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1.
Animal ; 18(4): 101118, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38508133

ABSTRACT

Nowadays, several countries are developing or adopting genomic selection in the dairy goat sector. The most used method to estimate breeding values is Single-Step Genomic Best Linear Unbiased Prediction (ssGBLUP) which offers several advantages in terms of computational process and accuracy of the estimated breeding values (EBVs). Saanen and Alpine are the predominant dairy goat breeds in Italy, and both have similar breeding programs where EBVs for productive traits are currently calculated using BLUP. This work describes the implementation of genomic selection for these two breeds in Italy, aligning with the selection practices already carried out in the international landscape. The available dataset included 3 611 genotyped animals, 11 470 lactation records, five traits (milk, protein and fat yields, and fat and protein percentages), and three-generation pedigrees. EBVs were estimated using BLUP, GBLUP, and ssGBLUP both with single and multiple trait approaches. The methods were compared in terms of correlation between EBVs and genetic trends. Results were also validated with the linear regression method excluding part of the phenotypic data. In both breeds, EBVs and GEBVs were strongly correlated and the trend of each trait was similar comparing the three methods. The average increase in accuracy across traits and methods amounted to +13 and +10% from BLUP to ssGBLUP for Alpine and Saanen breeds, respectively. Results indicated higher prediction accuracy and correlation for GBLUP and ssGBLUP compared to BLUP, implying that the use of genotypes increases the accuracy of EBVs, particularly in the absence of phenotypic data. Therefore, ssGBLUP is likely to be the most effective method to enhance genetic gain in Italian Saanen and Alpine goats.


Subject(s)
Genome , Genomics , Female , Animals , Genomics/methods , Genotype , Milk/metabolism , Phenotype , Goats/genetics , Pedigree , Models, Genetic
2.
JDS Commun ; 5(2): 124-128, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38482122

ABSTRACT

In the dairy cattle sector, the number of crossbred genotypes increased in the last years, and therefore, the need for accurate genomic evaluations for crossbred animals has also increased. Thus, this study aimed to investigate the feasibility of including crossbred genotypes in multibreed, single-step genomic BLUP (ssGBLUP) evaluations. The Council of Dairy Cattle Breeding provided more than 47 million lactation records registered between 2000 and 2021 in purebred Holstein and Jersey and their crosses. A total of 27 million animals were included in the analysis, of which 1.4 million were genotyped. Milk, fat, and protein yields were analyzed in a 3-trait repeatability model using BLUP or ssGBLUP. The 2 models were validated using prediction bias and accuracy computed for genotyped cows with no records in the truncated dataset and at least one lactation in the complete dataset. Bias and accuracy were better in the genomic model than in the pedigree-based one, with accuracies for crossbred cows higher than those of purebreds, except for fat yield in Holstein. Our study shows that genotypes for crossbred animals can be included in a ssGBLUP analysis with their purebred ancestors to estimate genomic estimated breeding values in a single run.

3.
Animal ; 18(3): 101102, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38430665

ABSTRACT

Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.


Subject(s)
Gastrointestinal Microbiome , Humans , Cattle , Animals , Eating , Feces/microbiology , Weaning , Gastrointestinal Tract , Bacteria/genetics , Animal Feed/analysis , Rumen/microbiology
4.
J Dairy Sci ; 106(12): 9016-9025, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37641333

ABSTRACT

Until now, the genetic evaluation of the Italian Mediterranean Buffalo has been mainly focused on production traits. However, female fertility affects the efficiency of the dairy industry as it is essential to maintain the profitability of dairy farms. Indeed, the estimation of its genetic component is crucial for its improvement. In this study, 3 measures of buffalo's fertility were analyzed: the age at first calving (AFC), the interval between first and second calving (CIV1), and the interval between second and successive calvings (CIV2_12). Milk yield at 270 d (MY270) was used as a correlated trait. First, genetic parameters were estimated using 7,915 buffalo cows with first calving from 1991 to 2018, then breeding values were calculated from 236,087 buffalo cows. Genetic parameters were estimated by Bayesian inference fitting a multiple-trait animal model using the GIBBS1F90 program, and BLUPF90 was used for estimation of breeding value. The heritability and repeatability estimates of fertility traits were low. The genetic correlations among fertility traits ranged from 0.10 (AFC-CIV1) to 0.92 (CIV1-CIV2_12). Genetic correlation between MY270 and fertility traits was unfavorable, ranging from 0.23 to 0.48. The results from this study can be used as a basis for the future genetic improvement of fertility traits in the Italian Mediterranean Buffaloes.


Subject(s)
Buffaloes , Milk , Cattle/genetics , Female , Animals , Buffaloes/genetics , Lactation/genetics , Bayes Theorem , Fertility/genetics , Italy
5.
J Dairy Sci ; 106(5): 3312-3320, 2023 May.
Article in English | MEDLINE | ID: mdl-37028961

ABSTRACT

Lactose, the principal carbohydrate found in milk, plays an important role in the physiological processes of milk production because it is related to milk volume, and it is responsible for the osmotic equilibrium between blood and milk in the mammary gland. In this study, factors affecting lactose content (LC) in sheep milk are investigated. For this purpose, 2,358 test-day records were sampled from 509 ewes (3-7 records per animal). The LC and other main milk traits were analyzed using a mixed linear model that included days in milk (DIM) class, parity, lambing month, and type of lambing as fixed effects and animal, permanent environment, and flock test day as random effects. The pedigree-based approach was used to estimate the heritability and repeatability of LC. Moreover, the genomic background of LC was investigated through a GWAS. The LC was affected by all tested factors (i.e., DIM class, parity, lambing month, and type of lambing). Low heritability (0.10 ± 0.05) and moderate repeatability (0.42 ± 0.02) were estimated for LC. High negative genetic correlations were estimated between LC and NaCl (-0.99 ± 0.01) and between LC and somatic cell count (-0.94 ± 0.05). Only 2 markers passed the chromosome-wide Bonferroni threshold. Results of the present study, although obtained on a relatively small sample, suggest the possibility to include LC in the breeding programs, particularly because of its strong relationship with NaCl and somatic cell count.


Subject(s)
Lactose , Sodium Chloride , Pregnancy , Sheep/genetics , Animals , Female , Milk , Parity , Phenotype , Genetic Background , Lactation/genetics
6.
Animal ; 17(4): 100766, 2023 Apr.
Article in English | MEDLINE | ID: mdl-37001441

ABSTRACT

Nowadays, in some populations, the number of genotyped animals is too large to obtain the inverse of the genomic relationship matrix. The algorithm for proven and young animals (APY) can be used to overcome this problem. In the present work, different strategies for defining core animals in APY were tested using either simulated or real data. In particular, core definitions based on random choice or on the contribution to the genomic relationship matrix (GCONTR) calculated using Principal Component Analysis were tested. Core sizes able to explain 90, 95, 98, and 99% of the total variance of the genomic relationship matrix (G) were used. Analyzed phenotypes were three simulated traits for 3 000 individuals, and milkability records for 136 406 Italian Simmental cows. The number of genotypes was 4 100 for the simulated dataset, and 11 636 for the Simmental data, respectively. The GCONTR values in Simmental dataset were moderately correlated with the analyzed phenotype, and they showed a decreasing trend according to the year of birth of genotyped animals. The accuracy increased as the size of the core increased in both datasets. The inclusion in the core of animals with largest GCONTR values led to the lowest accuracies (0.50 and 0.71 for the simulated and Simmental datasets, respectively; average across traits and core sizes). On the contrary, the selection of animals with the lowest rank according to their contribution to the G provided slightly higher accuracies, especially in the simulated dataset (0.68 for the simulated dataset, and 0.76 for the Simmental data; average across traits and core sizes). In real data, particularly for larger sizes of core animals, the criteria of choice appear less important, confirming the results of earlier studies. Anyway, the inclusion in the core of animals with the lowest values of GCONTR led to increases in accuracy. These are preliminary results based on a small sample size that need to be confirmed on a larger number of genotypes.


Subject(s)
Genome , Genomics , Female , Cattle/genetics , Animals , Genomics/methods , Genotype , Phenotype , Algorithms , Models, Genetic
7.
J Dairy Sci ; 105(8): 6773-6782, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35840399

ABSTRACT

Milk coagulation ability is of central importance for the sheep dairy industry because almost all sheep milk is destined for cheese processing. The occurrence of milk with impaired coagulation properties is an obstacle to cheese processing and, in turn, to the profitability of the dairy companies. In this work, we investigated the causes of noncoagulation of sheep milk; specifically, we studied the effect of milk physicochemical properties on milk coagulation status [coagulating and noncoagulating (NC) milk samples, which do or do not coagulate within 30 min, respectively], and whether mid-infrared spectroscopy (MIR) could be used to assess variability in coagulation status. We also investigated the genetic background of milk coagulation ability. Individual milk samples were collected from 996 Sarda ewes farmed in 47 flocks located in Sardinia (Italy). Considered traits were daily milk yield, milk composition traits, and milk coagulation properties (rennet coagulation time, curd firming time, and curd firmness), and MIR spectra were acquired. About 9% of samples did not coagulate within 30 min. A logistic regression approach was used to test the effect of milk-related traits on milk coagulation status. A principal component (PC) analysis was carried out on the milk MIR spectra, and PC scores were then used as covariates in a logistic regression model to assess their relationship with milk coagulation status. Results of the present work demonstrated that the probability of having NC samples increases as milk contents of proteins and chlorides and somatic cell score increase. The analysis of PC extracted from milk spectra that influenced coagulation status highlighted key regions associated with lactose and protein concentrations, and others not associated with routinely collected milk composition traits. These results suggest that the occurrence of NC is mostly related to damage of the epithelium secretory mammary cells, which occurs with the advancement of a lactation or due to unhealthy mammary gland status. Genetic analysis of milk coagulation status and of the extracted PC confirmed the genetic background of the milk coagulability of sheep milk.


Subject(s)
Cheese , Milk , Animals , Cheese/analysis , Chymosin/metabolism , Dairying/methods , Female , Lactation , Lactose/analysis , Milk/chemistry , Phenotype , Sheep
8.
J Dairy Sci ; 105(6): 5141-5152, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35282922

ABSTRACT

Official multibreed genomic evaluations for dairy cattle in the United States are based on multibreed BLUP evaluation followed by single-breed estimation of SNP effects. Single-step genomic BLUP (ssGBLUP) allows the straight computation of genomic (G)EBV in a multibreed context. This work aimed to develop ssGBLUP multibreed genomic predictions for US dairy cattle using the algorithm for proven and young (APY) to compute the inverse of the genomic relationship matrix. Only purebred Ayrshire (AY), Brown Swiss (BS), Guernsey (GU), Holstein (HO), and Jersey (JE) animals were considered. A 3-trait model with milk (MY), fat (FY), and protein (PY) yields was applied using about 45 million phenotypes recorded from January 2000 to June 2020. The whole data set included about 29.5 million animals, of which almost 4 million were genotyped. All the effects in the model were breed specific, and breed was also considered as fixed unknown parent groups. Evaluations were done for (1) each single breed separately (single); (2) HO and JE together (HO_JE); (3) AY, BS, and GU together (AY_BS_GU); (4) all the 5 breeds together (5_BREEDS). Initially, 15k core animals were used in APY for AY_BS_GU and 5_BREEDS, but larger core sets with more animals from the least represented breeds were also tested. The HO_JE evaluation had a fixed set of 30k core animals, with an equal representation of the 2 breeds, whereas HO and JE single-breed analysis involved 15k core animals. Validation for cows was based on correlations between adjusted phenotypes and (G)EBV, whereas for bulls on the regression of daughter yield deviations on (G)EBV. Because breed was correctly considered in the model, BLUP results for single and multibreed analyses were the same. Under ssGBLUP, predictability and reliability for AY, BS, and GU were on average 7% and 2% lower in 5_BREEDS compared with single-breed evaluations, respectively. However, validation parameters for these 3 breeds became better than in the single-breed evaluations when 45k animals were included in the core set for 5_BREEDS. Evaluations for Holsteins were more stable across scenarios because of the greatest number of genotyped animals and amount of data. Combining AY, BS, and GU into one evaluation resulted in predictions similar to the ones from single breed, especially when using about 30k core animals in APY. The results showed that single-step large-scale multibreed evaluations are computationally feasible, but fine tuning is needed to avoid a reduction in reliability when numerically dominant breeds are combined. Having evaluations for AY, BS, and GU separated from HO and JE may reduce inflation of GEBV for the first 3 breeds.


Subject(s)
Genome , Models, Genetic , Animals , Cattle/genetics , Female , Genomics , Genotype , Male , Phenotype , Reproducibility of Results , United States
9.
J Dairy Sci ; 104(5): 5843-5853, 2021 May.
Article in English | MEDLINE | ID: mdl-33663836

ABSTRACT

The objective of this study was to assess the reliability and bias of estimated breeding values (EBV) from traditional BLUP with unknown parent groups (UPG), genomic EBV (GEBV) from single-step genomic BLUP (ssGBLUP) with UPG for the pedigree relationship matrix (A) only (SS_UPG), and GEBV from ssGBLUP with UPG for both A and the relationship matrix among genotyped animals (A22; SS_UPG2) using 6 large phenotype-pedigree truncated Holstein data sets. The complete data included 80 million records for milk, fat, and protein yields from 31 million cows recorded since 1980. Phenotype-pedigree truncation scenarios included truncation of phenotypes for cows recorded before 1990 and 2000 combined with truncation of pedigree information after 2 or 3 ancestral generations. A total of 861,525 genotyped bulls with progeny and cows with phenotypic records were used in the analyses. Reliability and bias (inflation/deflation) of GEBV were obtained for 2,710 bulls based on deregressed proofs, and on 381,779 cows born after 2014 based on predictivity (adjusted cow phenotypes). The BLUP reliabilities for young bulls varied from 0.29 to 0.30 across traits and were unaffected by data truncation and number of generations in the pedigree. Reliabilities ranged from 0.54 to 0.69 for SS_UPG and were slightly affected by phenotype-pedigree truncation. Reliabilities ranged from 0.69 to 0.73 for SS_UPG2 and were unaffected by phenotype-pedigree truncation. The regression coefficient of bull deregressed proofs on (G)EBV (i.e., GEBV and EBV) ranged from 0.86 to 0.90 for BLUP, from 0.77 to 0.94 for SS_UPG, and was 1.00 ± 0.03 for SS_UPG2. Cow predictivity ranged from 0.22 to 0.28 for BLUP, 0.48 to 0.51 for SS_UPG, and 0.51 to 0.54 for SS_UPG2. The highest cow predictivities for BLUP were obtained with the most extreme truncation, whereas for SS_UPG2, cow predictivities were also unaffected by phenotype-pedigree truncations. The regression coefficient of cow predictivities on (G)EBV was 1.02 ± 0.02 for SS_UPG2 with the most extreme truncation, which indicated the least biased predictions. Computations with the complete data set took 17 h with BLUP, 58 h with SS_UPG, and 23 h with SS_UPG2. The same computations with the most extreme phenotype-pedigree truncation took 7, 36, and 15 h, respectively. The SS_UPG2 converged in fewer rounds than BLUP, whereas SS_UPG took up to twice as many rounds. Thus, the ssGBLUP with UPG assigned to both A and A22 provided accurate and unbiased evaluations, regardless of phenotype-pedigree truncation scenario. Old phenotypes (before 2000 in this data set) did not affect the reliability of predictions for young selection candidates, especially in SS_UPG2.


Subject(s)
Genome , Models, Genetic , Animals , Cattle/genetics , Female , Genomics , Genotype , Male , Pedigree , Phenotype , Pregnancy , Reproducibility of Results
10.
J Dairy Sci ; 104(5): 5719-5727, 2021 May.
Article in English | MEDLINE | ID: mdl-33612221

ABSTRACT

Milkability is a trait related to the milking efficiency of an animal, and it is a component of the herd profitability. Due to its economic importance, milkability is currently included in the selection index of the Italian Simmental cattle breed with a weight of 7.5%. This lowly heritable trait is measured on a subjective scale from 1 to 3 (1 = slow, 3 = fast), and genetic evaluations are performed by pedigree-based BLUP. Genomic information is now available for some animals in the Italian Simmental population, and its inclusion in the genetic evaluation system could increase accuracy of breeding values and genetic progress for milkability. The aim of this study was to test the feasibility and advantages of having a genomic evaluation for this trait in the Italian Simmental population. Phenotypes were available for 131,308 cows. A total of 9,526 animals had genotypes for 42,152 loci; among the genotyped animals, 2,455 were cows with phenotypes, and the other were their relatives. The youngest cows with both phenotypes and genotypes (n = 900) were identified as selection candidates. Variance components and heritability were estimated using pedigree information, whereas genetic and genomic evaluations were carried out using BLUP and single-step genomic BLUP (ssGBLUP), respectively. In addition, a weighted ssGBLUP was assessed using genomic regions from a genome-wide association study. Evaluation models were validated using theoretical and realized accuracies. The estimated heritability for milkability was 0.12 ± 0.01. The mean theoretical accuracies for selection candidates were 0.43 ± 0.08 (BLUP) and 0.53 ± 0.06 (ssGBLUP). The mean realized accuracies based on linear regression statistics were 0.29 (BLUP) and 0.40 (ssGBLUP). No genomic regions were significantly associated with milkability, thus no improvements in accuracy were observed when using weighted ssGBLUP. Results indicated that genomic information could improve the accuracy of breeding values and increase genetic progress for milkability in Italian Simmental.


Subject(s)
Genome-Wide Association Study , Genome , Animals , Cattle/genetics , Female , Genome-Wide Association Study/veterinary , Genomics , Genotype , Italy , Models, Genetic , Pedigree , Phenotype
11.
J Dairy Sci ; 104(4): 5079-5094, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33516547

ABSTRACT

Fatty acid (FA) profile is one of the most important aspects of the nutritional properties of milk. The FA content in milk is affected by several factors such as diet, physiology, environment, and genetics. Recently, principal component analysis (PCA) and multivariate factor analysis (MFA) have been used to summarize the complex correlation pattern of the milk FA profile by extracting a reduced number of new variables. In this work, the milk FA profile of a sample of 993 Sarda breed ewes was analyzed with PCA and MFA to compare the ability of these 2 multivariate statistical techniques in investigating the possible existence of latent substructures, and in studying the influence of physiological and environmental effects on the new extracted variables. Individual scores of PCA and MFA were analyzed with a mixed model that included the fixed effects of parity, days in milking, lambing month, number of lambs born, altitude of flock location, and the random effect of flock nested within altitude. Both techniques detected the same number of latent variables (9) explaining 80% of the total variance. In general, PCA structures were difficult to interpret, with only 4 principal components being associated with a clear meaning. Principal component 1 in particular was the easiest to interpret and agreed with the interpretation of the first factor, with both being associated with the FA of mammary origin. On the other hand, MFA was able to identify a clear structure for all the extracted latent variables, confirming the ability of this technique to group FA according to their function or metabolic origin. Key pathways of the milk FA metabolism were identified as mammary gland de novo synthesis, ruminal biohydrogenation, desaturation performed by stearoyl-coenzyme A desaturase enzyme, and rumen microbial activity, confirming previous findings in sheep and in other species. In general, the new extracted variables were mainly affected by physiological factors as days in milk, parity, and lambing month; the number of lambs born had no effect on the new variables, and altitude influenced only one principal component and factor. Both techniques were able to summarize a larger amount of the original variance into a reduced number of variables. Moreover, factor analysis confirmed its ability to identify latent common factors clearly related to FA metabolic pathways.


Subject(s)
Fatty Acids , Milk , Animals , Diet/veterinary , Factor Analysis, Statistical , Female , Lactation , Pregnancy , Sheep , Sheep, Domestic
12.
J Dairy Sci ; 102(4): 3189-3203, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30799105

ABSTRACT

Fatty acid (FA) composition is one of the most important aspects of milk nutritional quality. However, the inclusion of this trait as a breeding goal for dairy species is hampered by the logistics and high costs of phenotype recording. Fourier-transform infrared spectroscopy (FTIR) is a valid and cheap alternative to laboratory gas chromatography (GC) for predicting milk FA composition. Moreover, as for other novel phenotypes, the efficiency of selection for these traits can be enhanced by using genomic data. The objective of this research was to compare traditional versus genomic selection approaches for estimating genetic parameters and breeding values of milk fatty acid composition in dairy sheep using either GC-measured or FTIR-predicted FA as phenotypes. Milk FA profiles were available for a total of 923 Sarda breed ewes. The youngest 100 had their own phenotype masked to mimic selection candidates. Pedigree relationship information and genotypes were available for 923 and 769 ewes, respectively. Three statistical approaches were used: the classical-pedigree-based BLUP, the genomic BLUP that considers the genomic relationship matrix G, and the single-step genomic BLUP (ssGBLUP) where pedigree and genomic relationship matrices are blended into a single H matrix. Heritability estimates using pedigree were lower than ssGBLUP, and very similar between GC and FTIR regarding the statistical approach used. For some FA, mostly associated with animal diet (i.e., C18:2n-6, C18:3n-3), random effect of combination of flock and test date explained a relevant quota of total variance, reducing the heritability estimates accordingly. Genomic approaches (genomic BLUP and ssGBLUP) outperformed the traditional pedigree method both for GC and FTIR FA. Prediction accuracies in the older cohort were larger than the young cohort. Genomic prediction accuracies (obtained using either G or H relationship matrix) in the young cohort of animals, where their own phenotypes were masked, were similar for GC and FTIR. Multiple-trait analysis slightly affected genomic breeding value accuracies. These results suggest that FTIR-predicted milk FA composition could represent a valid option for inclusion in breeding programs.


Subject(s)
Fatty Acids/analysis , Milk/chemistry , Sheep , Animals , Breeding , Female , Genomics , Genotype , Pedigree , Phenotype , Quantitative Trait, Heritable , Spectroscopy, Fourier Transform Infrared
13.
Anim Genet ; 49(5): 371-383, 2018 Oct.
Article in English | MEDLINE | ID: mdl-30070013

ABSTRACT

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo-Bruna and Sardo-Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within-breed genetic heterogeneity. The FST comparison revealing the largest number of significant SNPs was Sardo-Bruna vs. Sardo-Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo-Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo-Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi-dimensional scaling and the admixture analysis the Sardo-Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo-Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.


Subject(s)
Cattle/classification , Cattle/genetics , Genome , Animals , Crosses, Genetic , Gene Flow , Genetic Variation , Heterozygote , Pedigree , Polymorphism, Single Nucleotide
14.
Adv Gerontol ; 29(5): 795-799, 2016.
Article in Russian | MEDLINE | ID: mdl-28556652

ABSTRACT

The aim of the study was to evaluate a new test of speech audiometry while examining aged patients. 32 aged listeners from 60 to 88 years old were examined: 20 hearing aid (HA) users and 12 patients with normal hearing thresholds and mild cognitive impairment according to the results of the mini-mental state examination (MMSE). The speech audiometry consisted of the traditional polysyllabic words discrimination test and a new speech test with motor responses (Verbal Tasks and Motor Responses - VTMR); in both tests the signal was presented in background noise (polyphony) in free field. All listeners performed the VTMR test significantly better than the polysyllabic words discrimination test. In the group of hearing impaired patients the mean result in VTMR test was 73,2±29,2 % without HA and 88,6±20,5 % with it, in traditional test - 34,8±20,9 % without HA and 56±18,4 % with it. All patients of the group with normal hearing and mild cognitive impairment performed the VTMR test with 100 % result, their speech discrimination score in traditional test was 88±12 %. In the practice of the geriatric center the use of both the traditional speech audiometry and the new speech test with motor responses seems to be reasonable, that allows examining the auditory function in patients with significant deterioration of speech intelligibility or cognitive impairment.


Subject(s)
Audiometry, Speech/methods , Cognitive Dysfunction , Hearing Loss , Aged , Cognitive Dysfunction/diagnosis , Cognitive Dysfunction/physiopathology , Female , Geriatric Assessment/methods , Hearing Loss/diagnosis , Hearing Loss/psychology , Humans , Male , Mental Status and Dementia Tests , Middle Aged , Reproducibility of Results , Speech Intelligibility , Speech Perception
15.
Med Hypotheses ; 85(3): 336-8, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26115944

ABSTRACT

Melanoma is an aggressive form of cancer derived from neuroectodermal melanocytes. Melanocytes are present in the skin and hair follicles, as well as in the eye (iris and choroids), the leptomeninges, the anal canal and the inner ear. In the inner ear melanocytes are found both in the intermediate layer of the stria vascularis of the cochlea and in the dark cells of the vestibular organs. They are believed to play an important role in the production of endolymphatic potentials and in the maintenance of normal volumes of the inner ear fluids. Recently, audiovestibular dysfunctions have been demonstrated in patients treated with immunotherapy for metastatic melanoma and have been related to an autoimmune attack on the normal melanocytes of the inner ear. Melanoma is an immunogenic tumor type frequently associated with spontaneous autoimmune manifestations which seem to be associated with better prognosis. The melanoma-associated antigens are also expressed in normal melanocytes in the skin, eye and ear. We hypothesize that inner ear melanocytes could be a target of an autoimmune process in patients affected by melanoma. The immune system could produce antibodies that cross-react with both the melanoma cells and the labyrinth melanocytes causing an altered homeostasis of endolymphatic liquids and provoking some labyrinthic disorders such as vertigo, hearing loss, aural fullness and tinnitus resembling or influencing Ménière's disease. In this perspective, audiovestibular disorders could be interpreted as an attempt by the individual immune system to develop anti-tumor response. In patients affected by melanoma an autoimmune genesis has already been advocated for ocular symptoms in melanoma-associated retinopathy, where the cross-reaction happens against retinal cells. A possible role of inner ear melanocytes should be considered as a potential cause of audiovestibular disorders. Further research is needed to demonstrate a connection between melanoma and labyrinth dysfunctions such as in melanoma-associated retinopathy.


Subject(s)
Melanoma/immunology , Meniere Disease/pathology , Vestibule, Labyrinth/pathology , Humans , Immunotherapy/adverse effects , Melanoma/pathology , Melanoma/therapy
16.
Phlebology ; 28(5): 231-3, 2013 Aug.
Article in English | MEDLINE | ID: mdl-22490722

ABSTRACT

OBJECTIVES: We report a case of bilateral sudden sensorineural hearing loss (SSHL) in a patient suffering from chronic venous cerebrospinal insufficiency (CCSVI). METHODS: Audiometric testing confirmed bilateral sensorineural hearing loss with hypoexcitability to caloric stimulation on the left side and echo-colour Doppler examination showed abnormal cerebral venous deficiency. RESULTS: The patient's condition improved after 15 days following medical treatment. CONCLUSIONS: CCSVI may explain the anatomical background which provides a predisposing factor for SSHL although further studies are needed to verify whether this observation is casual or coincidental.


Subject(s)
Hearing Loss, Sensorineural/diagnosis , Venous Insufficiency/diagnosis , Audiometry , Cerebrovascular Circulation , Female , Hearing Loss, Sensorineural/complications , Humans , Hyperbaric Oxygenation , Middle Aged , Platelet Aggregation Inhibitors/chemistry , Steroids/therapeutic use , Treatment Outcome , Ultrasonography, Doppler , Venous Insufficiency/complications
17.
Acta Otorhinolaryngol Ital ; 32(3): 170-4, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22767982

ABSTRACT

Several studies have previously demonstrated that postural changes modify evoked otoacoustic emission. In order to evaluate a possible interaction between eye muscles and ciliated cells in the inner ear, we studied the effects of eye lateralization on the contralateral suppression of transient evoked otoacoustic emissions (TEOAEs). Thirty-eight normal hearing subjects with TEOAEs were recruited. Their TEAOEs at threshold level were recorded with contralateral suppression (white noise) via straight ahead fixation and right or left lateral fixation. Eye lateralization in the same direction of the white noise significantly decreased the suppression at 4 kHz (p = 0.003). The signal-to-noise ratio in the suppression condition with straight ahead was 1.54 (± 4.610) dB, while the ratio was 3.48 (± 4.631) dB in the suppression condition with gaze toward the white noise. Eye lateralization seems to reduce the contralateral suppression effect of TEOAEs at 4 kHz. However, further studies are necessary to investigate the possible mechanisms of this phenomenon.


Subject(s)
Eye Movements/physiology , Functional Laterality/physiology , Otoacoustic Emissions, Spontaneous/physiology , Adult , Aged , Female , Humans , Male , Middle Aged , Young Adult
18.
J Laryngol Otol ; 124(8): 859-63, 2010 Aug.
Article in English | MEDLINE | ID: mdl-20441674

ABSTRACT

OBJECTIVE: To assess whether different compact disk recording protocols, used to prepare speech test material, affect the reliability and comparability of speech audiometry testing. MATERIAL AND METHODS: We conducted acoustic analysis of compact disks used in clinical practice, to determine whether speech material had been recorded using similar procedures. To assess the impact of different recording procedures on speech test outcomes, normal hearing subjects were tested using differently prepared compact disks, and their psychometric curves compared. RESULTS: Acoustic analysis revealed that speech material had been recorded using different protocols. The major difference was the gain between the levels at which the speech material and the calibration signal had been recorded. Although correct calibration of the audiometer was performed for each compact disk before testing, speech recognition thresholds and maximum intelligibility thresholds differed significantly between compact disks (p < 0.05), and were influenced by the gain between the recording level of the speech material and the calibration signal. CONCLUSION: To ensure the reliability and comparability of speech test outcomes obtained using different compact disks, it is recommended to check for possible differences in the recording gains used to prepare the compact disks, and then to compensate for any differences before testing.


Subject(s)
Acoustics , Audiometry, Speech/instrumentation , Compact Disks/standards , Psychoacoustics , Tape Recording/standards , Adult , Audiometry, Speech/standards , Calibration , Female , Humans , Male , Reference Standards , Reproducibility of Results , Speech Reception Threshold Test/methods , Speech Reception Threshold Test/standards , Young Adult
20.
Am J Med Genet A ; 149A(2): 171-6, 2009 Feb.
Article in English | MEDLINE | ID: mdl-19161135

ABSTRACT

Since the first description of Kabuki syndrome (KS) in 1981, over 350 cases from a variety of countries have been reported. Even though otolaryngological manifestations are common in KS, only a limited number of the reports provide audiological and vestibular data. The aim of the present study was to investigate the vestibular function and describe the audiological findings in KS. The present study reports no audiological and vestibular features in a group of 10 KS patients (7 males, 3 females), with chronological age ranging from 10 to 25 years (mean age = 14.5): a complete otoneurological and audiological work-up was performed for each patient and included where possible, the measurement of vestibular evoked potentials, caloric tests and static posturography. Hearing loss was found in 65% showing a mix or a conductive impairment; moreover the vestibular function was normal in 95% of the examined ears. In conclusion, audiological and vestibular examination should be considered when evaluating KS subjects.


Subject(s)
Abnormalities, Multiple/diagnosis , Adolescent , Adult , Caloric Tests , Child , Evoked Potentials, Auditory , Face/abnormalities , Female , Hearing Loss , Humans , Male , Syndrome , Vestibular Diseases/diagnosis , Vestibular Function Tests , Young Adult
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