New insights into cadmium tolerance and accumulation in tomato: Dissecting root and shoot responses using cross-genotype grafting

Cadmium (Cd) is one of the most threatening soil and water contaminants in agricultural settings. In previous studies, we observed that Cd affects the metabolism and physiology of tomato (Solanum lycopersicum) plants even after short-term exposure. The objective of this research was to use cross-genotype grafting to distinguish between root- and shoot-mediated responses of tomato genotypes with contrasting Cd tolerance at the early stages of Cd exposure. This study provides the first report of organ-specific contributions in two tomato genotypes with contrasting Cd tolerance: Solanum lycopersicum cv. Calabash Rouge and Solanum lycopersicum cv. Pusa Ruby (which have been classified and further characterized as sensitive (S) and tolerant (T) to Cd, respectively). Scion S was grafted onto rootstock S (S/S) and rootstock T (S/T), and scion T was grafted onto rootstock T (T/T) and rootstock S (T/S). A 35 μM cadmium chloride (CdCl₂) treatment was used for stress induction in a hydroponic system. Both shoot and root contributions to Cd responses were observed, and they varied in a genotype- and/or organ-dependent manner for nutrient concentrations, oxidative stress parameters, antioxidant enzymes, and transporters gene expression. The findings overall provide evidence for the dominant role of the tolerant rootstock system in conferring reduced Cd uptake and accumulation. The lowest leaf Cd concentrations were observed in T/T (215.11 μg g^-1 DW) and S/T (235.61 μg g^-1 DW). Cadmium-induced decreases in leaf dry weight were observed only in T/S (-8.20%) and S/S (-13.89%), which also were the only graft combinations that showed decreases in chlorophyll content (-3.93% in T/S and -4.05% in S/S). Furthermore, the results show that reciprocal grafting is a fruitful approach for gaining insights into the organ-specific modulation of Cd tolerance and accumulation during the early stages of Cd exposure.

Purple acid phosphatases in coffee-genome-wide identification and the transcriptional profile of selected members in roots upon Pi starvation

Phosphorus (P) availability is determinant for crop productivity and, despite the sufficient amount of this nutrient in arable land, most of it remains insoluble, leading to the need of high fertilizer input. To cope with P scarcity forecasts and also for cropping costs alleviation, genotypes better adapted to promote P solubilization and absorption are required, especially for perennial crops. Coffee is one of these important perennial crops cultivated in soils with low P availability, and thus we aimed to study adaptive strategies to coffee genotypes in acquire phosphorus. In this study, we focused on rhizosphere phosphatase activity, a major characteristic related to P solubilization from organic pools. To explore the genetic basis of this characteristic, we firstly identified 29 Purple Acid Phosphatases (PAP) genes in C. canephora genome and selected five candidates with higher potential to encode secreted PAPs. We found that C. arabica genotypes have diverse profiles of rhizosphere phosphatase activity, as well as microbial biomass carbon, which we measured to explore the impact of the plant on microbiota and also to discriminate the phosphatase activity origin (plant or microorganism-derived). We selected two C. arabica cultivars with contrasting phosphatase activity and found that one PAP gene has a correlated gene expression profile with this characteristic. This work explores coffee adaptative responses to P starvation conditions, and the information provided can further contribute to breeding programs aiming better adapted genotypes for sustainable agriculture in face of current challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03399-6.

The SAUR gene family in coffee: genome-wide identification and gene expression analysis during somatic embryogenesis

BACKGROUND

Small auxin-up RNA (SAUR) genes form a wide family supposedly involved in different physiological and developmental processes in plants such as leaf senescence, auxin signaling and transport, hypocotyl development and tolerance to abiotic stresses. The transcription of SAUR genes is quickly induced by auxins, a group of phytohormones of major importance on embryo development. To better understand the distribution and expression profile of such still not explored family in Coffea sp., especially during the development of somatic embryogenesis (SE), SAUR members were characterized in silico using the available Coffea canephora genome data and analyzed for gene expression by RT-qPCR in C. arabica embryogenic samples.

METHODS AND RESULTS

Over C. canephora genome 31 CcSAURs were distributed by 11 chromosomes. Out of these 31 gene members, 5 SAURs were selected for gene expression analysis in C. arabica embryogenic materials. CaSAUR12 and CaSAUR18 were the members highly expressed through almost all plant materials. The other genes had more expression in at least one of the developing embryo stages or plantlets. The CaSAUR12 was the only member to exhibit an increased expression in both non-embryogenic calli and the developing embryo stages.

CONCLUSION

The identification of SAUR family on C. canephora genome followed by the analysis of gene expression profile across coffee somatic embryogenesis process on C. arabica represents a further additional step towards a better comprehension of molecular components acting on SE. Along with new research about this gene family such knowledge may support studies about clonal propagation methods via somatic embryogenesis to help the scientific community towards improvements into coffee crop.

Comprehensive characterization of the ALMT and MATE families on Populus trichocarpa and gene co-expression network analysis of its members during aluminium toxicity and phosphate starvation stresses

Aluminium (Al) toxicity and phosphate deficit on soils are some of the main problems of modern agriculture and are usually associated. Some plants are able to overcome these stresses through exuding organic acids on the rhizosphere, such as citrate and malate, which are exported by MATE (Multi drug and toxin extrusion) and ALMT (Aluminium-activated malate transporter) transporters, respectively. Despite its co-action on acidic soils, few studies explore these two families' correlation, especially on tree crops, therefore we performed a comprehensive description of MATE and ALMT families on Populus trichocarpa as a model species for arboreal plants. We found 20 and 56 putative members of ALMT and MATE families, respectively. Then, a gene co-expression network analysis was performed using broad transcriptomic data to analyze which members of each family were transcriptionally associated. Four independent networks were generated, one of which is composed of members putatively related to phosphate starvation and aluminum toxicity stresses. The PoptrALMT10 and PoptrMATE54 genes were selected from this network for a deeper analysis, which revealed that in roots under phosphate starvation stress the two genes have independent transcriptional profiles, however, on the aluminum toxicity stress they share some common correlations with other genes. The data presented here help on the description of these gene families, of which some members are potentially involved in plant responses to acid soil-related stresses and its exploration is an important step towards using this knowledge on breeding programs for P. trichocarpa and other tree crops.

Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

Background

Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants.

Results

We have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator.

Conclusion

Therefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.

Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp

The adaptation of crops to acid soils is needed for the maintenance of food security in a sustainable way, as decreasing fertilizers use and mechanical interventions in the soil would favor the reduction of agricultural practices' environmental impact. Phosphate deficiency and the presence of reactive aluminum affect vital processes to the plant in this soil, mostly water and nutrient absorption. From this, the understanding of the molecular response to these stresses can foster strategies for genetic improvement, so the aim was to broadly analyze the transcriptional variations in Poupulus spp. in response to these abiotic stresses, as a plant model for woody crops. A co-expression network was constructed among 3,180 genes differentially expressed in aluminum-stressed plants with 34,988 connections. Of this total, 344 genes presented two-fold transcriptional variation and the group of genes associated with those regulated after 246 hours of stress had higher number of connections per gene, with some already characterized genes related to this stress as main hubs. Another co-expression network was made up of 8,380 connections between 550 genes regulated by aluminum stress and phosphate deficiency, in which 380 genes had similar profile in both stresses and only eight with transcriptional variation higher than 20%. All the transcriptomic data are presented here with functional enrichment and homology comparisons with already characterized genes in another species that are related to the explored stresses, in order to provide a broad analysis of the co-opted responses for both the stresses as well as some specificity. This approach improves our understanding regarding the plants adaptation to acid soils and may contribute to strategies of crop genetic improvement for this condition that is widely present in regions of high agricultural activity.

Gene expression in two contrasting hybrid clones of Eucalyptus camaldulensis x Eucalyptus urophylla grown under water deficit conditions

The physiological and molecular responses to water stress are mediated by a range of mechanisms, many of which involve abscisic acid (ABA)-dependent signaling pathways. In addition, plants contain drought response genes that can be induced by ABA-independent routes, mediated by secondary messengers such as Ca²⁺, or regulated by epigenetic modifications. The complex processes involved in the response to water stress can be investigated using molecular techniques to evaluate the expression patterns of genes of interest and to infer the behavior of different genotypes and species. In the present study, we first analyzed the stability of a set of reference genes for normalization of the gene expression with real-time quantitative polymerase chain reaction (RT-qPCR), since there were no results related to the genotype used in this study. We verified that although there were some variations between algorithms used, the three most stable reference genes were SAND, PP2A-3 and EF-1α. The expressions of genes encoding for proteins associated with drought-tolerance responses, namely 9-cis-epoxycarotenoid dioxygenase 3 (EgrNCED3), pyrabactin resistance 1 (EgrPYR1), dehydration-responsive element-binding 2.5 (EgrDREB2.5) transcription factors, calcium-dependent protein kinase 26 (EgrCDPK26), methyl transferase 1 (EgrMET1) and deficient in DNA methylation 1 (EgrDDM1) protein, were determined by RT-qPCR in leaf samples from drought sensitive (VM05) and drought tolerant (VM01) clones of the hybrid Eucalyptus camaldulensis x Eucalyptus urophylla grown under water stress and irrigation conditions. When the two clones were maintained under conditions of water deficiency, VM01 exhibited higher expression levels of EgrNCED3 and EgrPYR1 genes than VM05 at all sampling times, implying that ABA biosynthesis and subsequent induction of the ABA-dependent cascade mediated by the PYR1-ABA receptor complex were enhanced in the tolerant clone. Under water-stress conditions, this clone also presented increased expression of the EgrDREB2.5 gene, representative of an ABA-independent cascade, and of the EgrCPK26 gene, related to stomatal opening and closure. On the other hand, the expression levels of EgrMET1 and EgrDDM1 genes in the sensitive clone were higher than in the tolerant clone under all conditions, showing a putative impact of epigenetic modifications on tolerance to water deficiency. The results obtained indicate that the superior ability of the VM01-tolerant clone to perceive water deficiency and activate drought-resistance genes is associated with the high expression levels of EgrNCED3, EgrPYR1 and EgrDREB2.5 under water-stress conditions. These findings will facilitate future research on the functional characterization of stress-related response genes, the identification of molecular markers, the evaluation of drought tolerance and genetic transformation in tree species.

Histodifferentiation of oil palm somatic embryo development at low auxin concentration

Large-scale propagation of oil palm (Elaeis guineensis, Jacq.) is difficult due to its single apical meristem. Thus, obtaining plants is mainly through seed germination, and a long growing period is required before oil production is possible. An alternative to large-scale seedling production is indirect somatic embryogenesis. The aim of this study was to analyze the somatic embryogenesis process in oil palm (E. guineensis Jacq.) with amino acids and low concentrations of auxins. The Tenera hybrid was analyzed by cytochemical and ultrastructural methods and was used to regenerate oil palm plants. First, calli were induced in MS culture media supplemented with 2,4-D and picloram. Two types of calli were obtained, characterized by beige or translucent color. Beige calli had embryogenic characteristics, such as large nuclei with prominent nucleoli, and they were multiplied for 8 months in MM culture (half strength MS, 1 mg L^-1 2,4-D, 2 mg L^-1 2iP, 1 mg L^-1 IBA, 250 mg L^-1 citric acid, 10 mg L^-1 cysteine, 100 mg L^-1 inositol, 1 mg L^-1 thiamine, 1 mg L^-1 pyridoxine, 1 mg L^-1 nicotinic acid, 1 mg L^-1 glycine, 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate). After multiplication, the MCB culture medium (half strength MS, supplemented with 0.25 mg L^-1 NAA, 2 mg L^-1 BAP, MM vitamins and 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate) was the most efficient for embryo formation, showing meristematic centers with totipotent cells in histochemical analyses. The somatic embryos were developed and germinated in MG medium (half strength MS, 0.45 mg L^-1 IAA, 0.25 mg L^-1 BAP, and MM vitamins), transplanted into polyethylene tubes containing pine bark substrates, and acclimatized in a greenhouse, achieving a 97% survival rate. The use of picloram for callus induction and somatic embryogenesis is advantageous and multiplication in MM medium is an important step for increasing cell mass. The calli with light beige color and nodular structures have meristematic cells with dense cytoplasm and totipotential features that later give rise to protoderm, procambium, and ground meristem during the globular, cordiform, and torpedo embryogenesis phases. In MCB medium, the concentration of vitamins and amino acids are crucial for somatic embryogenesis.

Expression of genes related to the regulation of muscle protein turnover in Angus and Nellore bulls

We aimed to evaluate the expression of genes related to the regulation of muscle protein turnover in the longissimus dorsi (LD) muscle of Angus and Nellore bulls and to estimate the within-breed correlations of gene expression and performance traits. Thirteen genes related to the IGF-1 and myostatin pathways were studied. Thirteen animals, with an initial average BW of 381.2 ± 11.8 kg, from each breed were used in a completely randomized 2 × 2 factorial design (2 breeds and 2 feeding levels). The diet consisted of corn silage and a corn-soybean meal concentrate in a roughage-to-concentrate ratio of 30:70. Cattle were fed ad libitum (with 9 animals from each breed) or feed restricted (a 55% restriction of total DMI of ad libitum-fed animals, calculated as percentage of metabolic BW, with 4 animals of each breed). The experimental period lasted for 82 d and it was preceded by a 28-d adaptation period. The performance traits evaluated were slaughter body weight, total ADG (from d 1 to 82 of the trial), initial ADG (from d 1 to 41 of the trial), final ADG (from d 42 to 82 of the trial), total DMI (from d 1 to 82 of the trial), initial DMI (from d 1 to 41 of the trial), final DMI (from d 42 to 82 of the trial), HCW, LD weight (LDW), and rib eye area (REA). After slaughter, samples were taken from the LD muscle between the 12th and 13th ribs for gene expression analysis by quantitative reverse transcription PCR. There was no difference ( > 0.05) in the expression of any of the genes studied between ad libitum-fed Angus and ad libitum-fed Nellore, whereas feed restriction increased the expression of (; < 0.001), (; = 0.05), and (; = 0.04) and decreased the expression of ( < 0.01). The REA was negatively correlated to (; = 0.01), (; = 0.02), and ( = 0.05). The HCW was negatively correlated to ( = 0.01) and ( = 0.01) and tended to be negatively correlated to ( = 0.07), whereas the LDW tended to be negatively correlated to ( = 0.08). The genes , , and seem to be important for muscle growth and may be worthy of further investigation as future strategies for increasing muscle in livestock.

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

Expression of genes involved in lipid metabolism in the muscle of beef cattle fed soybean or rumen-protected fat, with or without monensin supplementation

Degree of unsaturation of fatty acids, which is influenced by lipid source and level of metabolism in the rumen, is a major determinant in how dietary lipids affect genes that regulate beef marbling. A total of 28 Red Norte bulls with an initial live weight of 361±32 kg (P>0.05) were used in a completely randomized experimental design to analyze the expression of genes that are involved in lipid metabolism in the longissimus dorsi (LD) when diets contained soybean grain or rumen-protected fat, with or without monensin. Treatments were arranged as a 2×2 factorial, with 4 treatments and 7 replicates per treatment. Half of the animals that received soybean or rumen-protected fat were supplemented with 230 mg head(-1) d(-1) of monensin. Gene expression was analyzed by reverse-transcription quantitative PCR (RT-qPCR). Expression of sterol regulatory element-binding protein-1c (SREBP-1c) in the LD muscle was not affected by lipid source or monensin (P>0.05). There was an interaction effect (P<0.05) between lipid source and monensin for peroxisome proliferator-activated receptor α (PPAR-α) and stearoyl-CoA desaturase (SCD) expression, where greater gene expression was found in animals fed soybean plus monensin and the lower gene expression was found in animals fed rumen-protected fat plus monensin. Expression of lipoprotein lipase (LPL) and fatty acid-binding protein 4 (FABP4) were greater (P<0.05) in the LD muscle of animals fed soybean. Monensin had no effect on LPL and FABP4 expression when soybean without monensin was fed, but when rumen-protected fat was fed, monensin increased LPL expression and decreased FABP4 expression (P<0.05). Linoleic and arachidonic acids had negative correlations (P<0.05) with the expression of PPAR-α, SCD, FABP4, and LPL genes. PPAR-α gene expression was not correlated with SREBP-1c but was positively correlated with SCD, FABP4, LPL, and glutathione peroxidase (GPX1) gene expression (P<0.001). Lipid sources and monensin interact and alter the expression of PPAR-α, SCD, acetyl CoA carboxylase α (ACACA), LPL, FABP4, and GPX1. These changes in gene expression were most associated with arachidonic and α-linolenic acids and the ability of lipid sources and monensin to increase these fatty acids in tissues.

Identification of expressed sequences in the coffee genome potentially associated with somatic embryogenesis

Brazil possesses the most modern and productive coffee growing farms in the world, but technological development is desired to cope with the increasing world demand. One way to increase Brazilian coffee growing productivity is wide scale production of clones with superior genotypes, which can be obtained with in vitro propagation technique, or from tissue culture. These procedures can generate thousands of clones. However, the methodologies for in vitro cultivation are genotype-dependent, which leads to an almost empirical development of specific protocols for each species. Therefore, molecular markers linked to the biochemical events of somatic embryogenesis would greatly facilitate the development of such protocols. In this context, sequences potentially involved in embryogenesis processes in the coffee plant were identified in silico from libraries generated by the Brazilian Coffee Genome Project. Through these in silico analyses, we identified 15 EST-contigs related to the embryogenesis process. Among these, 5 EST-contigs (3605, 9850, 13686, 17240, and 17265) could readily be associated with plant embryogenesis. Sequence analysis of EST-contig 3605, 9850, and 17265 revealed similarity to a polygalacturonase, to a cysteine-proteinase, and to an allergenine, respectively. Results also show that EST-contig 17265 sequences presented similarity to an expansin. Finally, analysis of EST-contig 17240 revealed similarity to a protein of unknown function, but it grouped in the similarity dendrogram with the WUSCHEL transcription factor. The data suggest that these EST-contigs are related to the embryogenic process and have potential as molecular markers to increase methodological efficiency in obtaining coffee plant embryogenic materials.

Transcriptome analysis of resistant soybean roots infected by Meloidogyne javanica

Soybean is an important crop for Brazilian agribusiness. However, many factors can limit its production, especially root-knot nematode infection. Studies on the mechanisms employed by the resistant soybean genotypes to prevent infection by these nematodes are of great interest for breeders. For these reasons, the aim of this work is to characterize the transcriptome of soybean line PI 595099-Meloidogyne javanica interaction through expression analysis. Two cDNA libraries were obtained using a pool of RNA from PI 595099 uninfected and M. javanica (J(2)) infected roots, collected at 6, 12, 24, 48, 96, 144 and 192 h after inoculation. Around 800 ESTs (Expressed Sequence Tags) were sequenced and clustered into 195 clusters. In silico subtraction analysis identified eleven differentially expressed genes encoding putative proteins sharing amino acid sequence similarities by using BlastX: metallothionein, SLAH4 (SLAC1 Homologue 4), SLAH1 (SLAC1 Homologue 1), zinc-finger proteins, AN1-type proteins, auxin-repressed proteins, thioredoxin and nuclear transport factor 2 (NTF-2). Other genes were also found exclusively in nematode stressed soybean roots, such as NAC domain-containing proteins, MADS-box proteins, SOC1 (suppressor of overexpression of constans 1) proteins, thioredoxin-like protein 4-Coumarate-CoA ligase and the transcription factor (TF) MYBZ2. Among the genes identified in non-stressed roots only were Ser/Thr protein kinases, wound-induced basic protein, ethylene-responsive family protein, metallothionein-like protein cysteine proteinase inhibitor (cystatin) and Putative Kunitz trypsin protease inhibitor. An understanding of the roles of these differentially expressed genes will provide insights into the resistance mechanisms and candidate genes involved in soybean-M. javanica interaction and contribute to more effective control of this pathogen.