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Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (

The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two "local" ones, San Marzano and Vesuviano in two different locations of Campania region (Italy).Responses to environment were more pronounced in the two "local" genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted.Although similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup.

Abstract Background Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

IntroductionTomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored.MethodsHerein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits. ResultsThe results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential. DiscussionThe pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.

A pervasive assessment of air quality in an urban or mobile scenario is paramount for personal or city-wide exposure reduction action design and implementation. The capability to deploy a high-resolution hybrid network of regulatory grade and low-cost fixed and mobile devices is a primary enabler for the development of such knowledge, both as a primary source of information and for validating high-resolution air quality predictive models. The capability of real-time and cumulative personal exposure monitoring is also considered a primary driver for exposome monitoring and future predictive medicine approaches. Leveraging on chemical sensing, machine learning, and Internet of Things (IoT) expertise, we developed an integrated architecture capable of meeting the demanding requirements of this challenging problem. A detailed account of the design, development, and validation procedures is reported here, along with the results of a two-year field validation effort.

Presentiamo una metodologia basata sul telerilevamento per una rapida valutazione dello stato e delle tendenze della produttività del territorio (LP) a livello nazionale e subnazionale. Questa metodologia mira a sostenere le politiche ambientali nazionali e internazionali per raggiungere l'obiettivo di Land Degradation Neutrality nel quadro dell'Agenda 2030 delle Nazioni Unite e degli Obiettivi di sviluppo sostenibile. Il lavoro è stato eseguito utilizzando l'indice NDVI (Normalized Difference Vegetation Index) della NASA-MODIS come indicatore proxy dello stato e della tendenza di LP. Lo stato LP è stato identificato dalla media e dalla deviazione standard dei valori annuali LP 2000-2015. I trend di LP delle serie annuali sono state calcolate utilizzando i test Mann-Kendall (MK) e Contextual Mann-Kendal (CMK). La quantità di terreno con trend crescenti e decrescenti è stata valutata assumendo il livello di significatività del 95% nelle aree ove la qualità del dati NDVI è affidabile. L'area di trend LP crescenti e decrescenti è stimata per il territorio nazionale e per diverse coperture del suolo. Le variazioni di LP positive osservate sono sicumente correlate alla progressiva rinaturalizzazione del territorio in seguito alla diminuzione delle attività agricole e all'aumento delle precipitazioni nella stagione invernale nel periodo di riferimento. La diminuzione di LP ha interessato aree molto limitate correlate a variazioni delle precipitazioni stagionali e/o delle attività umane. I comuni maggiormente interessati dal declino o dall'aumento di LP vengono identificati allo scopo di individuare le aree ove possibilmente effettuare specifiche attività di monitoraggio e convalida future. We present a remote sensing-based methodology for rapid assessment of status and trends of Land Productivity (LP) at national and sub-national scales. This methodology aims at supporting environmental national and international policies to achieve the Land Degradation Neutrality target in the framework of the UN Agenda 2030 and the Sustainable Development Goals. The work was performed in Italy using the NASA-MODIS Normalized Difference Vegetation Index (NDVI) as proxy indicator of LP status and trend. LP status was identified by mean and standard deviation of 2000-2015 yearly LP values. LP trends of the yearly time series were computed using Mann-Kendall (MK) and Contextual MK (CMK) tests. The amount of land with valid increasing and decreasing trends is estimated assuming the 95% significance level of trends in the areas with good pixel reliability. The area of increasing and decreasing LP are estimated for the national territory and for different land covers. The widespread observed positive LP variations were correlated to the progressive renaturalization of lands subsequent to the decrease of agricultural activities and increasing precipitation trends in the winter season. LP decrease affected very limited areas and hot spots were correlated to changes of seasonal precipitation and human activities. The municipalities most affected by LP decline or increase are identified for future monitoring and validation activities.