RESUMO
About three decades of breeding and selection in the Valle del Belìce sheep are expected to have left several genomic footprints related to milk production traits. In this study, we have assembled a dataset with 451 individuals of the Valle del Belìce sheep breed: 184 animals that underwent directional selection for milk production and 267 unselected animals, genotyped for 40,660 single-nucleotide polymorphisms (SNPs). Three different statistical approaches, both within (iHS and ROH) and between (Rsb) groups, were used to identify genomic regions potentially under selection. Population structure analyses separated all individuals according to their belonging to the two groups. A total of four genomic regions on two chromosomes were jointly identified by at least two statistical approaches. Several candidate genes for milk production were identified, corroborating the polygenic nature of this trait and which may provide clues to potential new selection targets. We also found candidate genes for growth and reproductive traits. Overall, the identified genes may explain the effect of selection to improve the performances related to milk production traits in the breed. Further studies using high-density array data, would be particularly relevant to refine and validate these results.
Assuntos
Genômica , Herança Multifatorial , Animais , Ovinos/genética , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The objective of this study was to uncover genomic regions explaining a substantial proportion of the genetic variance in milk production traits and somatic cell score in a Valle del Belice dairy sheep. Weighted single-step genome-wide association studies (WssGWAS) were conducted for milk yield (MY), fat yield (FY), fat percentage (FAT%), protein yield (PY), protein percentage (PROT%), and somatic cell score (SCS). In addition, our aim was also to identify candidate genes within genomic regions that explained the highest proportions of genetic variance. Overall, the full pedigree consists of 5534 animals, of which 1813 ewes had milk data (15,008 records), and 481 ewes were genotyped with a 50 K single nucleotide polymorphism (SNP) array. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. We considered the top 10 genomic regions in terms of their explained genomic variants as candidate window regions for each trait. The results showed that top ranked genomic windows (1 Mb windows) explained 3.49, 4.04, 5.37, 4.09, 3.80, and 5.24% of the genetic variances for MY, FY, FAT%, PY, PROT%, and total SCS, respectively. Among the candidate genes found, some known associations were confirmed, while several novel candidate genes were also revealed, including PPARGC1A, LYPLA1, LEP, and MYH9 for MY; CACNA1C, PTPN1, ROBO2, CHRM3, and ERCC6 for FY and FAT%; PCSK5 and ANGPT1 for PY and PROT%; and IL26, IFNG, PEX26, NEGR1, LAP3, and MED28 for SCS. These findings increase our understanding of the genetic architecture of six examined traits and provide guidance for subsequent genetic improvement through genome selection.
RESUMO
The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test-day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock-test-day on milk production traits was also estimated. Significant genomic regions at either genome-wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep.
Assuntos
Lactação , Leite , Carneiro Doméstico/genética , Animais , Feminino , Genômica , Lactação/genética , Fenótipo , Gravidez , Ovinos/genéticaRESUMO
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
Assuntos
Variações do Número de Cópias de DNA , Lactação/genética , Locos de Características Quantitativas , Ovinos/genética , Animais , Mapeamento Cromossômico , Indústria de Laticínios , Feminino , Estudo de Associação Genômica Ampla , GenótipoRESUMO
Early vat bacterial biofilms developed spontaneously through contact with whey have been characterized on seven wood types (Castanea sativa Miller, Cedrus libani, A. Rich., Prunus avium L., Fraxinus ornus L., Juglans regia L., Pinus nigra J.F. Arnold and Populus nigra L.). The present study aimed to evaluate the influence of these biofilms on the microbiological, chemical, physical and sensory characteristics of PDO Vastedda della valle del Belìce (VdB) cheese, processed traditionally from raw ewe's milk using wooden tools. To this purpose, the experimental cheeses after 15â¯d of refrigerated storage were examined. Lactic acid bacteria (LAB) populations dominated the microbial community of all samples. The species more frequently identified were Lactococcus lactis among starter LAB and Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus fermentum and Pediococcus pentosaceus among non starter LAB. Culture-independent analysis of microbiota diversity was performed by MiSeq Illumina that identified Streptococcus as major group followed by members of Enterobacteriaceae family, Lactococcus and Lactobacillus. Generally, the seven tree species did not negatively affect the physicochemical composition of VdB cheeses. Chestnut (both Sicilian and Calabrian) vats produced cheeses with significant lower hue angle (a*/b*) than other wood types. Among chemical parameters, significant variations were registered for aw, primary and secondary lipid oxidation state (significantly lower for the VdB cheeses produced with poplar wood), and volatile organic compounds (VOCs). The significant differences detected among the VOCs emitted from cheeses were not perceived by the panelists who recognized all cheeses from the different trials as similar. This study confirmed the suitability of cedar, cherry, ash, walnut, black pine and poplar as alternative woods to chestnut for the production of the wooden vats employed in cheese making for the Sicilian traditional dairy productions.
Assuntos
Biofilmes , Queijo/microbiologia , Microbiota , Adulto , Animais , Queijo/análise , Fenômenos Químicos , Cor , Ácidos Graxos/análise , Manipulação de Alimentos , Microbiologia de Alimentos , Humanos , Lactobacillales/isolamento & purificação , Limosilactobacillus fermentum/isolamento & purificação , Lacticaseibacillus rhamnosus/isolamento & purificação , Lactococcus/isolamento & purificação , Lactococcus lactis/isolamento & purificação , Metabolismo dos Lipídeos , Pessoa de Meia-Idade , Leite/microbiologia , Pediococcus pentosaceus/isolamento & purificação , Fenótipo , Polifenóis/análise , Análise de Sequência de DNA , Ovinos , Streptococcus/isolamento & purificação , Compostos Orgânicos Voláteis/análise , Adulto JovemRESUMO
BACKGROUND: Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding ([Formula: see text]) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies. RESULTS: We identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of [Formula: see text] estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation. CONCLUSIONS: These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection.
Assuntos
Genética Populacional , Homozigoto , Endogamia , Polimorfismo de Nucleotídeo Único/genética , Ovinos/genética , Animais , Cromossomos/genética , Genótipo , Seleção GenéticaRESUMO
The essential role of the acetyl-CoA carboxylase (ACACA) enzyme in milk fatty acid (FA) synthesis suggests that it may be responsible for the phenotypic variability observed inmilk.Before attempting association analyses between this gene and/or enzyme and phenotypic traits, a study on the genetic variability within this locus is required. The aim of this work was to sequence the entire coding region of ACACA gene in Valle del Belice sheep breed to identify polymorphic sites. A total of 51 coding exons of ACACA gene were sequenced in 32 individuals of Valle del Belice sheep breed. Sequencing analysis and alignment of obtained sequences showed the presence of 23 polymorphic sites. The most polymorphic was exon 53 which showed presence of 12 single-nucleotide polymorphisms (SNPs), ofwhich eightweremissensemutations, caused amino acid changes and therefore may affect protein function or stability causing variation in phenotype. The identified polymorphisms showed high variability of the ACACA gene. Sequences analysis allowed to find six new SNPs in exon 53 (6832C>T; 6835C>A; 6840G>A; 6847G>T; 6852C>T and 6860G>C). A total of 31 haplotypes were inferred. Although this study could not provide association study with production traits, it shows finding of novel SNPs that might be important in future studies and laid the basis for further association analyses needed to evaluate the potential use of these SNPs as genetic markers for fat content and FAs composition in milk of Valle del Belice sheep breed.
Assuntos
Acetil-CoA Carboxilase/genética , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Ovinos/genética , Substituição de Aminoácidos , Animais , Cruzamento , Éxons , Marcadores Genéticos , Haplótipos , Mutação , FenótipoRESUMO
BACKGROUND: Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. RESULTS: The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ± 0.22), and CNS and ALL (0.92 ± 0.04). CONCLUSION: The results of our study support the presence of significant genetic variation for mastitis caused by Streptococci and suggest the importance of discriminating between different pathogens causing mastitis due to the fact that they most likely influence different genetic traits. Low heritabilities for pathogen specific-mastitis resistance may be considered when including bacteriological status as a measure of mastitis presence to implement breeding strategies for improving udder health in dairy ewes.