Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses

Understanding the role of P-type ATPases in regulating pollen fertility and development in pigeonpea

The P-type ATPase superfamily genes are the cation and phospholipid pumps that transport ions across the membranes by hydrolyzing ATP. They are involved in a diverse range of functions, including fundamental cellular events that occur during the growth of plants, especially in the reproductive organs. The present work has been undertaken to understand and characterize the P-type ATPases in the pigeonpea genome and their potential role in anther development and pollen fertility. A total of 59 P-type ATPases were predicted in the pigeonpea genome. The phylogenetic analysis classified the ATPases into five subfamilies: eleven P1B, eighteen P2A/B, fourteen P3A, fifteen P4, and one P5. Twenty-three pairs of P-type ATPases were tandemly duplicated, resulting in their expansion in the pigeonpea genome during evolution. The orthologs of the reported anther development-related genes were searched in the pigeonpea genome, and the expression profiling studies of specific genes via qRT-PCR in the pre- and post-meiotic anther stages of AKCMS11A (male sterile), AKCMS11B (maintainer) and AKPR303 (fertility restorer) lines of pigeonpea was done. Compared to the restorer and maintainer lines, the down-regulation of CcP-typeATPase22 in the post-meiotic anthers of the male sterile line might have played a role in pollen sterility. Furthermore, the strong expression of CcP-typeATPase2 in the post-meiotic anthers of restorer line and CcP-typeATPase46, CcP-typeATPase51, and CcP-typeATPase52 in the maintainer lines, respectively, compared to the male sterile line, clearly indicates their potential role in developing male reproductive organs in pigeonpea.

Genome-wide identification of heavy-metal ATPases genes in Areca catechu: investigating their functionality under heavy metal exposure

Heavy-metal ATPases (HMAs) play a vital role in plants, helping to transport heavy metal ions across cell membranes.However, insufficient data exists concerning HMAs genes within the Arecaceae family.In this study, 12 AcHMA genes were identified within the genome of Areca catechu, grouped into two main clusters based on their phylogenetic relationships.Genomic distribution analysis reveals that the AcHMA genes were unevenly distributed across six chromosomes. We further analyzed their physicochemical properties, collinearity, and gene structure.Furthermore, RNA-seq data analysis exhibited varied expressions in different tissues of A. catechu and found that AcHMA1, AcHMA2, and AcHMA7 were highly expressed in roots, leaves, pericarp, and male/female flowers. A total of six AcHMA candidate genes were selected based on gene expression patterns, and their expression in the roots and leaves was determined using RT-qPCR under heavy metal stress. Results showed that the expression levels of AcHMA1 and AcHMA3 genes were significantly up-regulated under Cd2 + and Zn2 + stress. Similarly, in response to Cu2+, the AcHMA5 and AcHMA8 revealed the highest expression in roots and leaves, respectively. In conclusion, this study will offer a foundation for exploring the role of the HMAs gene family in dealing with heavy metal stress conditions in A. catechu.

Genome-Wide Identification and Expression Profiling of Heavy Metal ATPase (HMA) Genes in Peanut: Potential Roles in Heavy Metal Transport

The heavy metal ATPase (HMA) family belongs to the P-type ATPase superfamily and plays an essential role in the regulation of metal homeostasis in plants. However, the gene family has not been fully investigated in peanut. Here, a genome-wide identification and bioinformatics analysis was performed on AhHMA genes in peanut, and the expression of 12 AhHMA genes in response to Cu, Zn, and Cd was evaluated in two peanut cultivars (Silihong and Fenghua 1) differing in Cd accumulation. A total of 21 AhHMA genes were identified in the peanut genome, including ten paralogous gene pairs derived from whole-genome duplication, and an additional gene resulting from tandem duplication. AhHMA proteins could be divided into six groups (I-VI), belonging to two clades (Zn/Co/Cd/Pb-ATPases and Cu/Ag-ATPases). Most AhHMA proteins within the same clade or group generally have a similar structure. However, significant divergence exists in the exon/intron organization even between duplicated gene pairs. RNA-seq data showed that most AhHMA genes are preferentially expressed in roots, shoots, and reproductive tissues. qRT-PCR results revealed that AhHMA1.1/1.2, AhHMA3.1/3.2, AhHMA7.1/7.4, and AhHMA8.1 might be involved in Zn transport in peanut plants, while AhHMA3.2 and AhHMA7.5 might be involved in Cd transport. Our findings provide clues to further characterize the functions of AhHMA genes in metal uptake and translocation in peanut plants.

Alleviation of microplastic toxicity in soybean by arbuscular mycorrhizal fungi: Regulating glyoxalase system and root nodule organic acid

Microplastic accumulation in the soil-plant system can stress plants and affect products quality. Currently, studies on the effect of microplastics on plants are not consistent and underlying molecular mechanisms are yet unknown. Here for the first time, we performed a study to explore the molecular mechanism underlying the growth of soybean plants in soil contaminated with various types of microplastics (PS and HDPE) and arbuscular mycorrhizal fungi (AMF) (presence/absence). Our results revealed that a dose-dependent decline was observed in plant growth, chlorophyll content, and yield of soybean under MPs stress. The addition of MPs resulted in oxidative stress closely related to hydrogen peroxide generation (H2O2), methylglyoxal (MG) levels, lipid peroxidation (MDA), and lipoxygenase (LOX). In contrast, MPs addition enhanced mycorrhizal colonization and dependency relative to control while the rubisco and root activity declined. All the genes (GmHMA13 and GmHMA19) were downregulated in the presence of MPs except GmHMA18 in roots. AMF inoculation alleviated MPs-induced phytotoxic effects on colonization, rubisco activity, root activity and restored the growth of soybean. Under MPs exposure, AMF inoculation induced plant defense system via improved regulation of antioxidant enzymes, ascorbate, glutathione pool, and glyoxalase system. AMF upregulated the genes responsible for metals uptake in soybean under MPs stress. The antioxidant and glyoxalase systems coordinated regulation expressively inhibited the oxidative and carbonyl stress at both MPs types. Hence, AMF inoculation may be considered an effective approach for minimizing MPs toxicity and its adverse effects on growth of soybean grown on MPs-contaminated soils.

Insights into heavy metal tolerance mechanisms of Brassica species: physiological, biochemical, and molecular interventions

Heavy metal (HM) contamination of soil due to anthropogenic activities has led to bioaccumulation and biomagnification, posing toxic effects on plants by interacting with vital cellular biomolecules such as DNA and proteins. Brassica species have developed complex physiological, biochemical, and molecular mechanisms for adaptability, tolerance, and survival under these conditions. This review summarizes the HM tolerance strategies of Brassica species, covering the role of root exudates, microorganisms, cell walls, cell membranes, and organelle-specific proteins. The first line of defence against HM stress in Brassica species is the avoidance strategy, which involves metal ion precipitation, root sorption, and metal exclusion. The use of plant growth-promoting microbes, Pseudomonas, Psychrobacter, and Rhizobium species effectively immobilizes HMs and reduces their uptake by Brassica roots. The roots of Brassica species efficiently detoxify metals, particularly by flavonoid glycoside exudation. The composition of the cell wall and callose deposition also plays a crucial role in enhancing HMs resistance in Brassica species. Furthermore, plasma membrane-associated transporters, BjCET, BjPCR, BjYSL, and BnMTP, reduce HM concentration by stimulating the efflux mechanism. Brassica species also respond to stress by up-regulating existing protein pools or synthesizing novel proteins associated with HM stress tolerance. This review provides new insights into the HM tolerance mechanisms of Brassica species, which are necessary for future development of HM-resistant crops.

A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress

The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.

Strigolactone decreases cadmium concentrations by regulating cadmium localization and glyoxalase defense system: Effects on nodules organic acids and soybean yield

To decrease environmental and human health risks associated with crop and soil contamination, alternative solutions are still needed. The information on strigolactones (SLs)-mediated elicitation of abiotic stress signaling and triggering physiological alterations is scarce in the plant. To unravel the same, soybean plants were subjected to cadmium (Cd) stress (20 mg kg^-1), presence or absence of foliar applied SL (GR24) at the concentration of 10 μM. Excess Cd accumulation causes reduced growth (-52% shoot and +24% root), yield (-35%), physio-biochemical markers, organic acid production, and genes encoding heavy metal resilience in soybean. SL exogenous application decreased the growth and yield suppression (-12%), shielded chlorophyll (+3%), and prominently declined Cd-induced oxidative stress biomarkers accumulation in soybean. Moreover, SL effectively alleviates Cd-induced suppression in organic acids, superoxide dismutase (+73%), catalase activities (+117%), and increments ascorbate glutathione (ASA-GSH) cycle activities comprising ascorbate peroxidase, glutathione peroxidase, glutathione reductase, dehydroascorbate reductase, and monodehydroascorbate reductase. SL-mediated upregulation of genes encoding heavy metals tolerance and glyoxalase defense system in Cd stressed plants. The results of this work point out that SL could be a promising player in mitigating Cd-induced injuries effectively in soybean. It acts through the antioxidant system modulation for redox homeostasis, shielding chloroplasts, enhancing photosynthetic apparatus, and elevating organic acid production in soybean plants.

Genome-wide analysis of heavy metal ATPases (HMAs) in Poaceae species and their potential role against copper stress in Triticum aestivum

Plants require copper for normal growth and development and have evolved an efficient system for copper management based on transport proteins such as P_1B-ATPases, also known as heavy metal ATPases (HMAs). Here, we report HMAs in eleven different Poaceae species, including wheat. Furthermore, the possible role of wheat HMAs in copper stress was investigated. BlastP searches identified 27 HMAs in wheat, and phylogenetic analysis based on the Maximum Likelihood method demonstrated a separation into four distinct clades. Conserved motif analysis, domain identification, gene structure, and transmembrane helices number were also identified for wheat HMAs using computational tools. Wheat seedlings grown hydroponically were subjected to elevated copper and demonstrated toxicity symptoms with effects on fresh weight and changes in expression of selected HMAs TaHMA7, TaHMA8, and TaHMA9 were upregulated in response to elevated copper, suggesting a role in wheat copper homeostasis. Further investigations on these heavy metal pumps can provide insight into strategies for enhancing crop heavy metal tolerance in the face of heavy metal pollution.

Temporal Comparative Transcriptome Analysis on Wheat Response to Acute Cd Toxicity at the Seedling Stage

Cadmium (Cd) is a non-essential and toxic metal that accumulates in plant's tissues and diminishes plant growth and productivity. In the present study, differential root transcriptomic analysis was carried out to identify Cd stress-responsive gene networks and functional annotation under Cd stress in wheat seedlings. For this purpose, the Yannong 0428 wheat cultivar was incubated with 40 µm/L of CdCl₂·2.5H₂O for 6 h at three different seedling growth days. After the quality screening, using the Illumina Hiseq 2000 platform, more than 2482 million clean reads were retrieved. Following this, 84.8% to 89.3% of the clean reads at three time points under normal conditions and 86.5% to 89.1% of the reads from the Cd stress condition were mapped onto the wheat reference genome. In contrast, at three separate seedling growth days, the data analysis revealed a total of 6221 differentially expressed genes (DEGs), including 1543 (24.8%) up-regulated genes and 4678 (75.8%) down-regulated genes. In total, 120 DEGs were co-expressed throughout all the growth days, whereas 1096, 1088, and 2265 DEGs were found to be selectively up-/down-regulated at 7d, 14d, and 30d, respectively. However, the clustering of DEGs, through utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that the DEGs in the metabolic category were frequently annotated for phenylpropanoid biosynthesis. In comparison, a considerable number of DEGs were linked to protein processing in the endoplasmic reticulum under the process of genetic information processing. Similarly, in categories in organismal systems and cellular processes, DEGs were found in plant hormone signal transduction pathways, and DEGs were identified in the plant-pathogen interaction pathway, respectively. However, DEGs in "endocytosis pathways" were enriched in environmental information processing. In addition, in-depth annotations of roughly specific heavy metal stress-response genes and pathways were also mined, and the expression patterns of eight DEGs were studied using quantitative real-time PCR. The results were congruent with the findings of RNA sequencing regarding transcript abundance in the studied wheat cultivar.

The stimulatory effect and mechanism of low-dose lanthanum on soybean leaf cells

Light rare earth elements (LREEs) have been long used in agriculture (i.e., mainly via aerially applied LREE fertilizers) based on the fact that low-dose LREEs promote plant growth. Meanwhile, the toxic effects of low-dose LREEs on organisms have also been found. However, the cellular and molecular mechanism of low-dose LREEs acting on organisms remain unclear. Plants are at the beginning of food chains, so it is critical to uncover the cellular and molecular mechanism of low-dose LREEs on plants. Here, lanthanum (La) and soybean were the representatives of LREEs and plants, respectively. The effects of low-dose La on soybean leaves were investigated, and the stimulatory effect and mechanism of low-dose LREEs on leaf cells were revealed. Specifically, clathrin-mediated endocytosis (CME) activated by low-dose La is an influx channel for La in soybean leaf cells. The intracellular La and La-activated CME jointly disturbed multiple forms of intracellular homeostasis, including metallic element homeostasis, redox homeostasis, gene expression homeostasis. The disturbed homeostasis either stimulated cell growth or caused damage to the plasma membrane of soybean leaf cells. These results provide new insights for clarifying the cellular and molecular mechanisms of low-dose LREEs as a class of stimulators instead of nutrients to stimulate plants.

Genome-wide analysis elucidates the roles of GhHMA genes in different abiotic stresses and fiber development in upland cotton

The heavy metal-binding domain is involved in heavy metal transporting and plays a significant role in plant detoxification. However, the functions of HMAs are less well known in cotton. In this study, a total of 143 GhHMAs (heavy metal-binding domain) were detected by genome-wide identification in G. hirsutum L. All the GhHMAs were classified into four groups via phylogenetic analysis. The exon/intron structure and protein motifs indicated that each branch of the GhHMA genes was highly conserved. 212 paralogous GhHMA gene pairs were identified, and the segmental duplications were the main role to the expansion of GhHMAs. The Ka/Ks values suggested that the GhHMA gene family has undergone purifying selection during the long-term evolutionary process. GhHMA3 and GhHMA75 were located in the plasma membrane, while GhHMA26, GhHMA117 and GhHMA121 were located in the nucleus, respectively. Transcriptomic data and qRT-PCR showed that GhHMA26 exhibited different expression patterns in each tissue and during fiber development or under different abiotic stresses. Overexpressing GhHMA26 significantly promoted the elongation of leaf trichomes and also improved the tolerance to salt stress. Therefore, GhHMA26 may positively regulate fiber elongation and abiotic stress. Yeast two-hybrid assays indicated that GhHMA26 and GhHMA75 participated in multiple biological functions. Our results suggest some genes in the GhHMAs might be associated with fiber development and the abiotic stress response, which could promote further research involving functional analysis of GhHMA genes in cotton.

Genome-wide identification and transcriptome analysis of the heavy metal-associated (HMA) gene family in Tartary buckwheat and their regulatory roles under cadmium stress

Heavy metal-associated (HMA) genes are those related to heavy metal transport and detoxification in plants. HMA genes have not been reported in Tartary buckwheat so far. In this study, we accessed the HMA genes of Tartary buckwheat by genome-wide identification for the first time. A total of 56 HMA genes were identified, including 36 ATX1 (antioxidant protein1) genes, 13 HIPP (heavy metal-associated isoprenylated plant protein) genes, and 7 P_1B-ATPase (P_1B-type adenosine triphosphatase) genes. These gene structures, motif compositions, chromosomal distribution, phylogenetic relationship, duplication events, interaction networks, cis-acting elements, and transcriptional expression under cadmium (Cd) stress were investigated. Among them, genes in HIPP and ATX1 subfamilies were more closely related. The 56 HMA genes were involved in the regulation of metal ion transport and homeostasis by binding metal ions, likely triggered by signals transducted by plant hormones. Fifteen of these HMA genes played regulatory roles under Cd stress. FtP1bA1 was identified to be a core gene involved in the defense regulation of Cd stress. Our results provide not only the first overview and characteristics of HMA genes in the whole genome of Tartary buckwheat but also a valuable reference for the functional analysis of HMA genes under Cd stress. Understanding changes in gene regulation induced by Cd stress lays the foundation for breeding resistant varieties.

Genome wide analysis of the heavy-metal-associated (HMA) gene family in tomato and expression profiles under different stresses

The heavy-metal-associated (HMA) family plays a major role in the transportation of metals. Despite having the genome sequence of the tomato (Solanum lycopersicum), the HMA gene family has not been studied yet. In this study, we identified 48 HMA genes and categorized them into Cu/Ag P1B-ATPase and Zn/Co/Cd/Pb P1BATPase sub-families according to their phylogenic relationship with Arabidopsis and rice. The SlHMA genes were distributed throughout the 12 chromosomes. Analysis of gene structure, chromosomal position, and synteny, revealed that segmental duplications bestowed their evolution. The high numbers of stress-related cis-elements were found to be present in the putative promoter regions indicate the involvement of SlHMAs in stress modulation pathways. RNA-seq data revealed that SlHMAs had divergent expression in different tissues and developmental stages, where members of Cu/Ag P1B-ATPase subfamily were strongly expressed in the roots. RT-qPCR analysis of nine selected SlHMAs showed that most of the genes were up-regulated in response to heavy metals and moderately regulated in response to different abiotic stresses such as salt, drought, and cold.

Impact of arbuscular mycorrhiza on maize P1B-ATPases gene expression and ionome in copper-contaminated soils

Arbuscular mycorrhizal (AM) fungi, symbionts of most land plants, increase plant fitness in metal contaminated soils. To further understand the mechanisms of metal tolerance in the AM symbiosis, the expression patterns of the maize Heavy Metal ATPase (HMA) family members and the ionomes of non-mycorrhizal and mycorrhizal plants grown under different Cu supplies were examined. Expression of ZmHMA5a and ZmHMA5b, whose encoded proteins were predicted to be localized at the plasma membrane, was up-regulated by Cu in non-mycorrhizal roots and to a lower extent in mycorrhizal roots. Gene expression of the tonoplast ZmHMA3a and ZmHMA4 isoforms was up-regulated by Cu-toxicity in shoots and roots of mycorrhizal plants. AM mitigates the changes induced by Cu toxicity on the maize ionome, specially at the highest Cu soil concentration. Altogether these data suggest that in Cu-contaminated soils, AM increases expression of the HMA genes putatively encoding proteins involved in Cu detoxification and balances mineral nutrient uptake improving the nutritional status of the maize plants.

Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress

Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.

Genome-Wide Characterization of Sedum plumbizincicola HMA Gene Family Provides Functional Implications in Cadmium Response

Heavy-metal ATPase (HMA), an ancient family of transition metal pumps, plays important roles in the transmembrane transport of transition metals such as Cu, Zn, Cd, and Co. Although characterization of HMAs has been conducted in several plants, scarcely knowledge was revealed in Sedum plumbizincicola, a type of cadmium (Cd) hyperaccumulator found in Zhejiang, China. In this study, we first carried out research on genome-wide analysis of the HMA gene family in S. plumbizincicola and finally identified 8 SpHMA genes and divided them into two subfamilies according to sequence alignment and phylogenetic analysis. In addition, a structural analysis showed that SpHMAs were relatively conserved during evolution. All of the SpHMAs contained the HMA domain and the highly conserved motifs, such as DKTGT, GDGxNDxP, PxxK S/TGE, HP, and CPx/SPC. A promoter analysis showed that the majority of the SpHMA genes had cis-acting elements related to the abiotic stress response. The expression profiles showed that most SpHMAs exhibited tissue expression specificity and their expression can be regulated by different heavy metal stress. The members of Zn/Co/Cd/Pb subgroup (SpHMA1-3) were verified to be upregulated in various tissues when exposed to CdCl₂. Here we also found that the expression of SpHMA7, which belonged to the Cu/Ag subgroup, had an upregulated trend in Cd stress. Overexpression of SpHMA7 in transgenic yeast indicated an improved sensitivity to Cd. These results provide insights into the evolutionary processes and potential functions of the HMA gene family in S. plumbizincicola, laying a theoretical basis for further studies on figuring out their roles in regulating plant responses to biotic/abiotic stresses.

Genome-wide identification and characterization of the heavy metal ATPase (HMA) gene family in Medicago truncatula under copper stress

In nature, the normal growth, development, and quality of plants are significantly affected by many abiotic stresses, such as drought, salinity, low temperature, and heavy metals. Among heavy metals, copper is an essential element for plant growth and development but also has a toxic effect on plants when its concentration is excessive. Therefore, plants have evolved a complex regulatory network to regulate the balance of copper ions in cells. Heavy metal ATPases (HMAs), which transport heavy metals to intracellular compartments or detoxify heavy metals present at excessive concentrations, have been extensively studied in model plant species. However, no comprehensive and systematic surveys of members of the HMA gene family have been conducted in the model legume species Medicago truncatula. Here, nine putative MtHMAs were identified in the M. truncatula genome. These MtHMAs were phylogenetically divided into two distinct groups. The members in each group had a relatively conserved gene structure and motif composition. The number of introns in the MtHMAs varied from 5 to 16, with the majority of these genes containing 8 introns. The expression patterns showed that MtHMAs exhibit preferential or distinct expression patterns among different tissues. Finally, the expression patterns of the members of this gene family were verified in the leaves and roots of plants under Cu stress. Our findings will be valuable for the functional investigation and application of members of this gene family in M. truncatula and other related legume species.

Genome-Wide Identification of the HMA Gene Family and Expression Analysis under Cd Stress in Barley

In recent years, cadmium (Cd) pollution in soil has increased with increasing industrial activities, which has restricted crop growth and agricultural development. The heavy metal ATPase (HMA) gene family contributes to heavy metal stress resistance in plants. In this study, 21 HMA genes (HvHMAs) were identified in barley (Hordeumvulgare L., Hv) using bioinformatics methods. Based on phylogenetic analysis and domain distribution, barley HMA genes were divided into five groups (A-E), and complete analyses were performed in terms of physicochemical properties, structural characteristics, conserved domains, and chromosome localization. The expression pattern analysis showed that most HvHMA genes were expressed in barley and exhibited tissue specificity. According to the fragments per kilobase of exon per million fragments values in shoots from seedlings at the 10 cm shoot stage (LEA) and phylogenetic analysis, five HvHMA genes were selected for expression analysis under Cd stress. Among the five HvHMA genes, three (HvHMA1, HvHMA3, and HvHMA4) were upregulated and two (HvHMA2 and HvHMA6) were downregulated following Cd treatments. This study serves as a foundation for clarifying the functions of HvHMA proteins in the heavy metal stress resistance of barley.

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton

BACKGROUND

Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have been identified in plants, such as rice, but there is little research on the WAK gene family in cotton.

RESULTS

In the present study, we identified 29 GhWAK genes in Gossypium hirsutum. Phylogenetic analysis showed that cotton WAK proteins can be divided into five clades. The results of synteny and Ka/Ks analysis showed that the GhWAK genes mainly originated from whole genome duplication (WGD) and were then mainly under purifying selection. Transcriptome data and real-time PCR showed that 97% of GhWAK genes highly expressed in cotton fibers and ovules. β-glucuronidase (GUS) staining assays showed that GhWAK5 and GhWAK16 expressed in Arabidopsis leaf trichomes. Fourteen GhWAK genes were found to possess putative gibberellin (GA) response elements in the promoter regions, 13 of which were significantly induced by GA treatment. Ten GhWAK genes contained auxin (IAA) response elements and the expression level of nine GhWAKs significantly increased under auxin treatment.

CONCLUSIONS

We provide a preliminary analysis of the WAK gene family in G. hirsutum, which sheds light on the potantial roles of GhWAK genes in cotton fiber cell development. Our data also provides a useful resource for future studies on the functional roles of GhWAK genes.

Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis

Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.

Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

P-type ATPases are integral membrane transporters that play important roles in transmembrane transport in plants. However, a comprehensive analysis of the P-type ATPase gene family has not been conducted in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. Here, we identified 419 P-type ATPase genes from seven Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, Prunus mume, Pyrus communis and Pyrus betulifolia). Structural and phylogenetic analyses revealed that P-type ATPase genes can be divided into five subfamilies. Different subfamilies have different conserved motifs and cis-acting elements, which may lead to functional divergence within one gene family. Dispersed duplication and whole-genome duplication may play critical roles in the expansion of the P-type ATPase family. Purifying selection was the primary force driving the evolution of P-type ATPase family genes. Based on the dynamic transcriptome analysis and transient transformation of Chinese white pear fruit, Pbr029767.1 in the P_3A subfamily were found to be associated with malate accumulation during pear fruit development. Using a co-expression network, we identified several transcription factors that may have regulatory relationships with the P-type ATPase gene family. Overall, this study lays a solid foundation for understanding the evolution and functions of P-type ATPase genes in Chinese white pear and six other Rosaceae species.

Interactive effect of drought and cadmium stress on soybean root morphology and gene expression

Recent climatic changes and low water availability due to unpredictable precipitation have reduced the productivity of soybean (Glycine max [L.] Merr.) cultivars. Limited information is available on how drought affects the accumulation and translocation of cadmium (Cd) by affecting soybean root. In this study, we investigated the effect of polyethylene glycol (PEG; 5% and 10%)-induced drought and Cd (0.2 and 0.5 mg L-1) stresses on soybean root morphology, Cd uptake and gene expression; plants not exposed to these stress (0% PEG and 0 mg L-1 Cd) served as a control. The results showed that drought affected roots morphology and Cd uptake. The reduction in root length, root area and root diameter and increase in catalase activity was less prominent in drought tolerant cultivars (Shennong20 and Liaodou32) than in drought sensitive cultivars (Liaodou3 and Liaodou10). Genes involved in abscisic acid (ABA) degradation, gibberellin and salicylic acid biosynthesis, hydrogen peroxide (H2O2) production and Cd transport were up-regulated, while those involved in zeatinriboside (ZR), indole 3-acetic acid (IAA) and methyl jasmonate (MeJA) biosynthesis were down-regulated under Cd and drought stress. Biosynthesis genes of gibberellin (Glyma03G019800.1), IAA (Glyma02G037600), ZR (XM_003550461.3) and MeJA (Glyma11G007600) were expressed to higher levels in drought tolerant cultivars than in drought sensitive cultivars. These genes represent potential candidates for the development of drought and Cd tolerant soybean cultivars.

Arbuscular mycorrhiza augments cadmium tolerance in soybean by altering accumulation and partitioning of nutrient elements, and related gene expression

Arbuscular mycorrhizal (AM) fungi can protect plants against cadmium (Cd) stress, and are the most prominent symbiotic fungi for contribution to phytoremediation. However, the tolerance mechanism for AM symbiosis on Cd toxicity still remains unclear, especially the related molecular mechanisms. In this study, different Cd treatments were applied to two soybean genotypes with different Cd tolerance in the presence or absence of AM fungal inoculation. The results showed that Cd addition obviously decreased AM colonization. AM symbiosis significantly increased plant dry weight, root growth, and P acquisition in Cd-tolerant HX3 genotype at Cd addition treatments. The effectiveness was associated with a concomitant increased expression of the AM inducible phosphate (Pi) transporter genes GmPT8, GmPT9, GmPT10, and upregulated expression of P-type heavy metal ATPase gene GmHMA19. Additionally, AM fungal inoculation effectively impacted the partitioning of Mg, Cu and Zn, including increased Mg, and decreased Cu and Zn relative concentrations in shoots of Cd tolerant HX3. Taken together, these results suggest that AM symbiosis can alleviate Cd toxicity in soybean through enhanced P nutrition, up-regulated expression of AM inducible GmPTs and GmHMA19, as well as, the alteration of the partitioning of essential nutrient elements.

Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections

The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.

Annotation and characterization of Cd-responsive metal transporter genes in rapeseed (Brassica napus)

In higher plants, heavy metal transporters are responsible for metal uptake, translocation and homeostasis. These metals include essential metals such as zinc (Zn) or manganese (Mn) and non-essential metals like cadmium (Cd) or lead (Pb). Although a few heavy metal transporters have been well identified in model plants (e.g. Arabidopsis and rice), little is known about their functionality in rapeseed (Brassica napus). B. napus is an important oil crop ranking the third largest sources of vegetable oil over the world. Importantly, B. napus has long been considered as a desirable candidate for phytoremediation owning to its massive dry weight productivity and moderate to high Cd accumulation. In this study, 270 metal transporter genes (MTGs) from B. napus genome were identified and annotated using bioinformatics and high-throughput sequencing. Most of the MTGs (74.8%, 202/270) were validated by RNA-sequencing (RNA-seq) the seedling libraries. Based on the sequence identity, nine superfamilies including YSL, OPT, NRAMP, COPT, ZIP, CDF/MTP, HMA, MRP and PDR have been classified. RNA-sequencing profiled 202 non-redundant MTGs from B. napus seedlings, of which, 108 MTGs were differentially expressed and 62 genes were significantly induced under Cd stress. These differentially expressed genes (DEGs) are dispersed in the rapeseed genome. Some of the genes were well confirmed by qRT-PCR. Analysis of the genomic distribution of MTGs on B. napus chromosomes revealed that their evolutional expansion was probably through localized allele duplications.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.