Genome-wide detection of signatures of selection in three Valdostana cattle populations

The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F_ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.     

Bioassays and application of olive pomace compost on emmer: effects on yield and soil properties in organic farming

Abstract

Composting olive oil pomace could solve the problem of disposal, by recycling this organic waste for agricultural purposes. Furthermore, application of composted organic waste could be a way to sustain both soil fertility and production, especially in organic farming. Therefore, the aim of this research was to evaluate the phytotoxicity and the effects of application of olive pomace composts on emmer performance and soil properties. Two types of olive pomace composts, with a different initial C/N ratio, were stopped at the active phase and processed until maturation. The obtained four olive pomace composts were compared with a commercial fertilizer in a two-year field experiment. Before the field trial, a bioassay was performed to assess phytotoxicity both for the raw pomace and the not-stabilized composts. Growing and yielding data for emmer were determined during the two-year period and soil characteristics were measured at the start and at the end of the experiment.

The composts were not phytotoxic (germination index was higher than 90%) and their total organic carbon content was always higher than the minimum values established by the Italian fertilizers legislation. The emmer protein content was significantly higher in the matured compost treatment with low C/N, than in the other compost treatments. Its value was comparable with that of the commercial fertilizer, suggesting a good performance on crop yield quality. Although not significant, this compost showed an increase of 9.8% in grain yield compared with commercial fertilizer treatment. On the whole, it can be suggested that repeated compost application might preserve the soil organic carbon content and supply macronutrients to a crop.     

Fundamental evaluation of the impact of high Hydrostatic Pressure on oat batters

The use of grains alternative to wheat or rye is a challenging task for cereal technologists, and currently new technologies are under investigation as tools to improve the performances of these alternative grains. In this work the effects of high Hydrostatic Pressure (HP) on oat batters were investigated. Oat batters were treated for 10 min at 200, 300, 350, 400 or 500 MPa. Scanning electron microscopy and bright field microscopy showed that high HP significantly affected oat batter microstructure, and both starch and proteins were affected. Treatment at high HP significantly improved batter viscosity and elasticity. At pressures ≤300 MPa the increase in the viscous component was higher than the increase in the elastic component. On the contrary, at pressures ≥350 MPa the elastic component was predominant. Differential scanning calorimetry revealed that high HP induced starch gelatinisation, which started at 300 MPa and was almost complete after treatment at 500 MPa. High HP also affected water- and salt-soluble as well as urea-soluble oat proteins. Analysis of proteins soluble in different buffers revealed that pressures ≥300 MPa induced the formation of urea-insoluble complexes and/or disulfide bonds. Overall, the extent of starch gelatinisation and protein modification was dependent on the applied pressure, but the results collected so far clearly show that high HP can be used to improve the functionality of oat batters.     

Microstructure, fundamental rheology and baking characteristics of batters and breads from different gluten-free flours treated with a microbial transglutaminase

Gluten is a fundamental component for the overall quality and structure of breads. The replacement of the gluten network in the development of gluten-free cereal products is a challenging task for the cereal technologist. The functionality of proteins from gluten-free flours could be modified in order to improve their baking characteristics by promoting protein networks. Transglutaminase (TGase) has been successfully used in food systems to promote protein cross-linking. In this study, TGase was investigated for network forming potential on flours from six different gluten-free cereals (brown rice, buckwheat, corn, oat, sorghum and teff) used in breadmaking. TGase was added at 0, 1 or 10 U/g of proteins present in the recipe. The effect of TGase on batters and breads was evaluated by fundamental rheological tests, Texture Profile Analysis and standard baking tests. Three-dimensional elaborations of Confocal Laser Scanning Microscopy (CLSM) images were performed on both batters and breads to evaluate the influence of TGase on microstructure. Fundamental rheological tests showed a significant increase in the pseudoplastic behaviour of buckwheat and brown rice batters when 10 U of TGase were used. The resulting buckwheat and brown rice breads showed improved baking characteristics as well as overall macroscopic appearance. Three-dimensional CLSM image elaborations confirmed the formation of protein complexes by TGase action. On the other side, TGase showed negative effects on corn flour as its application was detrimental for the elastic properties of the batters. Nevertheless, the resulting breads showed significant improvements in terms of increased specific volume and decreased crumb hardness and chewiness. Under the conditions of this study, no effects of TGase could be observed on breads from oat, sorghum or teff. Overall, the results of this study show that TGase can be successfully applied to gluten-free flours to improve their breadmaking potentials by promoting network formation. However, the protein source is a key element determining the impact of the enzyme.     

Characterisation of thirteen cowpea landraces from Umbria (Italy). Strategy for their conservation and promotion

Thirteen landraces of cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata cv. gr. Unguiculata) have been morphologically and agronomically characterised as part of a plan for safeguarding and protecting plant biodiversity typical of Lake Trasimeno (Umbria, central Italy). Sixty plants per accession were scored for plant vigour, growth habit, flower colour, days to flowering, days to first mature pod, pod length, total number of pods produced, seed colour pattern, 100 seed weight, total seed yield and virus susceptibility. With the exception of vigour and growth habit, all landraces appeared to be well differentiated from one another for all the characters considered. Strategies and problems related to their in situ conservation are discussed.     

Fruit characterization of Cocos nucifera L. (ARECACEAE) cultivars from the Pacific coast of Costa Rica and the Philippines

Tall coconut cultivars from the Pacific coast of Costa Rica and the Philippines (San Ramón, Tagnanán, and Laguna), were evaluated for fruit characteristics. Most of the introduced cultivars showed extremely large heterogeneity. A cluster analysis, based on the Ward method, classified the palms into four groups with high internal homogeneity. Some of the evaluated coconut palms from the Costa Rican Pacific area had nut characteristics similar to the San Ramon and Tagnanan palm groups but not to the Laguna group. At the association level used (semipartial R ² = 0.10), another group which included the remaining palms sampled from the Costa Rican Pacific coast was constituted.     

Exploring connectivity between spawning and nursery areas of Mullus barbatus (L., 1758) in the Mediterranean through a dispersal model

Connectivity between spawning and nursery areas plays a major role in determining the spatial structure of fish populations and the boundaries of stock units. Here, the potential effects of surface current on a red mullet population in the Central Mediterranean were simulated using a physical oceanographic model. Red mullet larvae were represented as Lagrangian drifters released in known spawning areas of the Strait of Sicily (SoS), which represents one of the most productive demersal fishing‐grounds of the Mediterranean. To consider the effect of inter‐annual variability of oceanographic patterns, numerical simulations were performed for the spawning seasons from 1999 to 2012. The main goal was to explore connectivity between population subunits, in terms of spawning and nursery areas, inhabiting the northern (Sicilian‐Maltese) and southern (African) continental shelves of the SoS. The numerical simulations revealed a certain degree of connectivity between the Sicilian–Maltese and the African sides of the SoS. Connectivity is present in both directions, but it is stronger from the Sicilian–Maltese spawning areas to the African nurseries owing to the marine circulation features of the region. However, because the majority of the larvae are transported to areas unsuitable for settlement or outside the SoS, the dispersal process is characterized by a strong loss of potential settlers born in the spawning areas. These results are in agreement with the low genetic heterogeneity reported for this species in the Mediterranean Sea and support the existence of a metapopulation structure of red mullet in the SoS and the adjacent areas.     

Differing trophic niches of three French stygobionts and their implications for conservation of endemic stygofauna

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Effect of ascorbic acid supplementation on zootechnical performance,haematological parameters and sperm quality of lebranche mullet Mugil liza

The feed provided to breeding fish is one of the main factors influencing the quality of fish gametes. This study was carried out to evaluate the influence of ascorbic acid on growth, haematological parameters and sperm quality of Lebranche mullet males (Mugil liza). Six diets with different levels of ascorbic acid (0; 53; 107; 216; 482 and 708 mg/kg) were tested in triplicate for 75 days. During spermiation (first gonadal maturation), 144 individuals (205.7 ± 11.5 g and 25.7 ± 0.4 cm) were randomly distributed in 18 experimental tanks. Growth parameters were evaluated at the beginning and end of the experiment. Fish blood was collected to analyse glucose, total protein and erythrocyte count (EC) (n = 9). Fish (n = 12) from each treatment were euthanized to determine hepatosomatic index (HSI) and gonadosomatic index (GSI). Semen was collected to evaluate spermatic density, cell membrane integrity and sperm motility. No difference (p > .05) was found on growth parameters, GSI, HSI and total protein. However, EC was lower in fish fed without ascorbic acid (the control group). Ascorbic acid supplementation provided positive effects on sperm characteristics. Fish from treatments with 53 and 107 mg/kg presented the best results for motility time (133.30 ± 4.25 and 135.00 ± 2.77 respectively). Treatments with 107, 216 and 708 mg/kg provided the best results for motility rate (92.0 ± 2.9%, 93.0 ± 5.8% and 93.0 ± 5.8% respectively). Supplementation with 107 and 216 mg/kg provided the best results for plasma membrane integrity (70.12 ± 9.10% and 76.3 ± 3.1% respectively). Lower spermatic density was observed in fish without ascorbic acid supplementation, although no difference was found in sperm density among the treatments with ascorbic acid (p < .05). Considering these results, supplementation of dietary ascorbic acid between 107 and 216 mg/kg optimizes the spermatic quality in males of lebranche mullet.