Jonathan Nuñez

Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families

The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily.

Biological nitrification inhibition activity in a soil-grown biparental population of the forage grass, Brachiaria humidicola

AimUtilization of biological nitrification inhibition (BNI) strategy can reduce nitrogen losses in agricultural systems. This study is aimed at characterizing BNI activity in a plant-soil system using a biparental hybrid population of Brachiaria humidicola (Bh), a forage grass with high BNI potential but of low nutritional quality.MethodsSoil nitrification rates and BNI potential in root-tissue were analyzed in a hybrid population (117), obtained from two contrasting Bh parents, namely CIAT 26146 and CIAT 16888, with low and high BNI activity, respectively. Observed BNI activity was validated by measuring archaeal (AOA) and bacterial (AOB) nitrifier abundance in the rhizosphere soil of parents and contrasting hybrids. Comparisons of the BNI potential of four forage grasses were conducted to evaluate the feasibility of using nitrification rates to measure BNI activity under field and pot grown conditions.ResultsHigh BNI activity was the phenotype most commonly observed in the hybrid population (72%). BNI activity showed a similar tendency for genotypes grown in pots and in the field. A reduction in AOA abundance was found for contrasting hybrids with low nitrification rates and high BNI potential.ConclusionBh hybrids with high levels of BNI activity were identified. Our results demonstrate that the microcosm incubation and the in vitro bioassay may be used as complementary methods for effectively assessing BNI activity. The full expression of BNI potential of Bh genotypes grown in the soil (i.e. low nitrification rates) requires up to one year to develop, after planting.

Low 15N Natural Abundance in Shoot Tissue of Brachiaria humidicola Is an Indicator of Reduced N Losses Due to Biological Nitrification Inhibition (BNI)

The tropical forage grass Brachiaria humidicola (Bh) suppresses the activity of soil nitrifiers through biological nitrification inhibition (BNI). As a result, nitrate (NO3−) formation and leaching are reduced which is also expected to tighten the soil nitrogen (N) cycle. However, the beneficial relationship between reduced NO3− losses and enhanced N uptake due to BNI has not been experimentally demonstrated yet. Nitrification discriminates against the 15N isotope and leads to 15N depleted NO3−, but 15N enriched NH4+ in soils. Leaching of 15N depleted NO3− enriches the residual N pool in the soil with 15N. We hypothesized that altered nitrification and NO3− leaching due to diverging BNI magnitudes in contrasting Bh genotypes influence soil 15N natural abundance (δ15N), which in turn is reflected in distinct δ15N in Bh shoot biomass. Consequently, high BNI was expected to be reflected in low plant δ15N of Bh. It was our objective to investigate under controlled conditions the link between shoot value of δ15N in several Bh genotypes and leached NO3− amounts and shoot N uptake. Additionally, plant 15N and N% was monitored among a wide range of Bh genotypes with contrasting BNI potentials in field plots for 3 years. We measured leaf δ15N of young leaves (regrown after cutback) of Bh and combined it with nitrification rates (NRs) of incubated soil to test whether there is a direct relationship between plant δ15N and BNI. Increased leached NO3− was positively correlated with higher δ15N in Bh, whereas the correlation between shoot N uptake and shoot δ15N was inverse. Field cultivation of a wide range of Bh genotypes over 3 years decreased NRs in incubated soil, while shoot δ15N declined and shoot N% increased over time. Leaf δ15N of Bh genotypes correlated positively with NRs of incubated soil. It was concluded that decreasing plant δ15N of Bh genotypes over time reflects the long-term effect of BNI as linked to lower NO3− formation and reduced NO3− leaching. Accordingly, a low δ15N in Bh shoot tissue verified its potential as indicator of high BNI activity of Bh genotypes.

The Effect of Pre-Harvest Methyl Jasmonate Treatment on the SelectedVolatile Compounds and Endogenous Hormones Contends in the Pulp ofGrape Berries

Grapevine is one of the most valued and widely cultivated fruit crop worldwide, with their pleasant flavor and valuable health effects. During the consequent ripening at ambient temperature, the volatile compounds of table grape often decreased, to affect their sensory evaluation. The development of new and effective methods to increase the volatile compounds of berries is necessary. Present study was carried out to investigate the pre-harvest methyl jasmonate (MeJA) treatment on the selected volatile compounds and endogenous hormones content from ‘Shine Muscat’ berries pulp. The results indicated that, pre-harvest application of MeJA (0.1 mM or 0.01 mM) on grape berries generally enhanced the production of terpenes, like nerol, linalool, alpha-terpineol; While some C6 compounds were reduced, such as (E)-2-hexenol, hexanol, (Z)-3-hexenol, hexanal and (E)-2-hexenal. The endogenous hormones like IAA (indole acetic acid), ABA (abscisic acid) and JA (jasmonate acid) content were also changed after MeJA treatment. We also observed that MeJA palys a key role in fruit endogenous hormones level and volatile compounds by increasing the expression level of several related genes, such as aroma-related genes Vvter, Vv-syn and hormone-related genes VvOPR3, VvAuI, VvEth, VvNCED1. We hypothesize that, MeJA as an effective elicitor affects the volatile compounds by altering endogenous hormones level in berries pulp of ‘Shine Muscat’.

Evidence of Epigenetic Mechanisms Affecting Carotenoids

Epigenetic mechanisms are able to regulate plant development by generating non-Mendelian allelic interactions. An example of these are the responses to environmenal stimuli that result in phenotypic variability and transgression amongst important crop traits. The need to predict phenotypes from genotypes to understand the molecular basis of the genotype-by-environment interaction is a research priority. Today, with the recent discoveries in the field of epigenetics, this challenge goes beyond analyzing how DNA sequences change. Here we review examples of epigenetic regulation of genes involved in carotenoid synthesis and degradation, cases in which histone- and/or DNA-methylation, and RNA silencing at the posttranscriptional level affect carotenoids in plants.