Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses.

BACKGROUND AND AIMS: Bioenergy crops are central to climate mitigation strategies that utilize biogenic carbon, such as BECCS (bioenergy with carbon capture and storage), alongside the use of biomass for heat, power, liquid fuels and, in the future, biorefining to chemicals. Several promising lignocellulosic crops are emerging that have no food role - fast-growing trees and grasses - but are well suited as bioenergy feedstocks, including Populus, Salix, Arundo, Miscanthus, Panicum and Sorghum. SCOPE: These promising crops remain largely undomesticated and, until recently, have had limited germplasm resources. In order to avoid competition with food crops for land and nature conservation, it is likely that future bioenergy crops will be grown on marginal land that is not needed for food production and is of poor quality and subject to drought stress. Thus, here we define an ideotype for drought tolerance that will enable biomass production to be maintained in the face of moderate drought stress. This includes traits that can readily be measured in wide populations of several hundred unique genotypes for genome-wide association studies, alongside traits that are informative but can only easily be assessed in limited numbers or training populations that may be more suitable for genomic selection. Phenotyping, not genotyping, is now the major bottleneck for progress, since in all lignocellulosic crops studied extensive use has been made of next-generation sequencing such that several thousand markers are now available and populations are emerging that will enable rapid progress for drought-tolerance breeding. The emergence of novel technologies for targeted genotyping by sequencing are particularly welcome. Genome editing has already been demonstrated for Populus and offers significant potential for rapid deployment of drought-tolerant crops through manipulation of ABA receptors, as demonstrated in Arabidopsis, with other gene targets yet to be tested. CONCLUSIONS: Bioenergy is predicted to be the fastest-developing renewable energy over the coming decade and significant investment over the past decade has been made in developing genomic resources and in collecting wild germplasm from within the natural ranges of several tree and grass crops. Harnessing these resources for climate-resilient crops for the future remains a challenge but one that is likely to be successful.

A versatile method for gene dosage quantification: multiplex PCR and single base extension for copy number and gene-conversion identification of SMN genes.

A comparison of the individual genomes within a species demonstrates that structural variation, including copy number variation (CNV), is a major contributor to phenotypic diversity and evolutionary adaptation. CNVs lead to the under/over-expression of a gene, according to the changes in the gene dosage, which account for the development of a number of genomic disorders. Thus, the development of efficient, rapid and accurate CNV screening is of fundamental importance. We report a method that enables the simultaneous determination of the copy numbers of several different targets as well as the discrimination among highly similar/almost identical targets that differ by only one single nucleotide variant, which establishes their copy numbers. The PCR co-amplification and single-base extension technologies are used to identify the copy number of a target sequence relative to a reference sequence of known genomic copy number in a given sample. This efficient and accurate quantification platform was successfully used to quantify the copy numbers of the primary spinal muscular atrophy-determining gene, SMN1, and the disease modifier gene, SMN2. The reliability, low-cost and potential for high-throughput make our method suitable for screening large populations as well as for use as a tool in clinical settings for genetic diagnosis/prognosis.

Short communication: Association between udder health status and blood serum proteins in dairy cows.

The aim of this study was to investigate the association between udder health (UH) status and blood serum proteins (i.e., total protein, albumin, globulin, and albumin-to-globulin ratio) in dairy cows. Blood and milk samples were collected from 1,508 cows of 6 different breeds (Holstein Friesian, Brown Swiss, Jersey, Simmental, Rendena, and Alpine Grey) that were housed in 41 multibreed herds. Bacteriological analysis was performed on milk samples with somatic cell count (SCC) >100,000 cells/mL and bacteria identification was confirmed by multiplex-PCR assays. Milk samples were grouped into 7 clusters of UH status: healthy (cows with milk SCC <100,000 cells/mL and not cultured); culture-negative samples with low, medium, or high SCC; and culture-positive samples with contagious, environmental, and opportunistic intramammary infections. Data of blood serum proteins were analyzed using a linear mixed model that included the fixed effects of stage of lactation, parity, breed, herd productivity (high or low production) and UH status, and the random effect of herd-date within herd productivity. Culture-negative samples with high milk SCC, which were most likely undergoing a strong inflammatory response and whose pathogens could not be isolated because they were engulfed by macrophages or because they had already cleared, and milk samples infected by contagious and environmental bacteria were associated with greater globulin concentrations (and lower albumin-to-globulin ratio) in blood. Variation in blood serum proteins seems to be associated with inflammatory status rather than infection, as serum globulin significantly increased in UH status groups with the highest milk SCC and no differences were observed among intramammary infections pathogens. Blood serum proteins can be a mammary gland inflammation indicator, but cannot be used to differentiate among different UH status groups.

Variation in blood serum proteins and association with somatic cell count in dairy cattle from multi-breed herds.

Blood serum proteins are significant indicators of animal health. Nevertheless, several factors should be considered to appropriately interpret their concentrations in blood. Therefore, the objectives of this study were (1) to assess the effect of herd productivity, breed, age and stage of lactation on serum proteins and (2) to investigate association between serum proteins and somatic cell count (SCC) in dairy cattle. Milk and blood samples were collected from 1508 cows of six different breeds (Holstein Friesian, Brown Swiss, Jersey, Simmental, Rendena and Alpine Grey) that were housed in 41 multi-breed herds. Milk samples were analyzed for composition and SCC, while blood samples were analyzed for serum proteins (i.e. total protein, albumin, globulin and albumin-to-globulin ratio (A : G)). Herds were classified as low or high production, according to the cow's average daily milk energy yield adjusted for breed, days in milk (DIM) and parity. Data were analyzed using a linear mixed model that included the fixed effects of DIM, parity, SCS, breed, herd productivity and the random effect of the Herd-test date within productivity level. Cows in high producing herds (characterized also by greater use of concentrates in the diet) had greater serum albumin concentrations. Breed differences were reported for all traits, highlighting a possible genetic mechanism. The specialized breed Jersey and the two dual-purpose local breeds (Alpine Grey and Rendena) had the lowest globulin concentration and greatest A : G. Changes in serum proteins were observed through lactation. Total protein reached the highest concentration during the 4th month of lactation. Blood albumin increased with DIM following a quadratic pattern, while globulin decreased linearly. As a consequence, A : G increased linearly during lactation. Older cows had greater total protein and globulin concentrations, while albumin concentration seemed to be not particularly affected by age. A linear relationship between serum proteins and SCS was observed. High milk SCS was associated with greater total protein and globulin concentrations in blood. The rise in globulin concentration, together with a decrease in albumin concentrations, resulted in a decline in A : G as SCS of milk increased. In conclusion, such non-genetic factors must be considered to appropriately interpret serum proteins as potential animal welfare indicator and their evaluation represents an important first-step for future analysis based on the integration of metabolomics, genetic and genomic information for improving the robustness of dairy cows.

Associations between pathogen-specific cases of subclinical mastitis and milk yield, quality, protein composition, and cheese-making traits in dairy cows.

The aim of this study was to investigate associations between pathogen-specific cases of subclinical mastitis and milk yield, quality, protein composition, and cheese-making traits. Forty-one multibreed herds were selected for the study, and composite milk samples were collected from 1,508 cows belonging to 3 specialized dairy breeds (Holstein Friesian, Brown Swiss, and Jersey) and 3 dual-purpose breeds of Alpine origin (Simmental, Rendena, and Grey Alpine). Milk composition [i.e., fat, protein, casein, lactose, pH, urea, and somatic cell count (SCC)] was analyzed, and separation of protein fractions was performed by reversed-phase high performance liquid chromatography. Eleven coagulation traits were measured: 5 traditional milk coagulation properties [time from rennet addition to milk gelation (RCT, min), curd-firming rate as the time to a curd firmness (CF) of 20 mm (k20, min), and CF at 30, 45, and 60 min from rennet addition (a30, a45, and a60, mm)], and 6 new curd firming and syneresis traits [potential asymptotical CF at an infinite time (CFP, mm), curd-firming instant rate constant (kCF, % × min-1), curd syneresis instant rate constant (kSR, % × min-1), modeled RCT (RCTeq, min), maximum CF value (CFmax, mm), and time at CFmax (tmax, min)]. We also measured 3 cheese yield traits, expressing the weights of total fresh curd (%CYCURD), dry matter (%CYSOLIDS), and water (%CYWATER) in the curd as percentages of the weight of the processed milk, and 4 nutrient recovery traits (RECPROTEIN, RECFAT, RECSOLIDS, and RECENERGY), representing the percentage ratio between each nutrient in the curd and milk. Milk samples with SCC > 100,000 cells/mL were subjected to bacteriological examination. All samples were divided into 7 clusters of udder health (UH) status: healthy (cows with milk SCC < 100,000 cells/mL and uncultured); culture-negative samples with low, medium, or high SCC; and culture-positive samples divided into contagious, environmental, and opportunistic intramammary infection (IMI). Data were analyzed using a linear mixed model. Significant variations in the casein to protein ratio and lactose content were observed in all culture-positive samples and in culture-negative samples with medium to high SCC compared to normal milk. No differences were observed among contagious, environmental, and opportunistic pathogens, suggesting an effect of inflammation rather than infection. The greatest impairment in milk quantity and composition, clotting ability, and cheese production was observed in the 2 UH status groups with the highest milk SCC (i.e., contagious IMI and culture-negative samples with high SCC), revealing a discrepancy between the bacteriological results and inflammatory status, and thus confirming the importance of SCC as an indicator of udder health and milk quality.

Alexithymia and personality traits of patients with inflammatory bowel disease.

Psychological factors, specific lifestyles and environmental stressors may influence etiopathogenesis and evolution of chronic diseases. We investigate the association between Chronic Inflammatory Bowel Diseases (IBD) and psychological dimensions such as personality traits, defence mechanisms, and Alexithymia, i.e. deficits of emotional awareness with inability to give a name to emotional states. We analyzed a survey of 100 patients with IBD and a control group of 66 healthy individuals. The survey involved filling out clinical and anamnestic forms and administering five psychological tests. These were then analyzed by using a network representation of the system by considering it as a bipartite network in which elements of one set are the 166 individuals, while the elements of the other set are the outcome of the survey. We then run an unsupervised community detection algorithm providing a partition of the 166 participants into clusters. That allowed us to determine a statistically significant association between psychological factors and IBD. We find clusters of patients characterized by high neuroticism, alexithymia, impulsivity and severe physical conditions and being of female gender. We therefore hypothesize that in a population of alexithymic patients, females are inclined to develop psychosomatic diseases like IBD while males might eventually develop behavioral disorders.

Growth Plate Lesions of Fattening Bulls.

Lameness related to growth plate lesions is an important problem in the beef industry. This article describes the macroscopic and microscopic lesions in the distal metatarsal physis of bulls from an association of farmers in northeastern Italy. The metatarsal bones of 62 bulls (12 with severe lameness and 50 without lameness), average age 16.44 ± 1.72 months, were examined at the abattoir. The animals came from the same geographic area and shared intensive husbandry practices and a diet based on maize starch. A total of 124 metatarsal bones were sectioned, and the distal metaphyseal growth plate was grossly examined. Twenty-three cases, including 12 lame and 9 nonlame animals with visible lesions on macroscopic examination, and 2 controls (a total of 46 physes) were examined microscopically. Eight of 12 bulls with severe lameness had a chronic purulent physitis in at least 1 limb. Segmental thickening of the hypertrophic zone, consistent with osteochondrosis (OC), was present contralaterally ( n = 3 cases) and bilaterally ( n = 3 cases) in 6 of these animals. In the group of nonlame bulls, 19 of 50 (38%) had similar segmental thickening of the physis consistent with OC. In the remaining bulls, minor findings included partial closure of the physis and a variable degree of metaphyseal hyperemia. A high incidence of OC was found in both lame and nonlame fattening bulls. It is likely that lame animals were clinically more severe due to secondary hematogenous implantation of bacteria, resulting in a purulent physitis and severe lameness that required emergency slaughter in some cases.

New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

Evaluation of venous blood gas levels, blood chemistry and haemocytometric parameters in milk fed veal calves at different periods of livestock cycle.

An evaluation of blood chemistry profile in relation to specific stages of livestock cycle can help better understand variations in physiological conditions in order to adjust management systems to animal needs. In addition to basal hematological investigation, the acid-base balance and blood gases are essential tools in evaluating metabolism in calves. The relationship between blood gas parameters, diet and growth should be further investigated. The aim of this study was to evaluate changes in acid-base status, blood gases, serum chemistry and hematological parameters in veal calves at different periods of livestock cycle. One hundred twenty-eight healthy cross breeding calves were enrolled in a farm in North-East Italy. Blood samplings were carried out from the jugular vein on day 1 (t1), 60 (t2) and 150 (t3) after arrival. Blood gas analysis was performed and hematological parameters were evaluated. One-way ANOVA and Tukey-Kramer post-hoc test were performed to assess differences between blood parameter values at the different periods. The main differences in blood gas parameter levels during the livestock cycle concerned pH, Base Excess and HCO3 with higher values recorded in t3. Urea, creatinine, gamma-glutamyl transpeptidase and bilirubin mean values were significantly higher in t1 than in t2 and t3. Aspartate aminotransferase increased from t1 to t2 and t3. Alkaline Phosphatase was higher in t2. Fe levels severely dropped in t2 and in t3, and the decrease led to a restrained but significant reduction in haemoglobin values. A correspondent decrease in the other haemocytometric parameters was found.

Evaluation of the udder health status in subclinical mastitis affected dairy cows through bacteriological culture, somatic cell count and thermographic imaging.

Subclinical mastitis in dairy cows is a big economic loss for farmers. The monitoring of subclinical mastitis is usually performed through Somatic Cell Count (SCC) in farm but there is the need of new diagnostic systems able to quickly identify cows affected by subclinical infections of the udder. The aim of this study was to evaluate the potential application of thermographic imaging compared to SCC and bacteriological culture for infection detection in cow affected by subclinical mastitis and possibly to discriminate between different pathogens. In this study we evaluated the udder health status of 98 Holstein Friesian dairy cows with high SCC in 4 farms. From each cow a sample of milk was collected from all the functional quarters and submitted to bacteriological culture, SCC and Mycoplasma spp. culture. A thermographic image was taken from each functional udder quarter and nipple. Pearson's correlations and Analysis of Variance were performed in order to evaluate the different diagnostic techniques. The most frequent pathogen isolated was Staphylococcus aureus followed by Coagulase Negative Staphylococci (CNS), Streptococcus uberis, Streptococcus agalactiae and others. The Somatic Cell Score (SCS) was able to discriminate (p<0.05) cows positive for a pathogen from cows negative at the bacteriological culture except for cows with infection caused by CNS. Infrared thermography was correlated to SCS (p<0.05) but was not able to discriminate between positive and negative cows. Thermographic imaging seems to be promising in evaluating the inflammation status of cows affected by subclinical mastitis but seems to have a poor diagnostic value.

Serum acute phase proteins in cows with SARA (Subacute Ruminal Acidosis) suspect / Proteínas séricas de fase aguda em vacas com suspeita de SARA (Subacute Ruminal Acidosis)

The aim of this study was to evaluate the variations of Acute Phase Proteins (APPs) and other blood constituents during the onset of the sub-acute ruminal acidosis (SARA) pathological status. A total of 108 cows from 12 dairy herds were randomly selected and divided into three Groups of 36 animals each. All animals were subjected to a rumenocentesis. Group A was composed by subjects with a rumen pH>5.8, Group B was composed by subjects with a rumen pH ≤5.5≤5.8 and Group C was composed by subjects with a rumen pH<5.5. Blood samples were collected by jugular venipuncture and Haptoglobin (Hp), Serum Amyloid A (SAA), Total Proteins, Albumin and White Blood Cells (WBC) were determined. One-way ANOVA showed a statistical significance on Rumen pH, Hp, SAA. SARA seems not stimulate the APPs production from liver.

O objetivo deste estudo foi avaliar as variações de Proteínas de Fase Aguda (APPs) e outros constituintes sanguíneos durante o início do status patológico de sub-acute ruminal acidosis (SARA). O total de 108 vacas de 12 rebanhos leiteiros foram aleatoriamente selecionados e divididos em três grupos com 36 animais cada. Todos os animais foram submetidos a ruminocentesis. O Grupo A foi composto por sujeitos com rumen pH>5.8, o Grupo B foi composto por sujeitos com rumen pH ≤5.5≤5.8 e o Grupo C foi composto por sujeitos com rumen pH<5.5. Amostras sanguíneas foram coletas por punção venosa jugular e Haptoglobin (Hp), Serum Amyloid A (SAA), Proteínas totais, Albumin e células brancas do sangue (WBC) foram determinadas. ANOVA em via única mostrou significância estatística em Rumen pH, Hp, SAA. SARA não parece estimular a produção de APPs pelo fígado.

Influence of temperature and humidity on rumen pH and fatty acids in dairy cows.

The aim of this study was to investigate the variations of rumen pH and fatty acids (acetic acid, propionic acid, iso-butyric acid, n-butyric acid, iso-valerianic acid, n-valerianic, caproic acid and total fatty acids) in 245 early lactating dairy cows under different temperature and humidity conditions. The animals were divided into six groups and rumen fluid was collected by rumenocentesis on 22 dairy cows in April (Group A), 33 in May (Group B), 43 in June (Group C), 48 in July (Group D), 36 in September (Group E) and 60 in October (Group F). One-way analysis of variance (ANOVA), followed by the Bonferroni's test, showed a significant effect of environmental variations on all studied parameters (P < 0.0001). Changes in studied parameters can be explained in relation to the microbial population and shift in the optima for rumen conditions associated with variations of environmental conditions. We can affirm that the microbial assemblages that underlie energy and protein supply to wild ruminant are evident especially in relation to temperature and humidity conditions.

Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions.

Improved knowledge of genome composition, especially of its repetitive component, generates important informations in both theoretical and applied research. In this study, we provide the first insight into the local organization of the sunflower genome by sequencing and annotating 349,380 bp from 3 BAC clones, each including one single-copy gene. These analyses resulted in the identification of 11 putative gene sequences, 18 full-length LTR retrotransposons, 6 incomplete LTR retrotransposons, 2 non-autonomous LTR-retroelements (LINEs), 2 putative DNA transposons fragments and one putative helitron. Among LTR-retrotransposons, non-autonomous elements (the so-called LARDs), which do not carry any protein-encoding sequence, were discovered for the first time in the sunflower. The insertion time of intact retroelements was measured, based on sister LTRs divergence. All isolated elements were inserted relatively recently, especially those belonging to the Gypsy superfamily. Retrotransposon families related to those identified in the BAC clones are present also in other species of Helianthus, both annual and perennial, and even in other Asteraceae. In one of the three BAC clones, we found five copies of a lipid transfer protein (LTP) encoding gene within less than 100,000 bp, four of which are potentially functional. Two of these are interrupted by LTR retrotransposons, in the intron and in the coding sequence, respectively. The divergence between sister LTRs of the retrotransposons inserted within the genes indicates that LTP gene duplication started earlier than 1.749 MYRS ago. On the whole, the results reported in this study confirm that the sunflower is an excellent system to study transposons dynamics and evolution.

Good quality sheep embryos produced by superovulation treatment without the use of progesterone devices.

Multiple ovulation and embryo transfer (MOET) is a very important tool for the genetic improvement and preservation of endangered livestock. However, the success of a MOET programme highly depends on the number of transferable embryos in response to a superovulation treatment. Thus, the aim of this study was to compare the number and quality of embryos produced during natural oestrus under porcine FSH treatment without the use of progesterone devices to more traditional protocols. Forty Sarda sheep were divided into 2 groups: without sponges (WS) (n = 20) and with sponges (S) containing 40mg FGA for 12 d (n = 20) (control group); 350 I.U. of porcine FSH per sheep was administered in eight decreasing doses twice daily starting four days after estrus was detected (Day 0) in group WS and 48 h before sponge removal in group S. A single i.m. dose of 125 µg of cloprostenol was administered on Day 6 after estrus in group WS to induce luteolysis. Sheep were naturally mated 24 h after cloprostenol injection or sponge removal. Seven days after mating, an inguinal laparotomy was performed and the number of corpora lutea (CL) recorded. Embryos were recovered surgically by flushing each uterine horn. A total of 38 fresh and 22 vitrified embryos were transferred in pairs into 3 groups of recipients seven days after estrus detection: fresh embryos from group S (S-F) (n = 9), fresh embryos from group WS (WS-F) (n = 10) and vitrified embryos from group WS (WS-V) (n = 11). Data on the number of corpora lutea (CL), recovered ova and embryos (OER), and quality 1-2 and 3 embryos (EQ(1-2), EQ(3)) per ewe were analyzed by ANOVA. Recovery (RR), fertility (FR) and quality 1-2 embryo (Q(1-2)R) rates per treatment were analyzed by a Chi Square analysis. A Chi Square analysis was also applied to pregnancy rate (PR), lambing rate (LR) and twinning rate (TR) of fresh and vitrified embryos in order to analyze embryo transfer results. Among all superovulation variables analysed, results show statistically significant differences in mean number of CL/ ewe (9.3 ± 3.9 vs 7 ± 3.2), RR (67% vs 80 %) and FR (100% vs 80%) (P < 0.05) between WS and S groups respectively. There were no significant differences in PR (78%, 70% and 82%), LR (67%, 60% and 59%) and TR (71%, 71% and 44.4%) among S-F, WS-F and WS-V groups respectively. In conclusion, it is possible to produce a good number of transferable embryos during natural oestrus avoiding the use of sponges.

A comparison of daily total locomotor activity between the lactation and the dry period in dairy cattle.

The objective of this study was to investigate the influence of farming management on the total locomotor activity (TLA) behaviour in dairy cattle. We recorded 24h/day TLA in five not pregnant Holstein Friesian cows during parts of the lactation and dry periods, by means of an activity monitoring system (Actiwatch mini®) for seven days in each period. During mild lactation (period 1) animals were milked and fed twice a day. During the dry (period 2) they were kept to graze all day. In both periods hay and water were available ad libitum. Differences between the photophase and the scotophase were evaluated with a Student t-test. One-way repeated measure ANOVA was used to determine a statistical significant effect of time. A trigonometric statistical model was used to describe the main rhythmic parameters: mean level, amplitude, acrophase and robustness of rhythm. Our results showed a circadian rhythm of daily TLA in both periods, with different percentages of robustness, and acrophase in the middle of the photophase. The different patterns of activity in the two periods were attributed to the management practise during milking period. These results could be taken in consideration during farming management for the evaluation of such systems used in livestock, with respect to production and welfare.

An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.).

With the aim to study variability in genes involved in ecological adaptations, we have analysed sequence polymorphisms of eight unique genes putatively involved in drought response by isolation and analysis of allelic sequences in eight inbred lines of sunflower of different origin and phenotypic characters and showing different drought response in terms of leaf relative water content (RWC). First, gene sequences were amplified by PCR on genomic DNA from a highly inbred line and their products were directly sequenced. In the absence of single nucleotide polymorphisms, the gene was considered as unique. Then, the same PCR reaction was performed on genomic DNAs of eight inbred lines to isolate allelic variants to be compared. The eight selected genes encode a dehydrin, a heat shock protein, a non-specific lipid transfer protein, a z-carotene desaturase, a drought-responsive-element-binding protein, a NAC-domain transcription regulator, an auxin-binding protein, and an ABA responsive-C5 protein. Nucleotide diversity per synonymous and non-synonymous sites was calculated for each gene sequence. The π (a)/π (s) ratio range was usually very low, indicating strong purifying selection, though with locus-to-locus differences. As far as non-coding regions, the intron showed a larger variability than the other regions only in the case of the dehydrin gene. In the other genes tested, in which one or more introns occur, variability in the introns was similar or even lower than in the other regions. On the contrary, 3'-UTRs were usually more variable than the coding regions. Linkage disequilibrium in the selected genes decayed on average within 1,000 bp, with large variation among genes. A pairwise comparison between genetic distances calculated on the eight genes and the difference in RWC showed a significant correlation in the first phases of drought stress. The results are discussed in relation to the function of analysed genes, i.e. involved in gene regulation and signal transduction, or encoding enzymes and defence proteins.

Physiological values and factors affecting the metacarpal bone density of healthy feedlot beef cattle as measured by dual-energy X-ray absorptiometry.

The metacarpal bone mineral density of 136 healthy feedlot beef cattle of four different breeds (Charolaise, Limousine, Irish Crossbreed and Slovakian Crossbreed) raised and fed on standard conditions was measured by means of a dual-energy X-ray absorptiometry technique in an ex vivo study design. The average reference values (mean ± SD) of bone mineral density (BMD) for animals aged between 12 and 22 months and weighing between 236 and 546 kg have been reported and the effects of (i) breed, (ii) gender, (iii) age and (iv) body weight on bone mineral density have been considered. A significant difference (i) among different breeds and (ii) between genders resulted, whereas a high correlation between bone density and (iii) age and (iv) body weight was detected within the same breed and gender, with body weight being the most important factor affecting BMD. A modern new technological insight into the study of bovine bone physio-pathology is proposed.

HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.).

In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5' and 3' long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5' LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last approximately 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.

Phylogenetic relationships between annual and perennial species of Helianthus: evolution of a tandem repeated DNA sequence and cytological hybridization experiments.

The amplification and chromosomal localization of tandem repeated DNA sequences from Helianthus annuus (clone HAG004N15) and the physical organization of ribosomal DNA were studied in annual and perennial species of Helianthus. HAG004N15-related sequences, which did not show amplification in other Asteraceae except for Viguiera multiflora, were redundant in all the Helianthus species tested, but their frequency was significantly higher in perennials than in annuals. These sequences were located at the ends and intercalary regions of all chromosome pairs of annual species. A similar pattern was found in the perennials, but a metacentric pair in their complement was not labelled. Ribosomal cistrons were carried on two chromosome pairs in perennials and on three pairs in annuals except for H. annuus, where rDNA loci were on four pairs. No difference was observed between cultivated H. annuus and its wild accessions in the hybridization pattern of the HAG004N15 and ribosomal probes. These findings support the hypothesis that the separation between annual and perennial Helianthus species occurred through interspecific hybridization involving at least one different parent. However, GISH in H. annuus using genomic DNA from the perennial Helianthus giganteus as blocking DNA failed to reveal different genomic assets in annual and perennial species.