Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat

Physiological responses of processing tomato in organic and conventional Mediterranean cropping systems

Processing tomato is a globally important horticultural crop. It is generally grown in high-input conventional systems, and there is little knowledge regarding its physiological responses in organic cultivation. Therefore, the aim of this work was to determine the influence of organic management on the physiological behavior of cultivars of processing tomato usually cultivated in conventional management in a Mediterranean area. The study was performed by means of: (1) field testing of a set of commercial cultivars for 2 years, in two systems, in one location in Southern Italy, and (2) crop physiological investigations during the growth cycle of processing tomato. Results of the two-year trials indicate that, under the organic cropping system, processing tomato showed, as 2 years average, higher intercellular CO2 concentration (Ci) (+10.3%), transpiration (E) (+15.5%) and stomatal conductance (gs) (+16.5%). Average net assimilation (A) was similar in the two systems and differences were only observed depending on years. In contrast, average leaf area index (LAI) and water use efficiency (WUE) were lower in the organic cropping system ( 1242% and 1217.8%), as were average fruit (FDW) and total (TDW) dry weight ( 1237.5% and 1229%). In our conditions, LAI at the end of the cultivation was highly correlated with total and fruit dry weight. As differences in fruit and total dry weight of processing tomato cannot be explained by differences in net assimilation per leaf area unit, other reasons may be linked to the effects of the organic management on the crop as weeds and pathogens

A Preliminary Approach in Mendelizing Barley FR-H1 and FR-H2 QTLs

Freezing temperatures is one of the major limitations among the abiotic stresses in Triticeae crops, and two major Quantitative Trait Loci of frost resistance (namely, FR-H1 and FR-H2) have been mapped in barley on the long arm of chromosome 5. FR-H1 co-segregated with the vernalization requirement gene VRN-H1, while FR-H2 encompasses a cluster of at least 13 different C-repeat Binding Factor (CBF) genes that activate cold acclimation. To disentangle the effect of FR-H1 and FR-H2, four reciprocals Near Isogenic Lines (NILs) were developed. The donor of the winter/resistance alleles was cv. Nure, while the donor of the spring/susceptible alleles was cv. Tremois. Marker-assisted backcross scheme was used to separate FR-H1 and FR-H2 in alternative backgrounds. PCR-based molecular markers for HvCBF3 (FR-H2) and HvBM5 (FR-H1) were used for selection, and after at least four backcrossing generations, selected plants underwent multiple selfing. The genotypic status of the lines was initially tested using 19 SSR markers scattered throughout the genome, then with via 9k iSelect array genotyping. After preliminary experiments in controlled conditions , two locations were selected to assess the winter survival rate (WSR) and agronomical traits: Reggio Emilia, Po valley area, and Wooster, Ohio, USA. In Wooster the winter was cold enough to assess the WSR and the winter allele of FR-H2 increased the WSR in the susceptible (Trèmois) background; conversely, the winter allele of FR-H1 did not significantly increase the resistance in the susceptible (Trèmois) background. For the lines with the Nure genomic background, allele substitution at either FR-H1 or FR-H2 with spring alleles did not reduce WSR, indicating an important role by the other factors in winter (Nure) genomic background in regulating the frost resistance. In Reggio Emilia WSR was the same for QTL-NILs, Nure and Tremois due to mild winter. These results indicate that winter FR-H2 allele is sufficient to enhance freezing tolerance in susceptible genotypes, but that the winter FR-H1 allele might require other factors for winter survival. In addition, the QTL-NILs, Nure and Tremois were tested for a preliminary experiment aimed at evaluating the immediate and early changes in CBF’s expression in the first two days of cold acclimation. Plants at third-leaf stage were sampled in the morning, afternoon, and night for three consecutive days, grown under control (20/15°C, 8/16 h day/night) and acclimation (3/1°C, 8/16 h day/night) conditions. RT-qPCR analysis showed different expression patterns in the CBF gene cluster. Phenotypic characterization for agronomic traits is currently underway, and, combined with gene expression results, will be preparatory for more in-depth (RT-ddPCR and RNAseq) studies

Iodine uptake and distribution in horticultural and fruit tree species.

Iodine is an essential microelement for humans and iodine deficiency disorder (IDD) is one of the most widespread nutrient-deficiency diseases in the world. Iodine biofortification of plants provides an attractive opportunity to increase iodine intake in humans and to prevent and control IDD. This study was conducted to investigate the iodine uptake and accumulation in edible portion of two fruit trees: plum and nectarine, and two horticultural crops: tomato and potato. Two type of iodine treatments (soil and foliar spray application), and, for fresh market tomato, two production systems (open field and greenhouse hydroponic culture) were tested. The distribution of iodine in potato stem and leaves, and in plum tree fruits, leaves, and branches was investigated. Iodine content of potato tubers after postharvest storage and processing (cooking), and iodine content of nectarine fruits after postharvest storage and processing (peeling) were also determined. Differences in iodine accumulation were observed among the four crops, between applications, and between production systems. In open field, the maximum iodine content ranged from 9.5 and 14.3 \u3bcg 100 g 121 for plum and nectarine fruit, to 89.4 and 144.0 \u3bcg 100 g 121 for potato tuber and tomato fruit, respectively. These results showed that nectarine and plum tree accumulated significantly lower amounts of iodine in their edible tissues, in comparison with potato and tomato. The experiments also indicated hydroponic culture as the most efficient system for iodine uptake in tomato, since its fresh fruits accumulated up to 2423 \u3bcg 100 g 121 of iodine. Iodine was stored mainly in the leaves, in all species investigated. Only a small portion of iodine was moved to plum tree branches and fruits, and to potato stems and tubers. No differences in iodine content after fruit peeling was observed. A significant increase in iodine content of potato was observed after baking, whereas a significant decrease was observed after boiling. We concluded that iodine biofortified fresh market tomato salad, both from field and hydroponics cultivation, and baked potatoes can be considered as potential functional foods for IDD prevention

Barley: Omics approaches for abiotic stress tolerance

Abiotic stresses such as frost, drought, salinity, hypoxia, and mineral deficiency or toxicity frequently limit growth and productivity of temperate cereal crops, for which barley (Hordeum vulgare L. ssp. vulgare) could represent a model. Improving barley resistance to such constraints is thus fundamental in view of the expected climate change for minimizing the gap between potential and actual yield (the so-called yield gap), increasing the yield stability, and guaranteeing the sustainability of the crop. As different omics technologies have been developed during the past few decades, they enabled systematic analysis of changes that occur in plants in response to abiotic stresses. In this chapter, we focus on the omics contribution to the improvement of abiotic stress tolerance in barley. After a brief summary of the most relevant abioticstresses that limit the crop yields worldwide, successful genomics approaches have been described, starting from the exploitation of germplasm resources. Structural and functional approaches that helped in understanding the mechanisms and the genetic bases of abiotic stress tolerance, when applied to barley and model species(mainly Arabidopsis, rice, and Brachypodium), have been reviewed as an important step toward crop tolerance improvement. Quantitative genetics and genetical genomics of abiotic stress tolerance have been discussed, as they represent both a huge source of information and a challenge for future holistic approaches. Then, we present an overview of the contribution of other omics sciences (e.g., proteomics, epigenomics, metabolomics, ionomics, and phenomics). In the last section, integrative (systems) biology, together with a series of strategies for the future, is proposed and discussed

Linkage mapping of the alpha-B-crystallin (CRYAB) gene to porcine chromosome 9.

An expressed sequence tag (EST) that showed homology with human (M28638) a-B-crystallin (CRYAB) gene sequence was isolated from a porcine skeletal muscle cDNA library (Z98816). Two alleles were identified in the 115-bp fragment of the porcine CRYAB 3'-untranslated region. A multipoint sex-averaged map of porcine chromosome 9, placed CRYAB between markers PPP2ARB and APOA

Identification of tomato genes differentially expressed during compatible interaction with Pyrenochaeta lycopersici.

Breeding for resistance is the most effective tool for controlling the corky root disease of tomato caused by the fungus Pyrenochaeta lycopersici. However, little is known about the molecular bases of tomato-P. lycopersici interaction. In order to identify genes involved in the basal defence response activated in a susceptible cultivar and in disease symptom development, a set of cDNA-AFLP fragments derived from a profiling experiment was analysed. A total of 247 differentially expressed TDFs (transcript-derived fragments), identified as putative tomato genes, were characterized by similarity searches, and classified into 11 broad functional classes. Timings ranging between the early [48, 72 and 96 h post-infection (hpi)] and the late infection stages (20 and 27 dpi) were used. The changes of tomato root transcriptional profiles showed large differences in quantity and quality between the early and late stages of infection. Mechanisms of basal defence were most likely activated at early stages, when a gene coding for a receptor-like serine-threonine protein kinase and other genes of the signalling class were upregulated. At 20 dpi some of the mechanisms involved in defence were still activated, while at 27 dpi a general repression of gene expression was observed

dBase CEREALAB

The CEREALAB database; an information system for breeders is a source of molecular and phenotypic data, realized by integrating two already existing web databases, Gramene and Graingenes together with the source storing the information achieved by research groups of the CEREALAB project. The new data derives from a systematic genotyping work using already known markers and some brandly new protocols developed by the discovery workpackage of the project.This integration is obtained using the MOMIS system (Mediator Environment for Multiple Information Sources). The result obtained is a queriable virtual view that integrates the three sources and allows performing selection of cultivars of barley, wheat and rice based on molecular data and phenotypic traits, regardless of the specific languages of the three source databases. The phenotypic characters to be included in the database have been chosen among those of major interest for the breeders and divided into six categories: Abiotic Stress, Biotic Stress, Growth and Development, Quality and Yield. As far as molecular data is concerned the major categories for the query are: Trait, Qtl, Gene and Marker

The porcine sarcolipin (SLN) gene: identification of an SNP and linkage mapping to chromosome 9.

Sarcolipin (SLN) is a 31-amino acid proteolipid that regulates the activity of SERCA1 (ATP2A1), a fasttwitch skeletal muscle sarcoplasmic reticulum Ca2+-ATPase. Two alleles were identified by SSCP analysis in the 218 bp fragment of the porcine SLN gene. Mendelian segregation was confirmed in three-generation families of the PiGMaP Consortium. The DNA samples belonging to six threegeneration families of the PiGMaP Consortium were genotyped at the SLN locus obtaining 98 informative meiosis. Multipoint sex-averaged map of porcine chromosome 9, placed SLN between markers PPP2ARB and CRYAB (PPP2ARB± 24.7 cM ± SLN ± 3.1 cM ± CRYAB ±). This assignment confirms the physical mapping of the porcine SLN gene to chromosome9p24-(1/3p21) previously obtaine