This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F ). The better results of F suggest that F can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

BackgroundRuns of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED).ResultsROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length.ConclusionsGenes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.

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BackgroundFatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique.ResultsDifferential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids. For the respective sums of the individual fatty acids, 51 differentially expressed genes for saturated fatty acids (SFA), 336 for monounsaturated (MUFA), 131 for polyunsaturated (PUFA), 92 for PUFA/SFA ratio, 55 for ω3, 627 for ω6, and 22 for ω6/ω3 ratio were identified. Functional annotation analyses identified several genes associated with fatty acid metabolism, such as those involved in intra and extra-cellular transport of fatty acid synthesis precursors in intramuscular fat of longissimus thoracis muscle. Some of them must be highlighted, such as: ACSM3 and ACSS1 genes, which work as a precursor in fatty acid synthesis; DGAT2 gene that acts in the deposition of saturated fat in the adipose tissue; GPP and LPL genes that support the synthesis of insulin, stimulating both the glucose synthesis and the amino acids entry into the cells; and the BDH1 gene, which is responsible for the synthesis and degradation of ketone bodies used in the synthesis of ATP.ConclusionSeveral genes related to lipid metabolism and fatty acid composition were identified. These findings must contribute to the elucidation of the genetic basis to improve Nellore meat quality traits, with emphasis on human health. Additionally, it can also contribute to improve the knowledge of fatty acid biosynthesis and the selection of animals with better nutritional quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3232-y) contains supplementary material, which is available to authorized users.

BackgroundThe aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories: i) farm phenotypes, assessing body condition score (BCS), degree of anemia assessed by the famacha chart (FAM), fur score (FS) and feces consistency (FC); and ii) lab phenotypes, comprising blood analyses for hematocrit (HCT), white blood cell count (WBC), red blood cell count (RBC), hemoglobin (HGB), platelets (PLT) and transformed (log10) egg per gram of feces (EPGlog). A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.), that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait model by single step genomic BLUP procedure.ResultsThe overall linkage disequilibrium (LD) mean between pairs of markers measured by r 2 was 0.23. The overall LD mean between markers considering windows up to 10 Mb was 0.07. The mean LD between adjacent SNPs across autosomes ranged from 0.02 to 0.10. Heritability estimates were low for EPGlog (0.11), moderate for RBC (0.18), PLT (0.17) HCT (0.20), HGB (0.16) and WBC (0.22), and high for FAM (0.35). A total of 22, 21, 23, 20, 26, 25 and 23 windows for EPGlog for FAM, WBC, RBC, PLT, HCT and HGB traits were identified, respectively. Among the associated windows, 10 were shown to be common to HCT and HGB traits on OAR1, OAR2, OAR3, OAR5, OAR8 and OAR15.ConclusionThe traits indicating gastrointestinal parasites resistance presented an adequate genetic variability to respond to selection in Santa Inês breed, and it is expected a higher genetic gain for FAM trait when compared to the others. The level of LD estimated for markers separated by less than 1 Mb indicated that the Ovine SNP12k BeadChip might be a suitable tool for identifying genomic regions associated with traits related to gastrointestinal parasite resistance. Several candidate genes related to immune system development and activation, inflammatory response, regulation of lymphocytes and leukocytes proliferation were found. These genes may help in the selection of animals with higher resistance to parasites.Electronic supplementary materialThe online version of this article (doi:10.1186/s40104-017-0190-4) contains supplementary material, which is available to authorized users.