Genome-wide association study for antibody response to Mycobacterium avium ssp. paratubeculosis in goats.

Mycobacterium avium ssp. paratuberculosis (MAP), causes Johne's disease (JD), or paratuberculosis, a chronic enteritis of ruminants, which in goats is characterized by ileal lesions. The work described here is a case-control association study using the Illumina Caprine SNP50 BeadChip to unravel the genes involved in susceptibility of goats to JD. Goats in herds with a high occurrence of Johne's disease were classified as healthy or infected based on the level of serum antibodies against MAP, and 331 animals were selected for the association study. Goats belonged to the Jonica (157) and Siriana breeds (174). Whole-genome association analysis identified one region suggestive of significance associated with an antibody response to MAP on chromosome 7 (p-value = 1.23 × 10-5 ). These results provide evidence for genetic loci involved in the antibody response to MAP in goats.

Analysis of Complementary Sex-Determiner (csd) Allele Diversity in Different Honeybee Subspecies from Italy Based on NGS Data.

Sexual regulation in Apis mellifera is controlled by the complementary sex-determiner (csd) gene: females (queens and workers) are heterozygous at this locus and males (drones) are hemizygous. When homozygous diploid drones develop, they are eaten by worker bees. High csd allelic diversity in honeybee populations is a priority for colony survival. The focus of this study is to investigate csd variability in the genomic sequence of the hypervariable region (HVR) of the csd gene in honeybee subspecies sampled in Italy. During the summer of 2017 and 2018, worker bees belonging to 125 colonies were sampled. The honeybees belonged to seven different A. mellifera subspecies: A. m. ligustica, A. m. sicula, A. m cecropia, A. m. carnica, A. m. mellifera, Buckfast and hybrid Carnica. Illumina genomic resequencing of all samples was performed and used for the characterization of global variability among colonies. In this work, a pipeline using existing resequencing data to explore the csd gene allelic variants present in the subspecies collection, based on de novo assembly of sequences falling within the HVR region, is described. On the whole, 138 allelic sequences were successfully reconstructed. Among these, 88 different alleles were identified, 68 of which match with csd alleles present in the NCBI GenBank database.

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera).

At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee's population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.

High biodiversity in a limited mountain area revealed in the traditional production of Historic Rebel cheese by an integrated microbiota-lipidomic approach.

Historic Rebel (HR) cheese is an Italian heritage cheese, produced from raw milk during the summer grazing period in the Alps. The aim of this work was (i) to characterize the cheese microbiota, by 16S rRNA gene amplicons sequencing, and the volatile and non-volatile lipophilic fraction, by Gas Chromatography and Dynamic Headspace Extraction-Gas Chromatography-Mass Spectrometry, and (ii) to evaluate their respective associations. HR cheese was dominated by Firmicutes phylum (99% of the entire abundance). The core microbiota was formed by Streptococcus, Lactobacillus, Lactococcus, Leuconostoc and Pediococcus genera together representing 87.2-99.6% of the total abundance. The polyunsaturated fatty acids composition showed a high PUFA n-3, PUFA n-6 and CLA content, two fold higher than typical plain cheeses, positively correlated with pasture altitude. A complex volatilome was detected, dominated in terms of abundance by ketones, fatty acids and alcohols. Total terpene levels increased at higher altitudes, being the main terpenes compounds α-pinene, camphene and ß-pinene. The HR cheese showed a great diversity of bacterial taxa and lipophilic fractions among producers, despite belonging to a small alpine area, revealing a scarce cheese standardization and a chemical fingerprint of a typical mountain cheese produced during the grazing period. A deeper knowledge of the variability of HR cheese due to its composition in microbial community and volatile compounds will be appreciated, in particular, by elite consumers looking for niche products, adding economic value to farming in these alpine areas.

Combinatorial Discriminant Analysis Applied to RNAseq Data Reveals a Set of 10 Transcripts as Signatures of Exposure of Cattle to Mycobacterium avium subsp. paratuberculosis.

Paratuberculosis or Johne's disease in cattle is a chronic granulomatous gastroenteritis caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). Paratuberculosis is not treatable; therefore, the early identification and isolation of infected animals is a key point to reduce its incidence. In this paper, we analyse RNAseq experimental data of 5 ELISA-negative cattle exposed to MAP in a positive herd, compared to 5 negative-unexposed controls. The purpose was to find a small set of differentially expressed genes able to discriminate between exposed animals in a preclinical phase from non-exposed controls. Our results identified 10 transcripts that differentiate between ELISA-negative, clinically healthy, and exposed animals belonging to paratuberculosis-positive herds and negative-unexposed animals. Of the 10 transcripts, five (TRPV4, RIC8B, IL5RA, ERF, CDC40) showed significant differential expression between the three groups while the remaining 5 (RDM1, EPHX1, STAU1, TLE1, ASB8) did not show a significant difference in at least one of the pairwise comparisons. When tested in a larger cohort, these findings may contribute to the development of a new diagnostic test for paratuberculosis based on a gene expression signature. Such a diagnostic tool could allow early interventions to reduce the risk of the infection spreading.

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient.

Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across-habitat ß-diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil ß-diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below-ground biodiversity responses.

Challenges and opportunities in genetic improvement of local livestock breeds.

Sufficient genetic variation in livestock populations is necessary both for adaptation to future changes in climate and consumer demand, and for continual genetic improvement of economically important traits. Unfortunately, the current trend is for reduced genetic variation, both within and across breeds. The latter occurs primarily through the loss of small, local breeds. Inferior production is a key driver for loss of small breeds, as they are replaced by high-output international transboundary breeds. Selection to improve productivity of small local breeds is therefore critical for their long term survival. The objective of this paper is to review the technology options available for the genetic improvement of small local breeds and discuss their feasibility. Most technologies have been developed for the high-input breeds and consequently are more favorably applied in that context. Nevertheless, their application in local breeds is not precluded and can yield significant benefits, especially when multiple technologies are applied in close collaboration with farmers and breeders. Breeding strategies that require cooperation and centralized decision-making, such as optimal contribution selection, may in fact be more easily implemented in small breeds.

The costs of breed reconstruction from cryopreserved material in mammalian livestock species.

The aim of this work was to compare costs, in the horse, cattle, sheep, swine, and rabbit species, for the creation of gene banks for reconstruction of an extinct breed, using different strategies: embryos-only, embryos in combination with semen, and semen-only. Three cost measures were used: time required for population reconstruction, cost for creation of the gene bank, number of years-keeping-female to reach reconstruction. Semen costs were estimated across four scenarios: the presence or absence of a commercial market for semen, purchase of semen donors, and semen extracted from the epididymus. The number of cells were doubled to take into account the creation of two storage sites. The strategy embryos-only required the shortest time to reach reconstruction. With the strategy embryos + semen, time increased with decreasing proportions of embryos. With semen-only, reconstruction time varied from 2 to 21 years. A high variation of costs was observed across species and strategies, from 360 Euros in the rabbit to 1,092,300 in the horse. In all species, the embryos-only strategy was about 10% more expensive than using 90% embryos + semen. Decreasing the percentage of embryos further diminished costs. The number of years-keeping-female ranged across strategies, from 2 in the rabbit, to a maximum of 12,878 in the horse.

Performance of Cinta Senese pigs and their crosses with Large White 2. Physical, chemical and technological traits of Tuscan dry-cured ham.

Technological, chemical and physical traits of cured ham from Cinta Senese and Large White pigs, and their crosses were investigated. Hams were obtained from 29 Cinta Senese (CS), 29 Large White×Cinta Senese (LW×CS) and 12 Large White (LW) pigs, fed a commercial mixture. Sensory and chemical-physical analysis was performed on a sample-slice and on muscles (Biceps femoris - BF; Semimembranosus - SM; Semitendinosus - ST) and subcutaneous fat. CS showed the highest trimming loss and the lowest salting loss. Hams of CS pigs scored higher for fatness than those of LW pigs, LW×CS showing intermediate values. On sample-slice, CS exhibited higher firmness, redness and marbling of lean, and greater fat extension than LW, with crosses having intermediate scores. Muscle moisture was lowest in CS, while both SM and BF from LW had the highest percentage of protein and the lowest of ash. CS showed higher intramuscular fat content than LW×CS and LW. Shear force of BF was higher in CS than in LW×CS and LW. With respect to LW, CS had lower values of L(∗) in muscles, and higher values of a(∗) in subcutaneous fat. Subcutaneous fat of CS contained less SFA and more MUFA than LW×CS and LW.

The combined use of embryos and semen for cryogenic conservation of mammalian livestock genetic resources.

The objective of this empirical simulation study was to evaluate the use of a combination of semen and embryos in the creation of gene banks for reconstruction of an extinct breed. Such an approach was compared for banks with varying proportions of embryos on the basis of the amount of the material to be stored, time for reconstruction, maintenance of genetic variability, and probability of failure during reconstruction. Four types of populations were simulated, based on reproductive rate: single offspring, twinning, enhanced reproduction, and litter bearing. Reconstruction was simulated for banks consisting of different combinations of semen and reduced numbers of embryos (expressed as a percentage of the material needed for a bank containing exclusively embryos and ranging from 10 to 90%). The use of a combination of semen and embryos increased the number of insemination cycles needed for reconstruction and the level of genetic relatedness in the reconstructed population. The risk for extinction was unacceptably high when a very low proportion of embryos (<20%) was used. However, combining semen with embryos could decrease costs, allowing for the conservation of more breeds, and specific strategies for semen use could decrease the level of relationships in the reconstructed breed.

Performance of Cinta Senese pigs reared outdoors and indoors. 1. Meat and subcutaneous fat characteristics.

The effects of rearing system on tissue composition of a sample joint and on chemical-physical traits of meat and subcutaneous fat were studied in an Italian local pig breed. Forty-six Cinta Senese pigs were used; 17 pigs were reared on wood pasture, 29 pigs were reared in pens and fed commercial mixtures. Weight at slaughter was 136.2 and 127.7 kg for indoor and outdoor-pigs respectively. For sample joint composition outdoor-pigs showed a lower percentage of Longissimus lumborum (Ll) (46% vs. 48%) and higher percentages of intermuscular fat (7.2% vs. 4.7%) and bone (20.9% vs. 19.2%). In Ll outdoor-pigs showed higher percentages of intramuscular fat (4.04% vs. 3.29%) and crude protein (23.5% vs. 22.8%), lower drip and cooking losses by oven (0.66% vs. 2.14% and 28.6% vs. 32.3% respectively) and higher cooking loss by water-bath (30.3% vs. 26.6%). Lower values of L* (45.8 vs. 50.1) and higher values of a* (14.9 vs. 11.8) and chroma (15.9 vs. 12.8) were recorded on Ll of outdoor-pigs. Subcutaneous fat of outdoor-pigs showed higher percentages of MUFA (55.1% vs. 53.3%) and PUFA (13.2% vs. 10.4%). Outdoor-pigs had higher PUFA/SFA ratio (0.43 vs. 0.29).

Performance of Cinta Senese pigs and their crosses with Large White. 1 Muscle and subcutaneous fat characteristics.

Twenty-nine Cinta Senese (CS), 29 Large WhitexCinta Senese (LWxCS) and 12 Large White (LW) pigs were reared indoors and fed a commercial mixture. After slaughter (at avg. weight of 136, 139, 155 kg for CS, LWxCS, LW, respectively), a portion of the loin (sample cut) was dissected into lean and Longissimus lumborum (LL), intermuscular fat and bone. Chemical and physical analyses were conducted on LL. Chemical composition and fatty acid profile were determined on the outer layer of backfat. CS pigs had the highest percentage of bone and the lowest of lean in the sample cut, LWxCS showing intermediate values between parental breeds. In LL, CS showed lower moisture (73.23% vs. 74.28%) and higher fat content (3.19% vs. 0.87%) than LW; pH(24) was higher in CS (5.78) than in LWxCS (5.67) and LW (5.50); meat was more red in CS and LWxCS than in LW; CS showed higher water holding capacity than LW, with LWxCS at an intermediate position; raw meat was tougher in CS than in LW, but differences disappeared after cooking. In backfat CS had lower moisture (6.5% vs. 6.9% and 7.8%) and higher lipid content (81.4 vs. 78.1 and 77.5%) than LWxCS and LW; concerning fatty acid composition, CS showed less SFA (saturated fatty acids; 36.2% vs. 37.12% and 37.7%) than the other two genotypes, and, together with LWxCS, less PUFA (polyunsaturated fatty acids; 10.4% and 10.2% vs. 11.1%) and more oleic acid (50.3% and 49.8% vs. 48.5%) than LW. Overall, evidence of additive genetic effects was present for most qualitative parameters with crosses showing intermediate values between parental breeds.

Chemical and microbiological parameters and sensory attributes of a typical Sicilian salami ripened in different conditions.

A study was carried out on a typical Sicilian salami prepared from meat of the local Nero Siciliano pig in order to characterize this typical product. One formulation of salami was divided in two batches and ripened in two different environments, a traditional sicilian room (TR) and a controlled industrial ripening room (RR). Microbiological and physico-chemical analysis were performed on raw mixture and after 7 and 90 days of ripening. Sensory analysis was carried out on salami at the end of ripening, and flavour compounds were extracted by simultaneous distillation-extraction and analysed by gas chromatography/mass spectrometry. Commercial salami prepared from meat from white pig were purchased locally and used as comparative samples. The experimental salami at the end of ripening was characterized by a high level of fat and low level of moisture. Fatty acid analysis showed that experimental salami contained a higher percentage of oleic acid, vaccenic acid and palmitic acid and a lower percentage of stearic acid and linoleic acid, when compared to commercial salami (P<0.05). No significant differences were found in fatty acid composition of the experimental salami between the two types of ripening. Instrumental analysis of flavour volatile compounds in the experimental salami demonstrated that traditionally ripened salami contained the most volatiles, especially aldehydes (8217 vs. 3104 ng g(-1), P<0.05). Sensory analysis showed no significant differences as a consequence of different ripening conditions for firmness, saltiness, acidity, cohesiveness and elasticity. In contrast, there were significant differences for hardness and rancidity, which were higher in TR salami compared with RR and commercial salami. Lactic acid bacteria and Micrococcaceae counts were higher in controlled ripened salami although the hygienic quality of both products was satisfactory. The use of a controlled room for the ripening of this typical salami seems to be a potential technological improvement to maintain an all year around production of this salami, that otherwise cannot be produced in the summer period due to the higher environmental temperatures. However, the non traditionally ripened product showed some chemical differences that were not evidenced by sensory analysis.

Comparison of the performances of Nero Siciliano pigs reared indoors and outdoors. 1. Growth and carcass composition.

A total of 78 female and male Nero Siciliano pigs were used. Forty-one pigs were reared following the traditional management system, 37 pigs were reared in pens with a small outdoor paddock and fed to appetite using commercial rations according to the growing period. Both male and female pigs were castrated. All pigs were weighed and measured periodically. Body measurements included height at withers, chest girth, body length, width at shoulders and at rump. Age and body weight at slaughter ranged respectively from 371 to 572 days and from 79 to 113 kg. The carcasses were weighed and dissected into lean, fat and bone cuts. In the early and final stages indoor-pigs grew faster than those reared outdoors. Trends in body length were similar for the two rearing systems, for width at shoulders and rump, chest girth and height at withers, indoor pigs showed higher values than the outdoor ones. Carcasses of similar weight were longer in outdoor than in indoor pigs but the latter showed greater subcutaneous fat thickness. Outdoor pigs had the lowest dressing percentage and the highest percentage of lean cuts, such as shoulder and ham, but not of neck and loin. Sex did not significantly affect the analysed characteristics.