution rates of the components and components scores was taken as the comprehensive score of each superior plant. In C. oleifera grown in the low-hot valley area, the oil yield exhibited very significant positive correlations with the dry seed rate and kernel rate but a very significant negative correlation with the 100-seed weight. The dry seed rate exhibited very significant negative correlations with the fruit diameter and fresh seed rate. Among the 26 characteristics, the variations of the acid value, peroxide value, number of fertile seeds, 100-seed weight and single-fruit weight were great; those of the fruit diameter, fruit height, kernel yield, oleic acid and total unsaturated fatty acid were small, showing strong genetic stability. According to the obtained comprehensive scores, the top 10 plants were ordered as follows: CY-6 > CY-13 > CY-31 > CY-11 > CY-16 > CY-22 > CY-28 > CY-23 > CY-24 > CY-29. This result was basically consistent with the ranking result according to the average yield per unit crown width within five years. In the low-hot valley area of Guizhou, C. oleifera exhibits excellent performance in single-fruit weight, total unsaturated fatty acids and kernel rate, 6 characteristics, i.e., acid value, peroxide value, single-fruit weight, the number of fertile seeds, 100-seed weight and α-linolenic acid possess high breeding potentials.

Sustainable Intensification of Maize in the Industrial Revolution: Potential of Nitrifying Bacteria and Archaea

Sustainable intensification is a means that proffer a solution to the increasing demand for food without degrading agricultural land. Maize is one of the most important crops in the industrial revolution era, there is a need for its sustainable intensification. This review discusses the role of maize in the industrial revolution, progress toward sustainable production, and the potential of nitrifying bacteria and archaea to achieve sustainable intensification. The era of the industrial revolution (IR) uses biotechnology which has proven to be the most environmentally friendly choice to improve crop yield and nutrients. Scientific research and the global economy have benefited from maize and maize products which are vast. Research on plant growth-promoting microorganisms is on the increase. One of the ways they carry out their function is by assisting in the cycling of geochemical, thus making nutrients available for plant growth. Nitrifying bacteria and archaea are the engineers of the nitrification process that produce nitrogen in forms accessible to plants. They have been identified in the rhizosphere of many crops, including maize, and have been used as biofertilizers. This study's findings could help in the development of microbial inoculum, which could be used to replace synthetic fertilizer and achieve sustainable intensification of maize production during the industrial revolution.

Integrative analysis of transcriptome and proteome provides insights into adaptation to cadmium stress in Sedum plumbizincicola

Sedum plumbizincicola, a cadmium (Cd) hyperaccumulating herbaceous plant, can accumulate large amounts of Cd in the above-ground tissues without being poisoned. However, the molecular mechanisms regulating the processes are not fully understood. In this study, Transcriptional and proteomic analyses were integrated to investigate the response of S. plumbizincicola plants to Cd stress and to identify key pathways that are potentially responsible for Cd tolerance and accumulation. A total of 630 DAPs (differentially abundant proteins, using fold change >1.5 and adjusted p-value <0.05) were identified from Tandem Mass Tag (TMT)- based quantitative proteomic profiling, which were enriched in processes including phenylpropanoid biosynthesis, protein processing in endoplasmic reticulum, and biosynthesis of secondary metabolites. Combined with the previous transcriptomic study, 209 genes and their corresponding proteins showed the identical expression pattern. The identified genes/proteins revealed the potential roles of several metabolism pathways, including phenylpropanoid biosynthesis, oxidative phosphorylation, phagosome, and glutathione metabolism, in mediating Cd tolerance and accumulation. Lignin staining and Cd accumulation assay of the transgenic lines over-expressing a selected Cd up-regulated gene SpFAOMT (Flavonoid 3',5'-methyltransferase) showed its functions in adapting to Cd stress, and provided insight into its role in lignin biosynthesis and Cd accumulation in S. plumbizincicola during Cd stress.

Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.)

BACKGROUND

The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium.

RESULTS

A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress.

CONCLUSIONS

Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.

Maize bHLH55 functions positively in salt tolerance through modulation of AsA biosynthesis by directly regulating GDP-mannose pathway genes

Ascorbic acid (AsA) is an antioxidant and enzyme co-factor that is vital to plant development and abiotic stress tolerance. However, the regulation mechanisms of AsA biosynthesis in plants remain poorly understood. Here, we report a basic helix-loop-helix 55 (ZmbHLH55) transcription factor that regulates AsA biosynthesis in maize. Analysis of publicly available transcriptomic data revealed that ZmbHLH55 is co-expressed with several genes of the GDP-mannose pathway. Experimental data showed that ZmbHLH55 forms homodimers localized to the cell nuclei, and it exhibits DNA binding and transactivation activity in yeast. Under salt stress conditions, knock down mutant (zmbhlh55) in maize accumulated lower levels of AsA compared with wild type, accompanied by lower antioxidant enzymes activity, shorter root length, and higher malondialdehyde (MDA) level. Gene expression data from the WT and zmbhlh55 mutant, showed that ZmbHLH55 positively regulates the expression of ZmPGI2, ZmGME1, and ZmGLDH, but negatively regulates ZmGMP1 and ZmGGP. Furthermore, ZmbHLH55-overexpressing Arabidopsis, under salt conditions, showed higher AsA levels, increased rates of germination, and elevated antioxidant enzyme activities. In conclusion, these results have identified previously unknown regulation mechanisms for AsA biosynthesis, indicating that ZmbHLH55 may be a potential candidate to enhance plant salt stress tolerance in the future.

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

BACKGROUND

Lead (Pb) pollution in soil has become one of the major environmental threats to plant growth and human health. Safe utilization of Pb contaminated soil by phytoremediation require Pb-tolerant rapeseed (Brassica napus L.) accessions. However, breeding of new B. napus cultivars tolerance to Pb stress has been restricted by limited knowledge on molecular mechanisms involved in Pb tolerance. This work was carried out to identify genetic loci related to Pb tolerance during seedling establishment in rapeseed.

RESULTS

Pb tolerance, which was assessed by quantifying radicle length (RL) under 0 or 100 mg/L Pb stress condition, shown an extensive variation in 472 worldwide-collected rapeseed accessions. Based on the criterion of relative RL > 80%, six Pb-tolerant genotypes were selected. Four quantitative trait loci (QTLs) associated with Pb tolerance were identified by Genome-wide association study. The expression level of nine promising candidate genes, including GSTUs, BCATs, UBP13, TBR and HIPP01, located in these four QTL regions, were significantly higher or induced by Pb in Pb-tolerant accessions in comparison to Pb-sensitive accessions.

CONCLUSION

To our knowledge, this is the first study on Pb-tolerant germplasms and genomic loci in B. napus. The findings can provide valuable genetic resources for the breeding of Pb-tolerant B. napus cultivars and understanding of Pb tolerance mechanism in Brassica species.

SbMYB15 transcription factor mitigates cadmium and nickel stress in transgenic tobacco by limiting uptake and modulating antioxidative defence system

Plants require different inorganic minerals in an appropriate amount for growth; however, imbalance can limit growth and productivity. Heavy metal accumulation causes toxicity and generates signalling crosstalk with reactive oxygen species (ROS), phytohormones, genes and transcription factors (TFs). The MYB (myeloblastoma) TFs participate in plant processes such as metabolism, development, cell fate, hormone pathways and responses to stresses. This is the first report towards characterisation of R2R3-type MYB TF, SbMYB15, from succulent halophyte Salicornia brachiata Roxb. for heavy metal tolerance. The SbMYB15 showed >5-fold increased transcript expression in the presence of CdCl2 and NiCl2•6H2O. The constitutive overexpression of SbMYB15 conferred cadmium and nickel tolerance in transgenic tobacco, with improved growth and chlorophyll content. Further, the transgenics showed reduced generation of reactive oxygen species (H2O2 and O2•-) as compared with the wild-type (WT) with both Cd2+ and Ni2+ stress. Transgenics also showed low uptake of heavy metal ions, increased scavenging activity of the antioxidative enzymes (CAT and SOD) and higher transcript expression of antioxidative genes (CAT1 and MnSOD). Thus, the present study signifies that SbMYB15 can be deployed for developing heavy metal tolerance in crop plants via genetic engineering.