The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora,Coffea eugenioidesand their interspecific hybridCoffea arabica). A total of 1311 non-redundant NLR loci were identified inC. arabica, 927 inC. canephora, and 1079 inC. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. TheC. arabicagenome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, andC. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared betweenC. arabicaand the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.

Pathogen‐associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plasma membrane. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post‐inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or co-receptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species.

Setaria viridis (L.) P. Beauv. is a species proposed to be used as model plant in reverse genetics studies for the validation of gene function. Soil salinity is a recurring problem present in more than a 100 countries worldwide, and approximately 20% of the agricultural land in the world has saline and/or sodium soils. Saline stress affects all the main processes of the plant, such as germination, growth, and, consequently, the yield. The present study aimed at determining the tolerance levels of S. viridisA10.1 to saline stress and identify its potential as a model plant to validate salt-tolerance candidate genes/alleles as well as promoter sequences from salt-responsive genes. In an initial experiment, the seeds of the plant were sown on a germination medium containing an increasing concentration of NaCl (0, 30, 60, 90, 120, or 150 mM), and maintained there during the initial growth stage; and, in another experiment, the plants at the vegetative growth stage were submitted to increasing doses of NaCl (0.0, 0.2, 0.4, 0.6, 0.8, and 1.0g per 100g of the substrate). The germination rate was found to be affected a little by the salinity, while the seedlings development was impaired right after germination. Plant in the vegetative growth stage experienced a reduction in the evapotranspiration rates and pigment levels, along with an impairment in the system of capture and use of light, and a decrease in the leaf gas exchange rates, resulting in less accumulation of dry and fresh plant biomass proportional to the salt dose used. Plants started to die within a week at doses ≥19.4 dS/m. In conclusion, A10.1 is a glycophyte plant with some level of salt-tolerance and might be used as a model plant to validate salt-tolerance candidate genes/alleles, as well as promoters salt-responsive genes, depending on the right combination of plant age and level of stress. As seed germination is affected only little by salt stress at NaCl doses of about 15 dS/m or less, A10.1 might not be used to validate genes/alleles with a putative role regarding this trait.

The objective of this work was to determine the suitability of Setaria viridis as a model plant in studies to validate candidate genes for cold tolerance by evaluating the response of two of its accessions to different durations of abrupt or gradual cold stress in the vegetative and reproductive stages. Plants of accessions A10.1 and Ast-1, cultivated at 25°C, were subjected to the following cold stress treatments: gradual reduction in temperature from 25 to 0°C, 5°C at a time, every 24 hours in a same chamber; or abrupt reduction in temperature, by transferring plants from a chamber at 25°C to another at 0°C. Plants were kept at 0°C for 3, 5, or 10 days, after which temperature was increased back again to 25°C; a control group remained at 25ºC. Low temperatures – reduced abruptly or gradually – caused a decrease in the gas exchange rates and shoot and root biomass of the plants, besides damage to their photochemical apparatus; the longer the cold lasted, the more pronounced the effect was. Regardless of stress duration, plants recovered and completed their life cycle. The studied accessions are tolerant to cold and, therefore, are not suitable as a model plant in studies to validate candidate genes for cold tolerance.