The aim of this research was to characterize the genetic diversity of the Sarda (Sa, n = 131), Sardo Bruna (SB, n = 44) and Sardo Modicana (SM, n = 26) cattle breeds, reared in the island of Sardinia ...(Italy). A portion of the mitochondrial DNA hypervariable region was sequenced, in order to identify a potential signature of African introgression. The F
coefficients among populations ranged between 0.056 for Sa vs SB and 0.167 for SB vs SM. AMOVA analysis indicated there was a significant differentiation of the three breeds, although most of diversity was gathered at the within-breed level. The Median Joining Network of the Sardinian sequences showed a potential founder effect signature. A MJ network including Sardinian cattle plus African, Italian, Iberian and Asian sequences, revealed the presence of haplogroup T3, already detected in Sa cattle, and the presence of Hg T1 and Hg T1'2'3, in Sa and SB. The presence of a private haplotype belonging to haplogroup T1, which is characteristic of African taurine breeds, may be due to the introgression of Sardinian breeds with African cattle, either directly (most probable source: North African cattle) or indirectly (through a Mediterranean intermediary already introgressed with African blood).
The Anglo-Arabian horse breed (AA) is the result of crossing between Thoroughbred and Arabian horses renowned for versatility in show-jumping and racing. Southwest France and Sardinia in Italy are ...considered the historical nucleus of European AA breeding. Since little is known on genetic variability in the AA breed, especially those bred in the Sardinia region, this study investigates: i) inbreeding levels via pedigree and SNP genotyping; ii) runs of homozygosity (ROH) and selection signatures; iii) effective population size; and iv) distinctiveness of AA compared to Arabian and Thoroughbred horses. The ROH revealed an excessive amount of homozygosity, with a high kurtosis value observed in several chromosomes and an average inbreeding based on ROH of 21.1%. This latter value is higher compared to what was found based on pedigree data, highlighting the importance of complete pedigree records when estimating inbreeding based on genealogical data. The genomic inbreeding in AA horses was higher compared to other Italian horse breeds but lower than what was found in pure Thoroughbred and Arabian horses. This result suggests that the selection process for AA horses, may have prioritised racing ability over breed preservation which is the main goal in most local Italian breeds. The reduction in effective population size found in the latest 20 generations corroborates the potential presence of genetic diversity reduction due to selection in the AA breed. Remarkably, a large ROH island was identified on ECA17, which overlapped with two QTLs associated with racing performance.
This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and ...milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes
,
,
and
. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between
and
genes, in addition to two LD blocks within the
and two LD blocks within the
gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and
showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype.
Many studies focus on the identification of genomic regions that undergo selective processes, where evidence of selection is revealed and positional candidate genes are identified. The aim of the ...research was to evaluate the association between positional candidate genes, namely secreted phosphoprotein 1 (
, sheep chromosome
OAR6, 36.651-36.658 Mb), protein O-fucosyltransferase 1 (
, OAR13, 61.006-61.027 Mb) and prolactin receptor (
, OAR16, 38.969-39.028 Mb) with milk yield, composition and coagulation traits. Eight single nucleotide polymorphisms (SNPs) mapping to the three genes were genotyped in 380 Sarda dairy sheep. Statistical analysis revealed an association between SNP rs161844011 at
(chromosome position Oar_v3 OAR6:36651870, gene region exon 7) and somatic cell score, while
SNP rs424501869 (OAR13:61007495, intron 1) was associated with curd firmness both 45 and 60 min after rennet addition (
= 0.015 and
= 0.007, respectively). SNP rs400874750 at
gene (OAR16:39004070, intron 2) had a significant association with lactose content (
= 0.020), somatic cell score (
= 0.038), rennet coagulation time (
= 0.018) and curd firming time (
= 0.047). The outcome of this research confirmed predictions based on genomic studies, producing new information regarding the
,
and
genes, which may be useful for future breeding schemes.
The aim of the present research was to analyze the variability of 45 SNPs from different genes involved in metabolism and innate immunity to perform an association analysis with the milk yield, ...composition and milk coagulation traits. A population of 1112 Sarda breed sheep was sampled. Genotyping was generated by a TaqMan Open ArrayTM. Thirty out of the 45 SNPs were polymorphic, and 12 displayed a minor allele frequency higher than 0.05. An association analysis showed that the variability at genes PRKAG3 and CD14 was significantly associated with the daily milk yield. The variability at PRKAG3 was also associated with the protein and casein content, somatic cell score and bacterial score. The variation at the PRKAA2 gene was associated with the milk lactose concentration. The SNPs at CD14 were also associated with the traditional milk coagulation properties, while the SNPs at GHR and GHRHR were associated with kSR, a derived coagulation parameter related to the rate of syneresis. The information provided here is new and increases our knowledge of genotype–phenotype interactions in sheep. Our findings might be useful in appropriate breeding schemes to be set up for the Sarda sheep breed, but these should be confirmed by further studies, possibly performed on independent populations.
One hundred and eighty Anglo-Arabian horses running 1239 races were sampled for the present study. DNA was extracted from the blood and myostatin gene,
, was genotyped. Moreover, prizes won and ...places were achieved for the 1239 races to perform association analyses between the different genotypes and sport traits. Two SNPs already reported in previous studies regarding the Thoroughbred breed, rs69472472 and rs397152648, were revealed as polymorphic. The linkage disequilibrium analysis investigating the haplotype structure of
did not evidence any association block. Polymorphism at SNP rs397152648, previously known as g.66493737 T>C, significantly influenced sport traits, with heterozygous horses TC showing better results than homozygotes TT. The portion of variance due to the random effect of the individual animal, and the other phenotypic effects of sex, percentage of Arabian blood and race distance, computed together with the genotype at
in the statistical models, exerted a significant influence. Hence, this information is useful to improve knowledge of the genetic profile of Anglo-Arabian horses and a possible selection for better sport performance.
The Sardo-Modicana is a local cattle breed from Sardinia, Italy. No information about its dairy potential is available in the literature. This study investigated the genotype at the CSN3 gene and ...milk traits of the Sardo-Modicana cattle breed. Fifty-four cows were sampled for DNA extraction and genotyping at the κ-casein gene locus, CSN3. Forty individual milk samples were analyzed for milk composition, milk coagulation properties and cheese yield (CY%). All the Sardo-Modicana cows were BB homozygotes at CSN3. Hence, the results were compared with the other two local Sardinian breeds. Eighty-three Sarda and 21 Sardo-Bruna cows were genotyped, and the A allele was found (at frequencies of 0.416 and 0.405, respectively). As regards milk traits, the mean protein value was 3.74 g/100 mL, and the mean casein value was 2.98 g/100 mL. Total bacterial and somatic cell counts showed excellent levels of hygiene considering the extensive farming and hand milking. In addition, milk produced by Sardo-Modicana cows was characterized by favorable values of coagulation properties and cheese yield. This information may represent a starting point for the conservation and enhancement of this breed.
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA ...markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The F
values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
•In the European Union no limits have been fixed for somatic cell count in sheep milk.•The effect of somatic cells count on milk traits and coagulation properties was investigated.•Samples with ...somatic cells higher than 545,000/mL showed worst milk coagulation properties.•This value could be used as a theoretical reference for improving quality of sheep dairy products.
Milk traits and coagulation properties (MCP) were investigated in a population of 960 Sarda ewes distributed in 21 farms, in order to propose a limit of somatic cells (SCC) by using the statistical analysis of milk traits and MCP from a large population of ewes. At each farm, from 20 to 80 ewes were individually sampled (one sampling day for each farm), during the afternoon milking. Ewes were between two and seven months after parturition, and the first and seventh parity. Daily milk yield was recorded on the same day of sampling. Milk samples were analyzed to achieve traits of milk composition (fat, protein, casein, lactose, and pH), total bacterial count (TBC), SCC, traditional MCP (rennet coagulation time: RCT; curd-firming time: k20; curd firmness after 30, 45 or 60 min from rennet addition: respectively a30, a45 and a60) and model parameters of curd-firming (curd firmness at an infinite time: CFP; curd firming instant rate constant: kCF; RCT estimated from the equation: RCTeq; syneresis instant rate constant: kSR; maximum curd firmness: CFmax; and attainment time of the maximum curd firmness: tmax). TBC and SCC were log transformed in their respective scores LBC and SCS. The Pearson product moment correlation coefficient was used to investigate the supposed linear relationship between LBC and SCS and a regression analysis to obtain the plots, model and the values of SCS predicted by using LBC. Results evidenced a positive correlation between SCS and LBC. Despite the very low R2 from the regression analysis, two putative cut-off limit of SCC were calculated: 180,000 SCC/mL, corresponding to 500,000 TBC/mL, and 545,000 SCC/mL, corresponding to 1,500,000 TBC/mL. Later, three groups of SCC-related milk samples were obtained: Low-SCC group (L-SCC), with samples showing a SCC lower than the estimated limit of 180,000/mL; High-SCC group (H-SCC), samples with SCC higher than 545,000/mL; Intermediate-SCC group (I-SCC), samples showing a SCC between the two limits of L-SCC and H-SCC. The L-SCC group showed the highest daily milk yield and lactose content, and the lowest values of fat, protein and casein content and pH. H-SCC group showed delayed coagulation times (both RCT and RCTeq), k20, tmax and kCF. In conclusion, milk yield and coagulation properties registered significant worsening in those milk samples with SCC higher than 545,000 SCC/mL. This value could be the starting point for the improvement of milk traits and coagulation properties from the Sarda sheep.
The prediction of traditional goat milk coagulation properties (MCP) and curd firmness over time (CFt) parameters via Fourier-transform infrared (FTIR) spectroscopy can be of significant economic ...interest to the dairy industry and can contribute to the breeding objectives for the genetic improvement of dairy goat breeds. Therefore, the aims of this study were to (1) explore the variability of milk FTIR spectra from 4 goat breeds (Camosciata delle Alpi, Murciano-Granadina, Maltese, and Sarda), and to assess the possible discriminant power of milk FTIR spectra among breeds, (2) assess the viability to predict coagulation traits by using milk FTIR spectra, and (3) quantify the effect of the breed on the prediction accuracy of MCP and CFt parameters. In total, 611 individual goat milk samples were used. Analysis of variance of measured MCP and CFt parameters was carried out using a mixed model including the farm and pendulum as random factors, and breed, parity, and days in milk as fixed factors. Milk spectra for each goat were collected over the spectral range from wavenumber 5,011 to 925 × cm−1. Discriminant analysis of principal components was used to assess the ability of FTIR spectra to identify breed of origin. A Bayesian model was used to calibrate equations for each coagulation trait. The accuracy of the model and the prediction equation was assessed by cross-validation (CRV; 80% training and 20% testing set) and stratified CRV (SCV; 3 breeds in the training set, one breed in the testing set) procedures. Prediction accuracy was assessed by using coefficient of determination of validation (R2VAL), the root mean square error of validation (RMSEVAL), and the ratio performance deviation. Moreover, measured and FTIR predicted traits were compared in the SCV procedure by assessing their least squares means for the breed effect, Pearson correlations, and variance heteroscedasticity. Results showed the feasibility of using FTIR spectra and multivariate analyses to correctly assign milk samples to their breeds of origin. The R2VAL values obtained with the CRV procedure were moderate to high for the majority of coagulation traits, with RMSEVAL and ratio performance deviation values increasing as the coagulation process progresses from rennet addition. Prediction accuracy obtained with the SCV were strongly influenced by the breed, presenting general low values restricting a practical application. In addition, the low Pearson correlation coefficients of Sarda breed for all the traits analyzed, and the heteroscedastic variances of Camosciata delle Alpi, Murciano-Granadina, and Maltese breeds, further indicated that it is fundamental to consider the differences existing among breeds for the prediction of milk coagulation traits.
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