DALLA DOMESTICAZIONE ALLA GENOMICA, COME L’UOMO MODIFICA LE SPECIE ANIMALI CHE ALLEVA

The paper briefly reviews the main steps of animal breeding starting from livestock domestication. The major cultural changes in biology comprehension during XIX and XX centuries are reported with some emphasis on the meaning of the infinitesimal model interpreting quantitative phenotypes. Genomic analysis, dominant on the scenes since the beginning of this century, is explored in a wider way. Genomic selection, production traceability and association between economic traits and specific regions of genome are briefly discussed

Analysis of 22 mutations within milk protein genes in Italian Friesian cattle

The bovine milk protein caseins, αS1-CN, β-CN, αS2-CN, and κ-CN are codified by four well characterized genes, named CSN1S1, CSN2, CSN1S2, and CSN3 respectively and clustered in a region of 250-kb of chromosome 6. A recent revision of milk protein nomenclature considering only protein polymorphisms indicates 8 αS1-CN, 4 αS2-CN, 12 β-CN, and 11 κ-CN variants within the genus Bos. Other mutations were found in the non-coding regions of the cluster, such as the promoter regions or the 3'UTR. Many of these polymorphisms, together with others in various genes, such as the one coding for β-lactoglobulin (LGB), show important associations with different milk quality traits. Analyzing all these polymorphisms could help clarify the role of both the casein haplotype and the other polymorphisms in milk composition and cheese-making properties, and could explain which polymorphisms are really or mostly involved. The mPCR-LDR-UA approach recently developed to test simultaneously 22 SNPs in DNA regions responsible for milk protein expression was used to type 250 Italian Friesian cattle. In perfect agreement with literature, the most frequent alleles were CSN1S1*B, CSN2*A2, CSN3*A, variant 2 of CSN1S1 promoter, and variant A of Bov-A2 element. A quite balanced frequency was observed for the LGB*A and LGB*B. No CSN2*C, CSN3*C, and CSN3*H alleles were found. The CSN1S1*C, CSN2*A3, CSN2*I alleles were detected only at the heterozygous condition and at a frequency lower than 2%. The method allowed also finding some unusual intragenic haplotype, such as the Bov-A2 element-CSN3 haplotypes A-B and B-E. As to LGB one of the four SNPs tested was always homozygous for the same mutation, as already noticed. This finding confirms that this synonymous SNP is probably a sequencing mistake or a rare mutation not decisive for the LGB typing in the Italian Friesian. Reducing cost and time for typing simultaneously many SNPs, the method will be applied to a greater number of individuals and to other breeds, aiming to find out a number of animals for each haplotype sufficient for accurate statistical analysis to give a better understanding of the significance of milk protein polymorphism

Detection of selection signatures for ear carriage in Maltese goat breed

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity

Microarray analyses to identify differentially expressed genes for assessing meat quality in swine

In order to identify candidate genes and molecular mechanisms that influence meat quality and production in pigs, microarray experiments were carried out to find differences in gene expression levels between two pools of six individuals, constituting the extreme tails of the Gaussian distribution of seven adjusted phenotypes of 100 Landrace and Large White animals. The phenotypes considered in this study were: muscle compactness, marbling, colour uniformity, fat covering, colour, dorsal fat, thickness, ham fat thickness. 437 differentially expressed ESTs (Expressed Sequence Tags) were found, clustering in different pathways according to their ontology. In particular, 73 functional categories were identified and ten of them could have a role in meat quality. Among the ESTs belonging to these pathways, seven of them were selected to be validated in quantitative real-time RT-PCR

Chromosomal assignment of the ovine hairless (hr) gene by fluorescence in situ hybridization.

Congenital hypotrichosis in mammalian species consists of partial or complete absence of a hair coat at birth. Affected individuals having a partial hair coat at birth may loose it subsequently.The aim of this paper was to physically map the ovine hr gene using fluorescence in situ hybridization (FISH).A preliminary study on an internet data bank (http://www.informatics.jax.org) showed that the regions of the hr gene on murine chromosome 14 and human chromosome 8 present homology with ovine chromosome 2

Fine mapping of loci on BTA8 associated to antibody response to Mycobacterium avium paratuberculosis in cattle

Paratuberculosis (ParaTB) or Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis commonly known as MAP in cattle, is a chronic gastroenteritis characterized by diarrhoea, decreased milk production and ultimately death. MAP is responsible for huge economic losses, particularly in dairy cattle herds. Susceptibility to MAP infection has been found to be heritable with heritability estimates ranging from 0.06 to 0.102. The definition of an infected animal can be based either on the presence of anti-MAP antibodies in the serum, or by direct demonstration of MAP in tissue or faeces by culture or PCR. Several studies have addressed the identification of genetic loci associated with MAP susceptibility. The objective of this study was to refine a locus associated with antibody response to Mycobacterium avium paratuberculosi (MAP). Using a genome- wide association analysis, a single nucleotide polymorphism on Bos taurus autosome BTA8 namely the SNP rs43161947 at posi- tion 35398490 with a p-value of 7.02 e-05, has previously been identified by the authors as associated with MAP infection. Fine mapping of the region was conducted with 100 single nucleotide polymorphisms spanning a region between BTA8: 34422912 and BTA8: 364553881 covering 2 Mega bases (Mb) designed in to cover 1 Mb ahead and after the SNP identified on BTA8. The 2 Mb region on BTA8 was evaluated within a group of 966 Holstein cows collected from routine ParaTB screening in the province of Lodi in Italy, in an area with a high prevalence of ParaTB. Animals were defined as ParaTB positive based on the detection of serum antibodies produced in response to MAP infection using the ID-screen\uae ELISA test (ID VET Montpellier, France). Of the 966 samples, 483 were MAP antibody positive (cases) and 483 MAP antibody negative (MAP negative controls). All animals were female, and cases and MAP negative controls were from the same farm tested on the same day.Using a single marker associ- ation analysis, conducted within the R statistical environment, we identified 3 different QTLs within the 2 Mega base region, under the main QTL on BTA8 associated with antibody response to MAP, in position 34.700.000, 35.800.000 and 36.400.000 bp. This reveals the complexity of the genetic architecture of thetrait and confirms the need to further explore the genome with fine mapping approaches, or by the use of whole genome sequencing to investigate complex traits, such as disease resistance

Casein genetic polymorphisms in goat breeds of Lombardy

Polimorfismo genetico delle caseine in razze caprine allevate in Lombardia. E\u2019 stato condotto uno studio della variabilit\ue0 genetica delle caseine in sei razze caprine allevate in Lombardia. La tipizzazione, condotta a livello proteico mediante isoelettrofocalizzazione, \ue8 preliminare ad un approccio molecolare dettagliato su un numero pi\uf9 limitato di soggetti, scelti in base a particolari fenotipi caseinici

First Insights in the Genetics of Caseous Lymphadenitis in Goats

Abscesses are a common problem in goat farms worldwide. In most cases, the disease is caused by Corynebacterium pseudotuberculosis that is the aetiological agent of caseous lymphadenitis (CLA). CLA causes considerable economic losses, due to reduced milk production, and to carcase damage. At present, no effective therapy for CLA is available and vaccine use is limited. The current study presents evidence for loci associated to CLA susceptibility identified using the 50K Goat SNP panel in a case-control genome wide association study. The analysis of the genotype data identified four chromosomal regions associated with disease status: on chromosomes 5, 7, 8 and 11. These results provide the first evidence for genetic loci involved in the immunological response to CLA in goat. Knowledge of genetic variations related to susceptibility will facilitate the incorporation of this information for the improvement of health status in the goat species