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.

Background: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH 5000 ) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here,

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.

Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.

Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.

The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.

BackgroundBeef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals.ResultsAssociated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction.ConclusionsFew associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.Electronic supplementary materialThe online version of this article (doi:10.1186/s40104-017-0199-8) contains supplementary material, which is available to authorized users.

ABSTRACT. The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferroni's correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP GWAS for milk production traits in buffalo markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.