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

Polymorphism analysis of AMY1, AMY2, SLC5A1, SLC2A2 and SLC2A5 genes in Italian horse breeds

The dietary demand of modern competition horse relies on high-cereal feeding daily interspersed by limited forage and it is frequently characterized by marked changes in carbohydrate fractions, above all starch, compared to natural grazing conditions. These dietary variations influence digestion, metabolism, and increase the risk for colic and laminitis, both main causes of equine mortality. Aim of this work has been to analyze the polymorphism of genes related to digestion and absorption of complex carbohydrates, particularly starch, to make a comparison between different cosmopolite and Italian native horse breeds, characterized by marked differences in feeding and management conditions. The analyzed genes were: salivary and pancreatic alpha-amylases (AMY1 and AMY2, respectively), solute carrier family 2, facilitated glucose transporter member 2 (SLC2A2) and member 5 (SLC2A5) and sodium/glucose cotransporter 1 (SLC5A1), code for GLUT2, GLUT5 and SGLT1 enzymes, respectively, main routes for the transport of dietary sugars from the lumen of the intestine into enterocytes. Horses belonging to three cosmopolite breeds, Throughbred, Purebred Arabian and Friesian, and three southern Italian native breeds, Sanfratellano, Indigeno Siciliano and Murgese, 2 DNA samples per breed, were pooled. SNP detection was performed by sequencing one DNA pool per breed. A total of 13 novel single nucleotide polymorphisms were found. Six SNPs are located in AMY1 gene and 3 are in exons, of which 1 is non-synonymous. A non-synonymous SNP was also identified in exon 1 of AMY2 gene. No SNPs were found in the SLC2A2 gene region analyzed, while 4 SNPs were characterized in 3\u2019UTR of SLC2A5 gene. Finally, 4 SNPs were found in SLC5A1 gene, all located in intron 3. Three out of the SNPs found in AMY1 and AMY2 genes were genotyped in 121 horses belonging to the analyzed breeds, with the addition of Haflinger and Sella Italiano breeds samples. The results of the SNP genotyping are presented

A microarray technology for SNP detection in goat milk protein genes

The aim of this paper was to investigate the influence of housing systems on stillbirth and mortality rate in preweaning pigs farrowed by different gilt breeds. The investigation included first farrowings of 225 Large White (LW) gilts, 297 Swedish Landrace (SL) gilts and 260 crossbreed gilts (LWxSL) in the period of five years. Despite of positive influence of straw through decreased number of stillborn pigs, especially in LW gilts, in further process of production until weaning, less appropriate microclimatic conditions developed in farrowing houses with straw, especially if accompanied with poor ventilation, can result with higher number of perished pigs and lower number of weaned pigs. Most sensible to unsuitable microclimatic conditions in straw bedded farrowing houses, according to the number of perished pigs before weaning, were the pigs from SL gilts, while the pigs from crossbreed gilts LWxSL were the most resistant. These results suggest that adding straw requires special attention on influence of such production on microclimate conditions in pigs' biozone in order to maintain its initial benefits in the time of farrowing through the whole preweaning period, especially in pure breeds of gilts

Diacylglycerol acyltransferase 1, stearoyl-CoA desaturase 1, and sterol regulatory element binding protein 1 gene polymorphisms and milk fatty acid composition in Italian Brown cattle

Several lipogenic genes have been shown to have effects on lipid metabolism: stearoyl CoA desaturase 1 (SCD1) catalyzes the desaturation of several fatty acids (FA) in the cis-Delta(9) position in mammary glands of ruminant animals, diacylglycerol acyltransferase I (DGAT1) is a key enzyme in triacylglycerol synthesis in the mammary gland, and sterol regulatory element binding protein (SREBP-1) is a transcription factor that regulates expression levels of the SCD1 gene and other genes relevant to lipid and FA metabolism in adipose tissue and mammary gland. In this work, 351 Italian Brown cows were genotyped for polymorphisms in the SCD1, SREBP-1, and DGAT1 genes to reveal the allelic distribution in the population. Subsequently, effects on individual milk FA composition and on cis-9 unsaturated/saturated FA ratios, a proxy of mammary stearoyl CoA desaturase activity, were investigated. The genotypes of SCD1 (A293V) and DGAT1 (K232A) were determined by an approach based on the ligation detection reaction and a universal array, whereas the genotype of SREBP-1 (84-bp insertion-deletion) was revealed by PCR amplification of intron 5. The genotype analysis showed an unbalanced distribution of alleles within all genes, being the allele with higher gene frequency at 82, 84, and 98% for SCD1, SREBP-1, and DGAT1, respectively. Significant associations between SCD1 and DGAT1 polymorphisms and milk FA composition were found, whereas SREBP-1 polymorphism was not associated with milk FA composition. In particular, SCD1 showed significant association with C14:1 cis-9 and C14:1 cis-9/C14:0, which is considered the best proxy of the desaturation activity in mammary gland. The DGAT1 polymorphism had the strongest association with milk FA composition, which confirmed the key role of DGAT1 in lipid metabolism of mammary gland. However, the unbalanced distribution of alleles in all polymorphisms investigated suggested that the size of population should be increased to confirm the results of the present study

Evolution of alphaS1-casein polymorphism in Italian Alpine and Saanen breeds

AlphaS1-casein, coded by CSN1S1 gene, is one of the most important goat milk protein, although, in this species, it represents on average only the 5.6% of the total casein content. On the basis of the milk content of alphaS1-casein, the CSN1S1 variants can be grouped into 4 classes: strong alleles (A, B1, B2, B3, B4, C, H, L, and M), producing almost 3.5 g/L of \uf061S1-casein each; intermediate alleles (E and I; 1.1 g/L); weak alleles (F and G; 0.45 g/L); and null alleles (01, 02, and N) apparently producing no alphaS1-casein. Previous studies have reported that the CSN1S1 can affect casein, protein and fat levels, total solids, milk rheology, as well as cheese yield and quality. The aim of the study was to evaluate how the frequencies of the major CSN1S1 allelic variant have changed during the last 10 years in the two main dairy goat breeds raised in the North of Italy: Italian Alpine and Saanen. Two hundred and twenty three Alpine and 129 Saanen were sampled from 8 farms spread all over Lombardy. AS-PCR and RFLP-PCR were performed to genotype the major allelic variants at the alphaS1-casein locus. Only the Saanen breed proved to be in Hardy-Weinberg equilibrium at this locus. The allele frequencies observed in the present work showed statistically significant differences (\uf0632 test, P<0.005) compared to those reported in two studies published in 2004. This difference was due to an increase of the strong allele A (12 and 18%) and the intermediate allele E (15 and 8%) nearby a reduction of the weak allele F (17 and 12%) and the strong allele B (11 and 13%) respectively in Saanen and Alpine breeds. The A allele is well known for being associated to smaller micellar casein, with a consequent better cheese yield. Recent indications of selection concerning the Alpine and Saanen bucks favours both strong and intermediate alleles, consistent with the described strong frequency increase of CSN1S1*E. For the top farms analysed, with over 85% genotypes with strong alleles, these directive could lead to an increaseof the allele E and consequently to a reduction of protein content and cheese yield