Plant Genotype Research Articles

Pitting the olive seed microbiome

BackgroundThe complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed’s endosphere under sterile conditions.ResultsA diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.ConclusionsThis study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed’s microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.

Genotype-Dependent Response of Root Microbiota and Leaf Metabolism in Olive Seedlings Subjected to Drought Stress

Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in maintaining the host homeostasis remains insufficiently investigated. In this study, we aimed to assess the specificity of the foliar metabolic response of contrasting olive genotypes to microbial inoculation with wet-adapted consortia of plant-growth-promoting rhizobacteria (PGPR), to see if previously inoculated plants with indigenous or exogenous microbes would display any change in their leaf metabolome once being subjected to drought stress. Two Tunisian elite varieties, Chetoui (drought-sensitive) and Chemleli (drought-tolerant), were tested under controlled and stressed conditions. Leaf samples were analyzed by gas chromatography–mass spectrometry (GC-TOFMS) to identify untargeted metabolites. Root and soil samples were used to extract microbial genomic DNA destined for bacterial community profiling using 16S rRNA amplicon sequencing. Respectively, the score plot analysis, cluster analysis, heat map, Venn diagrams, and Krona charts were applied to metabolic and microbial data. Results demonstrated dynamic changes in the leaf metabolome of the Chetoui variety in both stress and inoculation conditions. Under the optimum state, the PGPR consortia induced noteworthy alterations in metabolic patterns of the sensitive variety, aligning with the phytochemistry observed in drought-tolerant cultivars. These variations involved fatty acids, tocopherols, phenols, methoxyphenols, stilbenoids, triterpenes, and sugars. On the other hand, the Chemleli variety displaying comparable metabolic profiles appeared unaffected by stress and inoculation probably owing to its tolerance capacity. The distribution of microbial species among treatments was distinctly uneven. The tested seedlings followed variety-specific strategies in selecting beneficial soil bacteria to alleviate stress. A highly abundant species of the wet-adapted inoculum was detected only under optimum conditions for both cultivars, which makes the moisture history of the plant genotype a selective driver shaping microbial community and thereby a useful tool to predict microbial activity in large ecosystems.

Unveiling the silver lining: examining the effects of biogenic silver nanoparticles on the growth dynamics of in vitro olive shoots

The current study aimed to evaluate the effects of biogenic silver nanoparticles (AgNPs) on growth behavior and leaf anatomy of in vitro growing shoots of ‘Picual’ and ‘Dolce’ olive cultivars. Biosynthesis of AgNPs was carried out using the cell-free filtrate of Fusarium oxysporum. The dimension and shape of the synthesized AgNPs have been analyzed using spectroscopy and topography analysis tools, confirming that the biosynthesis of AgNPs is a crystalline nanostructure with an average particle size of 37 nm. The shoots of the selected olive cultivars were cultured on Rugini olive medium-supplemented AgNPs at 0, 10, 20, and 30mg L− 1. The effect of genotypes on shoot multiplication was significant, ‘Picual’ recorded higher values of shoot growth parameters compared with ‘Dolce’ cultivar. Adding AgNPs to the culture medium significantly affected the growth of in vitro olive shoots. AgNPs at 20 and 30mg L− 1 produced higher values of the number of shoots, shoot length, and leaf number of Picual cv. compared with the control treatments, but the higher AgNPs concentration harmed the growth parameters of Dolce cv. and recorded lower growth values compared with the lower concentration (10mg L− 1). AgNPs had a significant effect on leaf morphology and their anatomical structure. The current results showed that the stimulatory effect of AgNPs on shoot growth of in vitro olive shoots is highly dependent on plant genotype and nanoparticle concentration.

Evaluation of Soybean Genotypes (Glycine max and G. soja) for Resistance to the Root-Knot Nematode, Meloidogyne enterolobii.

Potential resistance to the root-knot nematode (RKN) Meloidogyne enterolobii in 72 Glycine soja and 44 G. max soybean genotypes was evaluated in greenhouse experiments. Approximately 2,500 eggs of M. enterolobii were inoculated on each soybean genotype grown in a steam sterilized 1:1 sand to soil mixture. Sixty days postinoculation, plants were destructively harvested to determine the host status. The host status of each soybean genotype was determined by assessing root galling severity and calculating the final eggs per root system divided by the initial inoculum, or the reproduction factor (Rf). Five G. soja soybean genotypes were identified as resistant (Rf < 1) to M. enterolobii: '407202', '407239', '424083', '507618', and '639621'. None of the tested G. max soybean genotypes were identified as resistant to M. enterolobii. Some of the G. max genotypes determined to be susceptible to M. enterolobii include 'Hagood', 'Avery', 'Rhodes', 'Santee', and 'Bryan'. The genotype 'Bryan' had the lowest Rf values among the group at 5.06 and 6.67 in two independent trials, respectively, which represents a five- to sixfold increase in reproduction of M. enterolobii. Plant genotypes resistant to RKNs are effective in managing the disease and preserving yield, cost-efficient, and environmentally sustainable, and host resistance is often regarded as the most robust management tactic for controlling plant-parasitic nematodes. Resistance to RKNs in soybean genotypes has been identified for other Meloidogyne species, yet there is currently limited data regarding soybean host status to the highly aggressive nematode M. enterolobii. This study adds to the knowledge of potential native resistance to M. enterolobii in wild and cultivated soybean.

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process.

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Morphometric analysis of wild potato leaves

AbstractTo catalog and promote the conservation and use of crop wild relatives, comprehensive phenotypic and genotypic information must be available. Plant genotyping has the power to resolve the phylogenetic relationships between crop wild relatives, quantify genetic diversity, and identify marker-trait associations for expedited molecular breeding. However, access to cost-effective genotyping strategies is often limited in underutilized crops and crop wild relatives. Potato landraces and wild species, distributed throughout Central and South America, exhibit remarkable phenotypic diversity and are an invaluable source of resistance to pests and pathogens. Unfortunately, very limited information is available for these germplasm resources, particularly regarding phenotypic diversity and potential use as trait donors. In this work, more than 150 accessions corresponding to 12 species of wild and cultivated potatoes, collected from different sites across the American continent, were analyzed using computer vision and morphometric methods to evaluate leaf size and shape. In total, more than 1100 leaves and leaflets were processed and analyzed for nine traits related to size, shape, and color. The results produced in this study provided a visual depiction of the extensive variability among potato wild species and enabled a precise quantification of leaf phenotypic differences, including shape, color, area, perimeter, length, width, aspect ratio, convexity, and circularity. We also discussed the application and utility of inexpensive but comprehensive morphometric approaches to catalog and study the diversity of crop wild relatives. Finally, this study provided insights for further experimental research looking into the potential role of leaf size and shape variation in plant–insect interactions, agronomic productivity, and adaptation.

Performance of seedlings and yield of soybean genotypes under soil compaction

AbstractThe identification of soybean genotypes tolerant to soil compaction makes it possible to reduce productivity loss under stress conditions. Added to this, the prior selection of these genotypes will result in greater assertiveness in the positioning of cultivars in the field. Thus, the objective was to evaluate the susceptibility of soybean genotypes to compaction in greenhouse and field conditions; verify which characteristics of seedlings under high resistance to root penetration are correlated with crop production in compacted soil; and to validate the substrate mechanical impedance method for evaluating the susceptibility of plant genotypes to soil compaction. Seeds of 20 genotypes were sown in a substrate mechanical impedance system under controlled conditions. The characteristics evaluated were total root length, total root surface area, mean root diameter, total root volume, taproot length, shoot length, root dry matter and seedling shoot dry matter. In the field experiment, half of the planting area was compacted, constituting two treatments, soil with and without compaction. The percentage of seedling emergence, initial plant height, stem diameter, number of nodes, internode length, number of lateral branches, shoot dry matter, final plant height, absolute and relative growth rate, number of pods, weight of 100 seeds and grain yield. In addition, the number of days between soybean sowing until plant flowering and grain harvest was recorded according to genotype and soil compaction level. In a controlled environment, genotypes tolerant to soil compaction show greater plasticity of root characteristics and smaller alterations in the shoot of seedlings. In the field, these genotypes show smaller reductions in growth rate, height, number of pods and grain yield. The shoot dry matter and the root dry matter of soybean seedlings in a mechanical impedance system present a positive and negative correlation, respectively, with soybean yield in compacted soil, indicating that the genetically determined susceptibility to soil compaction stress was similar throughout ontogenesis. The substrate mechanical impedance system used to evaluate the performance of soybean seedlings under stress, facilitates the decision‐making in breeding programs focused on identifying genotypes expressing soil compaction tolerance.

Influence of different factors on in vitro multiplication and rooting of three local Juglans regia L. genotypes in Uzbekistan

The Persian walnut (Juglans regia L.) is one of the most lucrative and widely distributed nut crops. It is appreciated as a forestry and ornamental tree in addition to its benefits as a fruit crop. Although Central Asian countries, especially Uzbekistan, are among the origins of the Persian walnut; they are not considered as top industrial producers of walnuts. Uzbekistan possesses a wide range of walnut genetic resources and as a result of conducted research, several promising, fruitful, early-harvesting varieties and forms have been selected. The aim of this study is to optimize microclonal in vitro propagation of selected Uzbekistan local varieties and forms by evaluating concentrations of different plant growth regulators and genotype on multiplication and rooting stages. As mother plants, 2 forms and one variety were selected: the Ideal variety, 'Form PDM23' and 'Form 202YaKT'. ?n the proliferation stage, the growth rate of walnut microshoots on basal medium Driver and Kuniyuki Walnut Medium (DKW) with different concentrations of 6-benzylaminopurine (BAP) and Indole-3-butyric acid (IBA) (0.01 mg/L) was studied. The rooting stage was assessed in half strength macronutrient DKW medium containing different IBA concentrations (0.0, 2.0, 4.0 and 6.0 mg/L). The Ideal variety and 'Form PDM23' performed best in DKW medium supplied with 1.5 mg/L BAP and 0.01 mg/L IBA, whereas 'Form 202YaKT' performed best in DKW medium supplemented with 1.0 mg/L BAP and 0.01 mg/ L IBA for the proliferation stage. For all genotypes, 6.0 mg/L IBA provided the best rooting results.

Reaction of Brazilian genotypes of pulses (pea, chickpea and lentil) to the root-knot nematode Meloidogyne enterolobii

Summary The root-knot nematode, Meloidogyne enterolobii, is an important pathogen of numerous crops, including the so-called pulses. Hence, it is necessary to identify genetic resistance, as it is the most efficient, cost-effective, and environmentally sound way to manage nematodes in the field. The objective of this study was to screen a Brazilian germplasm collection of pulse crops (peas, chickpeas, and lentils) comprising accessions from the Embrapa Germplasm Bank and commercial cultivars against M. enterolobii under glasshouse conditions. The experiment was conducted with 23 treatments (genotypes), i.e., 14 pea, six chickpea and one lentil genotype, and two tomato cultivars, ‘Rutgers’ (susceptible) and ‘Nemadoro’ (resistant). Each plant (replication) was inoculated with 5000 eggs and second-stage juveniles (J2) of M. enterolobii and evaluated 65 days after inoculation, considering the following variables: gall index, egg mass index, number of eggs per g of roots, and reproduction factor. The experiments were conducted at two independent time points (summer and autumn/winter). Results showed that all 23 plant genotypes were susceptible to the nematode, with pea genotype ‘Itapuã’ being intolerant to infection. Cultivation of pulse crops has been steadily increasing both in Brazil and worldwide. Our research findings make a valuable contribution to the ongoing efforts to identify genetic resistance to nematode pathogens that can significantly affect the productivity of these crops. By identifying and developing resistant genotypes, pulse crop yields can be safeguarded, and sustainable agricultural practices can be supported.

Optimization of an Efficient Direct Shoot Induction System and Histological Evaluation of Shoot Formation in Cucurbita maxima Duch

Improving plant regeneration ability and shortening regeneration time can promote the development of genetic transformation breeding technology for horticultural crops. We optimized several culture conditions, including explant type, mother plant genotype, and medium, to improve shoot formation in winter squash (Cucurbita maxima Duch.). Histological analysis of the occurrence of shoots was also carried out. The results indicate that cotyledon was the most suitable explant for inducing the shoot regeneration of winter squash. We found that ‘Jin-li’ had a shorter shoot induction time and a higher average number of shoots. The highest induction rate of 95.23% among the five lines. The average shoot induction rate of five lines was the highest (84.85%) on Murashige and Skoog (MS) medium supplemented with 2.0 mg/L 6-benzylaminopurine (6-BA) and 0.2 mg/L indole-3-acetic acid (IAA). We also found that there was an interaction between genotypes and induction media, and their interaction had a greater impact on the shoot induction rate than individual effects. Histological observation revealed that the induced shoots of winter squash cotyledons originated from subepidermal cells. We also found that the optimal medium for de novo root regeneration was 1/2 MS. We acclimatized and cultivated regenerated plants and harvested their fruits, which maintained the characteristics of mother plants. These findings lay an important foundation for further research on direct shoot regeneration and accelerate its application in winter squash genetic transformation.

Potential of Cassava Clones for Iron, Zinc, and Selenium Biofortification

Cassava (Manihot esculenta Crantz) is a crucial staple food in South America, providing starchy storage roots that contribute to the sustenance of millions. To address deficiencies in iron (Fe), zinc (Zn), and selenium (Se), a global initiative is underway to identify plant species and genotypes that naturally accumulate these nutrients for human consumption, such as cassava. In this way, this study aims to identify potential cassava genotypes for biofortification in Fe, Zn, and Se, while also improving the overall cassava yield. We evaluated the accumulation potential of Fe, Zn, and Se in 20 South American cassava genotypes under traditional growing conditions, concurrently examining their photosynthetic and growth characteristics. Cassava roots exhibited Zn content ranging from 3.20 to 8.56 mg kg−1, Fe content from 2.20 to 10.73 mg kg−1, and Se content from 1.20 to 9.43 µg kg−1 (expressed on a dry basis). Genotypes MS018, DG014, and DG839 emerged as promising candidates for biofortification programs, displaying elevated levels of Fe, Zn, and Se, coupled with superior photosynthetic capacity. These genotypes, recommended for biofortification programs, also demonstrated increased yield potential. The findings from this study contribute to the development of cassava genotypes with enhanced agronomic biofortification and elevated yield potential.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria.

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

The effect of type and combination of fertilizers on eukaryotic microbiome of date palm rhizosphere

The date palm (Phoenix dactylifera) is an important cultivated crop in arid areas. Here, we studied the effect of plant genotype and type of fertilizers on the eukaryotic community structures of the date palm rhizosphere. Samples were collected from one wild population, five cultivars from two farms, and a factorial fertilizer experiment (organic, chemical, and biofertilizer) in Qatar. The eukaryotic communities were sequenced using a next-generation sequencing method. A total of 2422 Operational Taxonomic Units (OTUs) were identified as belonging to 15 phyla, Chlorophyta, Streptophyta, Imbricatea, Chytridiomycota, Ascomycota, Olpidiomycota, being dominant. The wild-type date palms showed a low number of OTUs compared to cultivated date palms, potentially due to the strong influence of soil salinity and low moisture level. However, the wild-type date palm hosted the highest number of unique OTUs. PCA revealed that the eukaryotic microbiome of the wild date palms was separated from the cultivated date palms and that the eukaryotic microbial diversity varied between date palm cultivars in similar environments. Using the highest amounts of biofertilizer and chemical fertilizer decreased the species diversity within the samples. However, a high concentration of biofertilizer combined with a low concentration of chemical fertilizers enhanced the eukaryotic diversity within the samples. We conclude that cultivar type (biotic factor), type of fertilizer, and dosage (abiotic factor) play significant roles in determining the microbiome diversity of the rhizosphere. The wild date palm population could potentially host salt and drought-tolerating eukaryotes that should be further investigated for future development of biofertilizers suitable for drylands.

Tomato plant response to heat stress: a focus on candidate genes for yield-related traits.

Climate change and global warming represent the main threats for many agricultural crops. Tomato is one of the most extensively grown and consumed horticultural products and can survive in a wide range of climatic conditions. However, high temperatures negatively affect both vegetative growth and reproductive processes, resulting in losses of yield and fruit quality traits. Researchers have employed different parameters to evaluate the heat stress tolerance, including evaluation of leaf- (stomatal conductance, net photosynthetic rate, Fv/Fm), flower- (inflorescence number, flower number, stigma exertion), pollen-related traits (pollen germination and viability, pollen tube growth) and fruit yield per plant. Moreover, several authors have gone even further, trying to understand the plants molecular response mechanisms to this stress. The present review focused on the tomato molecular response to heat stress during the reproductive stage, since the increase of temperatures above the optimum usually occurs late in the growing tomato season. Reproductive-related traits directly affects the final yield and are regulated by several genes such as transcriptional factors, heat shock proteins, genes related to flower, flowering, pollen and fruit set, and epigenetic mechanisms involving DNA methylation, histone modification, chromatin remodelling and non-coding RNAs. We provided a detailed list of these genes and their function under high temperature conditions in defining the final yield with the aim to summarize the recent findings and pose the attention on candidate genes that could prompt on the selection and constitution of new thermotolerant tomato plant genotypes able to face this abiotic challenge.

Potential of Endophytious Fungi from Rice Plant Local Genotype Kuantan Singingi in Improving Rice Plant Growth

This study aims to investigate the potential of endophytic fungi derived from local genotypes of Pulut Karate and white Sisgam rice plants to enhance the growth of rice plants. The research was conducted in a laboratory setting using an experimental approach. Initially, the endophytic fungi were isolated from the rice plants of Pulut Karate and white lionfish genotypes, which were previously collected in another research project. These fungi were then cultured on PDA media and incubated for seven days. Subsequently, the germination and growth of rice seedlings inoculated with each endophytic fungus isolate were examined. The growth parameters of the rice seedlings, including seed height, root length, and number of leaves, were carefully observed. The findings of this research were presented in the form of data and images. The results indicate that the seed germination rate ranged from 90% to 100%. Among all the isolates, isolate PB03 demonstrated the most significant impact on rice plant growth, as evidenced by its taller plant height (8.03 cm) and longer root length (6.27 cm) compared to the other isolates and the control group.

Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events

BackgroundThe aim of this study was to evaluate and characterize the mutations induced by two TALE-based approaches, double-strand break (DSB) induction by the FokI nuclease (mitoTALEN) and targeted base editing by the DddA cytidine deaminase (mitoTALECD), to edit, for the first time, the mitochondrial genome of potato, a vegetatively propagated crop. The two methods were used to knock out the same mitochondrial target sequence (orf125).ResultsTargeted chondriome deletions of different sizes (236–1066 bp) were induced by mitoTALEN due to DSB repair through ectopic homologous recombination of short direct repeats (11–12 bp) present in the target region. Furthermore, in one case, the induced DSB and subsequent repair resulted in the amplification of an already present substoichiometric molecule showing a 4288 bp deletion spanning the target sequence. With the mitoTALECD approach, both nonsense and missense mutations could be induced by base substitution. The deletions and single nucleotide mutations were either homoplasmic or heteroplasmic. The former were stably inherited in vegetative offspring.ConclusionsBoth editing approaches allowed us to obtain plants with precisely modified mitochondrial genomes at high frequency. The use of the same plant genotype and mtDNA region allowed us to compare the two methods for efficiency, accuracy, type of modifications induced and stability after vegetative propagation.

Elevated atmospheric CO2 combined with Epichloë endophyte may improve growth and Cd phytoremediation potential of tall fescue (Festuca arundinacea L.).

Complex environmental conditions like heavy metal contamination and elevated CO2 concentration may cause numerous plant stresses and lead to considerable crop losses worldwide. Cadmium is a non-essential element and potentially highly toxic soil metal pollution, causing oxidative stress in plants and human toxicity. In order to assess a combination of complex factors on the responses of two genotypes of Festuca arundinacea (75B and 75C), a greenhouse experiment was conducted on plants grown in two Cd-contaminated soil conditions and two soil textures under combined effects of elevated ambient CO2 (700ppm) and Epichloë endophyte infection. Plant biomass, Cd, Fe, Cu, Zn, and Mn concentrations in the plant shoots and roots, Fv/Fm, chlorophyll (a & b), and carotenoid contents were measured after 7months of growth in pots. Our results showed that endophyte-infected plants (E+) grown in elevated CO2 atmosphere (CO2+), clay-loam soil texture (H) with no Cd amendment (Cd-) in the genotype 75B had significantly greater shoot and root biomass than non-infected plants (E-) grown in ambient CO2 concentration (CO2-), sandy-loam soil texture (L) with amended Cd (Cd+) in the genotype 75C. Increased CO2 concentration and endophyte infection, especially in the genotype 75B, enabled Festuca for greater phytoremediation of Cd because of higher tolerance to Cd stress and higher biomass accumulation in the plant genotype. However, CO2 enrichment negatively influenced the plant mineral absorption due to the inhibitory effects of high Cd concentration in shoots and roots. It is concluded that Cd phytoremediation can be positively affected by the increased atmospheric CO2 concentration, tolerant plant genotype, heavy soil texture, and Epichloë endophyte. Using Taguchi and AIC design methodologies, it was alsopredicted that the most critical factors affecting Cd phytoremediation potential were CO2 concentration and plant genotype.

Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis

In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant’s OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.

Factors influencing yield, chemical composition and efficacy of essential oils

Essential oils are secondary metabolites that are produced by plants for the purpose of protection from pests, predators, attraction of pollinators and seed dispersal. The oil is produced in different parts of the plants and contains various chemical compounds that give plants a characteristic odour and flavor. These compounds vary between different plant species and also within plants of the same species. The yield and the efficacy of essential oils also vary between and within species. The variations in the essential oil compounds, the yield and the efficacy is influenced by both exogenous and endogenous factors. Endogenous factors such as plant age, plant density, plant genotype, part of the plant where the oil is extracted brings about variability in yield, chemical composition and the efficacy of essential oils. Similarly, exogenous factors such as light intensity and temperature, water availability, altitude and latitude, soil type and composition, preparation of the plant material before the essential oil extraction, method of extraction of the essential oil and the storage conditions after extraction also have a great influence on the chemical composition, yield and efficacy of essential oils. The factors then need to be moderated in order to ensure that the essential oil produced is of the quality required. Once extraction is done, proper storage conditions to avoid oxidation is necessary as the essential oils await to be used. They should be stored in dark cool conditions in tightly closed dark glass containers to ensure long term quality. Knowledge on the growth requirements of the individual plants that produce oils is necessary so as to produce quality oil.

Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping.

Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.