A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds.

BACKGROUND: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.

The effect of genotype and muscle type on the physico-chemical characteristics and taurine, carnosine and L-carnitine concentration in lamb meat.

An experiment was conducted to determine the chosen bioactive components and physico-chemical characteristics of lamb meat of different animal genotypes and the muscle types. The 22 ram lambs of Polish Merino (PM) and 22 crossbreeds of Polish Merino  × â€¯Berrichone du Cher (PMB) were fattened to achieve their slaughter weight of 40 kg. After slaughter, the carcasses were kept at 4  ∘ C for 24 h. Then, the samples of longissimus lumborum (LL) and gluteus medius (GM) muscle were collected to analyse the physico-chemical traits; fatty acid profile; and concentrations of taurine, carnosine, L-carnitine. The GM muscle compared to LL had the higher value ( P  < 0.05) of L * and a lower value ( P  < 0.05) of b * and H * both in PM and PMB lambs. The value of expressed juice was lower ( P  < 0.05) in both LL and GM muscles of PM lambs. A higher amount ( P  < 0.05) of collagen was found in LL muscle compared to GM both in PM and PMB lambs. The GM muscle of PM lambs showed higher ( P  < 0.05) conjugated linoleic acid (CLA) content, as well as higher total polyunsaturated acids (PUFAs), PUFA n-6, and PUFA n-3 ( P  < 0.05). The GM muscle was characterized by a higher ( P  < 0.05) content of taurine, while in the LL muscle there was a higher amount ( P  < 0.05) of carnosine. A larger amount ( P  < 0.05) of L-carnitine was found in GM muscle but only within PMB lambs. The obtained results showed a greater impact of the lamb's genotype on the physical characteristics of meat than on its chemical composition and the content of bioactive components. The muscle type had an effect on meat colour; collagen content; fatty acid profile; and amount of taurine, carnosine, and L-carnitine present.

The effect of aging and muscle type on the quality characteristics and lipid oxidation of lamb meat.

The research carried out on meat from 45 ram lambs of the Polish merino breed allowed to determine the effect of meat aging and muscle type on physicochemical characteristics and oxidative stability of lipids. Analysis of physicochemical traits (pH, meat color, expressed juice, cooking loss, shear force, moisture, protein, fat and total collagen content) was performed on fresh and meat aged for 14 d in the longissimus lumborum (LL) and gluteus medius (GM) muscles. The meat aging determined all physicochemical characteristics except protein and fat content. More changes in pH and meat color parameters were defined in the GM muscle compared to the LL muscle. The increase in the tenderness of meat expressed as a reduction ( P < 0.05 ) of shear force values was observed in both muscles aged for 14 d. A lower value ( P < 0.05 ) of the shear force, despite the higher content of collagen, was determined in the GM muscle compared to LL. The investigated muscles differed in the degree of lipid peroxidation expressed as thiobarbituric acid-reactive substances (TBARS) in both fresh and aged meat. The TBARS value was lower ( P < 0.05 ) in the LL muscle than in GM. In the longissimus lumborum muscle, the significantly lower content of polyunsaturated fatty acids (PUFAs) and PUFA n-6 has been recorded. The oxidation stability was not influenced by the meat aging.

Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease.

Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.

Design and implementation of microarray gene expression markup language (MAGE-ML).

BACKGROUND: Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies. RESULTS: To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. CONCLUSIONS: MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.