A. Talenti

B. Lazzari

C. Costa

E. Facchini

G. Gandini

G. Minozzi

G.G.A. Pagnacco

English

AIR Universita degli studi di Milano

[page 100] [Ital J Anim Sci vol.18:s1, 2019]
23rd Congress of Animal Science and Production Association
ANIMAL BREEDING AND GENOMICS – GENOMIC EDITING
incubating 0.75 g of diet with pepsin (1%; pH2) for 2 h at 39 °C; 
then a pancreatin solution (10%; pH 6.8) was added and incu-
bated for 4h at 39 °C. At the end, sulpho-salicylic acid (20%) was 
used to precipitate the residual protein. The undigested residue 
was filtered in glass crucibles, dried at 103 °C and ashed at 550 °C.
The mean chemical composition of the extruded diet was (% a.f.): 
dry matter 92.88 ± 1.05, ash 7.33 ± 0.79, crude protein 31.75 ± 3.64, 
ether extract 12.66 ± 2.13 and crude fibre 5.16 ± 2.26.
The determination coefficient (r2 = 0.7607) suggest that the pro-
posed in vitro method provided an accurate prediction of in vivo 
digestibility, even if on average OMD_iv values were lower than 
OMD ones. Correlating chemical composition parameters with 
OMD and OMD_iv values, the two methods showed similar trend. 
Only lipids content and structural carbohydrates significantly 
affected OM digestibility: crude fibre was the main factor that 
influenced negatively (p<.01) digestibility (−0.697 and −0.598 
for OMD and OMD_iv, respectively), while ether extract was pos-
itively correlated with digestibility (0.493; p<.05 and 0.589; p<.01, 
respectively).
These preliminary results suggest the goodness of the proposed 
method to predict OM digestibility, even if the digestibility of 
other nutrients have to be studied and a larger number of differ-
ent pet-food have to be tested in order to better represent the 
wide variation of pet-food which exists on the market and, con-
sequently, to achieve a better adjustment of the obtained 
equation.
O159
DogBiome: the gut microbiome project for 
dog
Elisa Scarsella1, Misa Sandri1, Michela Cintio1, Sandy 
Sgorlon1, Giuseppe Conte2, Bruno Stefanon1
1Department AgroFood, Environmental and Animal 
Science. University of Udine, Italy
2Department of Agricultural, Food and Agrenvironmental 
Sciences, University of Pisa, Italy
Contact: bruno.stefanon@uniud.it
Recently, a description of the microbial population of many niches 
of the organism, for example, the gastrointestinal tract, is feasible 
thanks to the use of advanced techniques such as High-throughput 
DNA sequencing that allows the simultaneous analysis of micro-
biota. Regarding the companion animals, a growing number of 
studies investigated faecal microbiome in healthy or affected 
subjects, although the methodologies used in the different labo-
ratories do not allow a straight comparison among results. 
Despite this, they still have the interest in studying microbiome 
in depth, also to see how diet modifications can affect this 
latter.
In the present study, we report data collected from several in house 
researches carried out in healthy dogs, with the aim to describe 
the variability of microbial taxa in the faeces, providing a global 
picture of the composition of faecal microbiota. Overall, the data-
base contains 334 samples from 132 dogs, which were collected 
during dietary intervention studies, where the diet composition 
and nutritional supply were under experimental control. According 
to the experimental design of the trials, for some dogs serial faecal 
samples were collected to assess the response of microbiota to 
the diet. The procedure of samples collection, storage, DNA 
extraction and sequencing, bioinformatic and statistical analysis 
followed a defined pipeline. The relative abundances (RA) of 
Firmicutes, Bacteroidetes and Fusobacteria represented more than 
90% of the phyla, with minor percentages of Proteobacteria and 
Actinobacteria. At a genus taxonomic level, 72 genera were found 
with an RA >0.001%, although 20 of these genera accounted for 
more than 90% of the total RA. The genera with a threshold of RA 
>5% were Clostridium, Blautia, Fusobacterium and Bacteroides. 
Alpha and beta biodiversity were relevant complementary infor-
mation to underpin faecal microbiome.
This DOGBIOME database represents a unique archive of dog 
faecal microbiota, which can form the basis for the identification 
of reference values, if any, of microbial community. The same 
data can also be used as a diagnostic tool to screen subject for 
gastrointestinal conditions. Nevertheless, the implementation of 
this archive will also help researchers to design diets and to inves-
tigate the effect of nutrients on gut functions.
Acknowledgement
The research was funded by the Department of AgroFood, Environmental 
and Animal Science. Grant PRID 2017.
ANIMAL BREEDING AND GENOMICS – GENOMIC 
EDITING
O160
Unveiling the Biodiversity of the Italian 
HONEYBEESBYNEXTGENERATIONSEQUENCING
Giulietta Minozzi1, Gustavo Gandini1, Barbara Lazzari1, 
Elena Facchini1, Cecilia Costa2, Andrea Talenti3, Giulio 
Pagnacco1
1Dipartimento di Medicina Veterinaria DIMEVET, 
University of Milano, Italy
2CREA-AA, Bologna, Italy
3Roslin Institute, University of Edinburgh, UK
Contact: Giulietta.Minozzi@unimi.it
Among the domestic animals, the honey bee (Apis mellifera) 
has an extremely important role both for the production of 
honey, wax, pollen and royal jelly, but above all for the pollination 
[page 101][Ital J Anim Sci vol.18:s1, 2019]
Italian Journal of Animal Science 2019; volume 18: supplement 1
ANIMAL BREEDING AND GENOMICS – GENOMIC EDITING
of arboreal and herbaceous species fundamental for human 
nutrition. Nevertheless, the genetic management of this species 
both at a selective and biodiversity conservation level has been 
proven to be difficult. One of the main reasons lies on the fact 
that the reproductive moment escapes possible human control 
as the virgin queen (VQ) is fertilised in flight by a variable 
number of drones present in the environment. Furthermore, 
free coupling opens the way to the genetic erosion of local vari-
eties by different genetic subtypes. The Apis mellifera, in fact, 
presents over 30 subtypes described in detail in the ‘80s by 
Friedrich Ruttner on a morphometric basis and by Father Adam 
(Karl Kehrle) of Buckfast Abbey based on the production and 
behavioural traits. In this scenario, it becomes urgent to provide 
protection of the local varieties from the phenomena of genetic 
erosion.
To implement a correct genetic conservation plan it is necessary 
to describe the biodiversity present today in a robust manner. 
The availability of the Honeybee genome allows using next-gen-
eration sequencing methods to define subtypes/subpopulations 
more precisely.
In this context, we analysed patterns of genetic variation of sev-
eral populations of Honeybees sampled in Italy. In detail, whole 
genome sequencing has been performed on 125 bee samples by 
Illumina technology. Sequences have been mapped to the refer-
ence genome obtaining a mean coverage of 18.6X (minimum 
coverage 7.33X and maximum coverage 29.75X). In total, after 
quality check, 4,095,663 SNPs have been identified. The SNP 
dataset has been pruned based on linkage disequilibrium (LD) 
and principal component analysis (PCA) has been performed. 
The resulting pruned dataset contains 1,032,587 SNP. Results of 
the PCA analysis of the 125 honeybees allowed to identify and 
subgroup bees according to their subtype. The SNP collection can 
be mined to create a SNP panel for subtype testing.
Acknowledgements
The research was funded by the BEENOMIX project funded by the 
Lombardy Region.
O161
The illumina® greater good initiative. A 
further step toward inclusion of camels in 
the ‘agrigenomic revolution’
Elena Ciani1, Pamela Burger2, Samantha Brooks3, Faisal 
Almathen4, International Camel Consortium for Genetic 
Improvement and Conservation†
1Dipartimento di Bioscienze, Biotecnologie e 
Biofarmaceutica, University of Bari, Italy
2Research Institute of Wildlife Ecology, Vetmeduni, Vienna, 
Austria
3Department of Animal Sciences, University of Florida, 
Gainesville, USA
4Department of Veterinary Public Health and Animal 
Husbandry, King Faisal University, Al Hofuf, Saudi Arabia
† https://icc-gic.weebly.com/
Contact: elena.ciani@uniba.it
Camels represent a key livestock resource in several low-income 
countries where they can positively impact food security and 
resilience. Unlike the other livestock species, the genomic revo-
lution is still in its early infancy for camels. Notwithstanding, a 
growing world-wide demand for innovation exists, as attested by 
(i) the recent establishment of the International Camel 
Consortium for Genetic Improvement and Conservation (ICC-
GIC), now counting over than 80 members from various coun-
tries; (ii) the ongoing work to establish the organisation of the 
camel genome at the chromosome level; (iii) the publication of 
various dromedary transcriptomes. Here, we describe the project, 
supported by the Illumina Greater Good Initiative Grant, aiming 
at developing an Illumina Camel Genotyping BeadChip. 
Implementation of a selection of SNP loci in a SNP genotyping 
platform may allow rapid and cost-effective genotyping of hun-
dreds of thousands markers in large numbers of animals, thus 
boosting downstream applications such as genome-wide associ-
ation studies for production traits and genome-based selective 
breeding. As the risk of the ‘SNP ascertainment bias’ phenome-
non has been shown to be one of the major drawbacks in SNP 
array design, the project will preliminary perform a whole-ge-
nome camel diversity study across the whole geographic range 
of camel distribution. Using the core collection of DNA samples 
available from the ICC-GIC members, a total amount of 20 tera-
bases of Illumina NovaSeq sequencing data will be produced, 
partly using the 10X Genomics Linked-Read sequencing approach. 
This strategy will allow to obtain a deep insight on the genomic 
variation at a large geographic scale (over 400 animals will be 
whole-genome sequenced), provide better resolution of haplo-
types, detect and characterise structural variants, improve the 
currently available reference genomes, deepen understanding of 
evolutionary processes (domestication, inter-specific hybridisa-
tion, dispersal and selection) that shaped the camel genomes, 
and possibly decipher the molecular basis of the peculiar physi-
ological adaptation traits of camels. Also, in line with the mission 
of ICC-GIC, this initiative will allow to strengthen the relation-
ships among the camel scientific community. Finally, the avail-
ability of a camel SNP genotyping platform may, in the mid-term, 
boosts national governments investments in country-based breed-
ing programmes based on systematic phenotype and genealogical 
recording.


Unveiling the Biodiversity of the Italian Honeybees by next generation sequencing

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Unveiling the Biodiversity of the Italian Honeybees by next generation sequencing

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