153 research outputs found
Insights into genetic diversity, runs of homozygosity and heterozygosity-rich regions in maremmana semi-feral cattle using pedigree and genomic data
No full textSemi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree-and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE = 0.261, HO = 0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r = 0.03 with FIS, r = 0.21 with FROH), while it was higher between FIS and FROH (r = 0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity
hnRNP H1 and intronic G runs in the splicing control of the human rpL3 gene
No full textBy generating mRNA containing a premature termination codon (PTC), alternative splicing (AS) can quantitatively regulate the expression of genes that are degraded by nonsense-mediated mRNA decay (NMD). We previously demonstrated that AS-induced retention of part of intron 3 of rpL3 pre-mRNA produces an mRNA isoform that contains a PTC and is targeted for decay by NMD. We also demonstrated that overexpression of rpL3 downregulates canonical splicing and upregulates the alternative splicing of its pre-mRNA. We are currently investigating the molecular mechanism underlying rpL3 autoregulation. Here we report that the heterogeneous nuclear ribonucleoprotein (hnRNP) H1 is a transacting factor able to interact in vitro and in vivo with rpL3 and with intron 3 of the rpL3 gene. We investigated the role played by hnRNP H1 in the regulation of splicing of rpL3 pre-mRNA by manipulating its expression level. Depletion of hnRNP H1 reduced the level of the PTC-containing mRNA isoform, whereas its overexpression favored the selection of the cryptic 3' splice site of intron 3. We also identified and characterized the cis-acting regulatory elements involved in hnRNP H1-mediated regulation of splicing. RNA electromobility shift assay demonstrated that hnRNP H1 specifically recognizes and binds directly to the intron 3 region that contains seven copies of G-rich elements. Site-directed mutagenesis analysis and in vivo studies showed that the G3 and G6 elements are required for hnRNP H1-mediated regulation of rpL3 pre-mRNA splicing. We propose a working model in which rpL3 recruits hnRNP H1 and, through cooperation with other splicing factors, promotes selection of the alternative splice site
Genome-wide association study identifies quantitative trait loci regions involved in muscle acidic profile in Large White heavy pigs
No full textThe widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic : palmitic and oleic : stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E-07). Of particular interest, the palmitoleic : palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products
Age prediction obtained by ultrasonographic fetal measurement in the buffalo.
No full textUltrasonography has been reported as the method of choice for early pregnancy diagnosis. The aim of this study was to evaluate the mesaurements of some specific somatic parameters in the foetus, such as crown rump length (CRL), biparietal diameter of the cranium (BPD), abdominal diameter (AD), muzzle occipital length (MOL) and femur, tibia and metatarsial bone lengths in order to estimate foetal growth. Several regression equations have been formulated in order to do this in buffalo species
Describing backfat and Semimembranosus muscle fatty acid variability in heavy pigs: Analysis of non–genetic factors
No full textThis study aimed to describe the multivariate structure of Semimembranosus muscle and backfat fatty acid (FA) composition in 798 Italian Large White heavy pigs and to investigate the effects of environmental factors and carcass characteristics on FA variations. The total FA variability in muscle and backfat was characterized by a negative correlation between saturated and polyunsaturated FAs, which strongly depended on the carcass adiposity. Slaughtering season was also relevant, with pigs slaughtered in autumn having more n-6 FAs and eicosadienoic acid in backfat, while pigs slaughtered in winter displayed more saturated FAs. Regarding Semimembranosus muscle, pigs with heavier belly cuts and slaughtered in autumn had higher proportions of cis-vaccenic and palmitoleic acids, while those slaughtered in summer had more saturated FAs. Slaughtering season emerged as a relevant factor shaping both backfat and muscle FA composition, indicating that more studies and attention should be paid to environmental factors, which may have effects on FA metabolism and deposition in finishing pigs
Genetic parameters and analysis of factors affecting variations between backfat and Semimembranosus muscle fatty acid composition in heavy pigs
No full textThis study was conceived to evaluate the variations between backfat (BF) and Semimembranosus (SM) muscle fatty acid (FA) composition in 789 heavy pigs and to estimate the genetic and phenotypic correlations and the heritability values of these variations. Most FAs showed a common genetic basis controlling their proportion in SM muscle and BF, while the n-6/n-3 ratio, α-linolenic and erucic acids displayed a genetic control more oriented towards tissue-specific molecular pathways. All variations between the FA composition of BF and SM muscle showed low-to-medium heritability values, suggesting that there are also genetic mechanisms capable of differentiating the deposition of FAs in BF from those in SM muscle. This result implies that a better knowledge of the genes differentiating the FA composition of BF and SM muscle could provide new tools allowing to select, in a partially independent manner, the FA composition of muscle and subcutaneous fat
LACTATION CURVES OF MILK PRODUCTION TRAITS IN ITALIAN WATER BUFFALOES ESTIMATED BY A MIXED LINEAR MODEL
No full textGenome-wide homozygosity in Maremmana Cattle
No full textThe current availability of large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of patterns of genetic diversity and of genome-wide homozygosity in animal populations. The aim of this work was to estimate genetic diversity and homozygosity in the Maremmana cattle breed. We used a sample of 149 animals (males and females) genotyped with the BovineSNP50 v2 (54K) Illumina BeadChip. After editing for call-rate >0.9 and removing SNP unassigned or on the sex chromosomes, 128 animals and 50,814 SNPs were left. We estimated the following genetic parameters: observed and expected heterozygosity (Ho and He), minor allele frequency (MAF), and the FIS statistic. We also scanned the genome for runs of homozygosity (ROH). In the present study, ROH were detected based on 20-SNP-long sliding-windows, and allowing for a maximum of 1 missing and 1 heterozygote genotype, and a maximum gap between consecutive SNP of 105 bp. ROH contained minimum 10 SNPs, and had a minimum length of 1 Mb and a minimum density of 1 SNP every 50 kbps. The average Ho and He were 0.374 ± 0.132 and 0.365 ± 0.120, respectively, and the average MAF was 0.274 ± 0.130. These values are consistent with the range observed in other cattle breeds. We obtained some negative values for FIS (-0.162 to 0.180) which corresponded to animals with lower than average homozygosity. In total, 10,465 ROH were detected (81.75 per animal), with an average length of 2.69 Mb. Most ROH (74%) had length 2 Mb. ROH are contiguous lengths of homozygous genomic segments where the two inherited haplotypes are identical. ROH indicate genomic regions where a reduction in heterozygosity occurred, and offer new opportunities to estimate inbreeding (F). The inbreeding coefficient based on ROH (FROH) was estimated by the ratio between the total ROH length and the size of the genome in each animal. Average FROH was 0.0869 ± 0.032. Unlike inbreeding estimated based on Ho, FROH is not influenced by allele frequencies (sampling) and can distinguish recent from ancient inbreeding. However, FROH requires SNP positions to be known (unlike Ho). Two genomic regions with ROH in over 60% of the animals were found: one on BTA6 (38.6-39.7 Mbps), one on BTA13 (54.3-54.8 Mbps). These may highlight regions where selective pressures have shaped the genome of the Maremmana breed
"Alternative splicing and nonsense-mediated mRNA decay (NMD) in the regulation of mammalian ribosomal protein expression
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