Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture

Two main distinct evolutionary stories describe the Italian grapevine assortment

A dataset of high-quality 7k SNP profiles of 1,038 unique Eurasian grapevine varieties was used to infer the most likely grapevine migration events, a spatial ancestry estimation, and a model about the origin of Eurasian grapevine germplasm. The comparison of putative gene flow scenarios from Caucasus throughout Europe aided to fit the more reliable spreading routes around the Mediterranean Basin. The same dataset was also used to assess the population genetic diversity, structure, and relatedness of Italian varieties. These data suggested a different history between Northern and Southern Italian grapevines, appearing clearly split into two different clusters. Interestingly, the Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The same SNP panel was used to determine parental relationships, identifying the main parents of traditional Italian and closely related cultivars. The parentage network suggested that Italian germplasm largely originated from a few key parents distributed into several geographical areas of genetic influence, with more or less large overlaps. These key cultivars are ‘Bombino bianco’, ‘Garganega’/‘Grecanico’, ‘Mantonico bianco’, ‘Orsolina’/‘Coccalona nera’, ‘Muscat à petits grains blanc’, ‘Malvasia odorosissima’, ‘Sangiovese’, ‘Sciaccarello’, ‘Visparola’ and ‘Vulpea’. The pedigree reconstruction by fullsib and second-degree relationships highlighted the pivotal role of some cultivars, such as ‘Visparola’, until now scarcely known. A hypothetic migration of this variety from Southern to Northern Italy along the Eastern side, as well as ‘Sangiovese’ migration from Southern to Central Italy along the Western side might be supposed. Moreover, ‘Muscat à petits grains blanc’, mainly through its offspring ‘Malvasia odorosissima’, furnished a consistent contribution to the development of many aromatic grapes grown in the Northern-Western part of the Italian Peninsula. These results represent the most complete study of grapevine Italian population genetics that has been carried out until now on the Italian germplasm

On the Intriguing Problem of Counting (n+1,n+2)-Core Partitions into Odd Parts

Tewodros Amdeberhan and Armin Straub initiated the study of enumerating subfamilies of the set of (s,t)-core partitions. While the enumeration of (n+1,n+2)-core partitions into distinct parts is relatively easy (in fact it equals the Fibonacci number F_{n+2}), the enumeration of (n+1,n+2)-core partitions into odd parts remains elusive. Straub computed the first eleven terms of that sequence, and asked for a "formula," or at least a fast way, to compute many terms. While we are unable to find a "fast" algorithm, we did manage to find a "faster" algorithm, which enabled us to compute 23 terms of this intriguing sequence. We strongly believe that this sequence has an algebraic generating function, since a "sister sequence" (see the article), is OEIS sequence A047749 that does have an algebraic generating function. One of us (DZ) is pledging a donation of 100 dollars to the OEIS, in honor of the first person to generate sufficiently many terms to conjecture (and prove non-rigorously) an algebraic equation for the generating function of this sequence, and another 100 dollars for a rigorous proof of that conjecture. Finally, we also develop algorithms that find explicit generating functions for other, more tractable, families of (n+1,n+2)-core partitions.Comment: 12 pages, accompanied by Maple package. This version announces that our questions were all answered by Paul Johnson, and a donation to the OEIS, in his honor, has been mad

Effetti della riduzione degli input di coltivazione sul girasole (<i>Helianthus annuus</i> L.) coltivato in diversi ambienti mediterranei

A two year field experiment was carried out on six different environmental sites of Middle and Southern Italy with the aim of evaluating the effects of some low input cultural techniques on yield of sunflower (Helianthus annuus L.). In each sites sunflower commerciai hybrids were sown at different dates between January to April. Normal and minimum soil tillage were included in the experimental design, and irrigation treatments were also tested in two sites. Yield response of sunflower to minimum tillage treatments did not show in most cases a significant variation in comparison with ordinary tillage methods. Early sowing enhanced or decreased sunflower performance according to the agrometeorological features of the sites. Irrigation determined a significant yield effect but in some cases water efficiency was lower in early sowing treatments. The results indicate the possibility of reducing energy input in sunflower without remarkable yield depression, by adapting cultural techniques and hybrid choice to the environmental characteristics. Due anni di sperimentazione in campo sono stati condotti in sei differenti ambienti dell'Italia Centro-Meridionale al fine di valutare la possibilità di una semplificazione della tecnica colturale in girasole. Sono stati saggiati ibridi di diversa precocità seminati in differenti epoche e sottoposti ad un diverso grado di intensificazione delle lavorazioni. In due delle unità operative (UUOO) sono stati sperimentati anche diversi trattamenti irrigui. Nella maggior parte dei casi la lavorazione ridotta non ha determinato differenze significative di resa rispetto alla tecniche tradizionali di preparazione del terreno, mettendo in evidenza la capacità del girasole di sfruttare l'effetto residuo delle lavorazioni. L'anticipo delle semine ha avuto un effetto sulle rese variabile a seconda del sito di sperimentazione, indicando che in alcuni ambienti questo accorgimento consente di utilizzare al meglio le eventuali piogge invernali e primaverili. L'eliminazione o la riduzione degli apporti irrigui ha invece determinato significative riduzioni di produzione, anche se in alcune situazioni questo effetto è risultato meno marcato con le epoche di semina anticipate. Il primo biennio di sperimentazione ha messo in evidenza che la riduzione degli input nella coltivazione del girasole sia proponibile anche dal punto di vista economico purché si adegui la scelta delle tecniche colturali e dei genotipi alle caratteristiche ambientali

Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance

The salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress responses, were identified. The expression of genes involved in trehalose metabolism, RNA processing, vesicle trafficking, cell wall organization, and signal transduction was significantly enhanced by the AMF symbiosis. A downregulation of genes involved in both enzymatic and non-enzymatic oxidative stress responses as well as amino acids, lipids, and carbohydrates metabolisms was also detected, suggesting a lower oxidative stress condition in the AMF inoculated plants. Interestingly, many transcription factor families, including WRKY, NAC, and MYB, already known for their key role in plant abiotic stress response, were found differentially expressed between treatments. This study provides valuable insights on AMF-induced gene expression modulation and the beneficial effects of plant-AMF interaction in durum wheat under salt stress

Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a “bridge” between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world

Salinity in Autumn-Winter Season and Fruit Quality of Tomato Landraces

Tomato landraces, originated by adaptive responses to local habitats, are considered a valuable resource for many traits of agronomic interest, including fruit nutritional quality. Primary and secondary metabolites are essential determinants of fruit organoleptic quality, and some of them, such as carotenoids and phenolics, have been associated with beneficial proprieties for human health. Landraces' fruit taste and flavour are often preferred by consumers compared to the commercial varieties' ones. In an autumn-winter greenhouse hydroponic experiment, the response of three Southern-Italy tomato landraces (Ciettaicale, Linosa and Corleone) and one commercial cultivar (UC-82B) to different concentrations of sodium chloride (0 mM, 60 mM or 120 mM NaCl) were evaluated. At harvest, no losses in marketable yield were noticed in any of the tested genotypes. However, under salt stress, fresh fruit yield as well as fruit calcium concentration were higher affected in the commercial cultivar than in the landraces. Furthermore, UC-82B showed a trend of decreasing lycopene and total antioxidant capacity with increasing salt concentration, whereas no changes in these parameters were observed in the landraces under 60 mM NaCl. Landraces under 120 mM NaCl accumulated more fructose and glucose in the fruits, while salt did not affect hexoses levels in UC-82B. Ultra-performance liquid chromatography-tandem mass spectrometry analysis revealed differential accumulation of glycoalkaloids, phenolic acids, flavonoids and their derivatives in the fruits of all genotypes under stress. Overall, the investigated Italian landraces showed a different behaviour compared to the commercial variety UC-82B under moderate salinity stress, showing a tolerable compromise between yield and quality attributes. Our results point to the feasible use of tomato landraces as a target to select interesting genetic traits to improve fruit quality under stress conditions

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution

High-throughput 18K SNP array to assess genetic variability of the main grapevine cultivars from Sicily

The viticulture of Sicily, for its vocation, is one of the most important and ancient forms in Italy. Autochthonous grapevine cultivars, many of which known throughout the world, have always been cultivated in the island from many centuries. With the aim to preserve this large grapevine diversity, previous studies have already started to assess the genetic variability among the Sicilian cultivars by using morphological and microsatellite markers. In this study, simple sequence repeat (SSR) were utilized to verify the true-to-typeness of a large clone collection (101) belonging to 21 biotypes of the most 10 cultivated Sicilian cultivars. Afterwards, 42 Organization Internationale de la Vigne et du Vin (OIV) descriptors and a high-throughput single nucleotide polymorphism (SNP) genotyping array (Vitis18kSNP) were applied to assess genetic variability among cultivars and biotypes of the same cultivar. Ampelographic traits and high-throughput SNP genotyping platforms provided an accuracy estimation of genetic diversity in the Sicilian germplasm, showing the relationships among cultivars by cluster and multivariate analyses. The large SNP panel defined sub-clusters unable to discern among biotypes, previously classified by ampelographic analysis, belonging to each cultivar. These results suggested that a very large number of SNP did not cover the genome regions harboring few morphological traits. Genetic structure of the collection revealed a clear optimum number of groups for K = 3, clustering in the same group a significant portion of family-related genotypes. Parentage analysis highlighted significant relationships among Sicilian grape cultivars and Sangiovese, as already reported, but also the first evidences of the relationships between Nero d’Avola and both Inzolia and Catarratto. Finally, a small panel of highly informative markers (12 SNPs) allowed us to isolate a private profile for each Sicilian cultivar, providing a new tool for cultivar identification