Association of apolipoprotein B and adiponectin receptor 1 genes with carcass, bone integrity and performance traits in a paternal broiler Line.

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers

Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle.

Abstract The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regions associated with the hornless trait in a commercial Nelore population. A total of 107,294 animals had phenotypes recorded and 2,238 were genotyped/imputed for 777k SNP. The weighted single-step approach for genome-wide association study (WssGWAS) was used to estimate the SNP effects and variances accounted for by 1 Mb sliding SNP windows. A centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631?3,987,104 bp) was found to be associated with hornless in the studied population. A total of 28 protein-coding genes are mapped in this region, including the taurine Polled locus and the IFNAR1, IFNAR2, IFNGR2, KRTAP11-1, MIS18A, OLIG1, OLIG2, and SOD1 genes, which expression can be related to the horn formation as described in literature. The functional enrichment analysis by DAVID tool revealed cytokine-cytokine receptor interaction, JAK-STAT signaling, natural killer cell mediated cytotoxicity, and osteoclast differentiation pathways as significant (P < 0.05). In addition, a runs of homozygosity (ROH) analysis identified a ROH island in polled animals with 2.47 Mb inside the region identified by WssGWAS. Polledness in Nelore cattle is associated with one region in the genome with 3.1 Mb size in chromosome 1. Several genes are harbored in this region, and they may act together in the determination of the polled/horned phenotype. Fine mapping the locus responsible for polled trait in Nelore breed and the identification of the molecular mechanisms regulating the horn growth deserve further investigation

Detection of potential genetic variants affecting gene function in Guzerat cattle.

Guzerat is a dual-purpose breed recognized for important traits to its adaptation to adverse tropical environments such as resistance to parasites, heat tolerance and ability to intake forage with low nutritional value. Once genetic variation responsible for this traits has so far not been well characterized, the aim of this study was to identity single nucleotide variants (SNVs) and insertion/deletions (Indels) in Guzerat cattle breed from whole genome re-sequencing in order to characterize loss-of-function variants which could be associated with complex traits in this cattle breed.X-meeting 2016

Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data.

Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24?945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75?2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30?kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, ?-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p?<?0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.First online

Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle.

Abstract The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the ad- ditive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient ab- sorption. Enrichment analysis revealed functional pathways (p-value&#57375;<&#57375;.05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/ Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste trans- duction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE- related traits

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits.

Abstract Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15&#8201;±&#8201;13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (&#8722;&#8201;0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (&#8722;&#8201;0.01 to &#8722;&#8201;0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH&#8201;>&#8201;8Mb (&#8722;&#8201;0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n&#8201;=&#8201;62) and their genomic location did not largely differ within lineages. Enriched terms (p&#8201;<&#8201;0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p <&#8201;0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle

A Gene Catalogue of the Euchromatic Male-Specific Region of the Horse Y Chromosome: Comparison with Human and Other Mammals

Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY) contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY gene catalogue was developed for the horse – an odd-toed ungulate. Using direct cDNA selection from horse testis, and sequence analysis of Y-specific BAC clones, 37 horse MSY genes/transcripts were identified. The genes were mapped to the MSY BAC contig map, characterized for copy number, analyzed for transcriptional profiles by RT-PCR, examined for the presence of ORFs, and compared to other mammalian orthologs. We demonstrate that the horse MSY harbors 20 X-degenerate genes with known orthologs in other eutherian species. The remaining 17 genes are acquired or novel and have so far been identified only in the horse or donkey Y chromosomes. Notably, 3 transcripts were found in the heterochromatic part of the Y. We show that despite substantial differences between the sequence, gene content and organization of horse and other mammalian Y chromosomes, the functions of MSY genes are predominantly related to testis and spermatogenesis. Altogether, 10 multicopy genes with testis-specific expression were identified in the horse MSY, and considered likely candidate genes for stallion fertility. The findings establish an important foundation for the study of Y-linked genetic factors governing fertility in stallions, and improve our knowledge about the evolutionary processes that have shaped Y chromosomes in different mammalian lineages