BackgroundCitrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.ResultsWe have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein.ConclusionWe have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?

BackgroundNelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.ResultsOur results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches.ConclusionsThe diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2535-3) contains supplementary material, which is available to authorized users.

Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material.

Gene expression profiling of in vivo- and in vitro-matured bovine oocytes can identify transcripts related to the developmental potential of oocytes. Nonetheless, the effects of in vitro culturing oocytes are yet to be fully understood. We tested the effects of in vitro maturation on the transcript profile of oocytes collected from Bos taurus indicus cows. We quantified the expression of 1488 genes in in vivo- and in vitro-matured oocytes. Of these, 51 genes were up-regulated, whereas 56 were down-regulated (≥2-fold) in in vivo-matured oocytes in comparison with in vitro-matured oocytes. Quantitative real-time polymerase chain reaction (PCR) of nine genes confirmed the microarray results of differential expression between in vivo- and in vitro-matured oocytes (EZR, EPN1, PSEN2, FST, IGFBP3, RBBP4, STAT3, FDPS and IRS1). We interrogated the results for enrichment of Gene Ontology categories and overlap with protein-protein interactions. The results revealed that the genes altered by in vitro maturation are mostly related to the regulation of oocyte metabolism. Additionally, analysis of protein-protein interactions uncovered two regulatory networks affected by the in vitro culture system. We propose that the differentially expressed genes are candidates for biomarkers of oocyte competence. In vitro oocyte maturation can affect the abundance of specific transcripts and are likely to deplete the developmental competence.

SUMMARYHeat stress (HS) is among the major limiting factors to growth of broilers. Heat stress also results in changes in the characteristics of the carcass, such as an increase in fat deposition. The molecular mechanisms responsible for fat deposition in broilers as a response to HS remain unknown. The current study aimed to describe the molecular mechanisms associated with the effects of high temperature and feed restriction due to chronic heat exposure at 32 °C, and to describe the resulting changes in the growth performance and carcass characteristics of the broilers at 21 and 42 days of age. In the current study, 441 male Cobb-500® broilers were subjected to three treatments that differed in rearing temperature and feeding regime: chronic HS fed ad libitum (HS/AL), thermoneutral environment fed ad libitum (TN/AL) and TN and pair-feeding on the feed intake (FI) of the heat-exposed group (TN/PF). HS increased fat content in the breast and wings and decreased fat content in the legs, but did not influence abdominal fat. These effects occurred regardless of reducing consumption induced by HS. Furthermore, HS, independently of reduced FI, increased liver sterol-regulatory element-binding protein-1 (SREBP-1) mRNA in both ages and growth hormone receptor (GHR) mRNA at 42days, whereas feed restriction reduced GHR mRNA only at 21days. In conclusion, increased fat content in the breast and wings was accompanied by a higher gene expression of GHR and SREBP-1, suggesting the involvement of both genes in the control of fat deposition in broilers exposed to HS.

The growth hormone 1 gene (GH1) is a candidate gene for body weight and weight gain in cattle since it plays a fundamental role in growth regulation. We investigated the GH1 gene AluI and DdeI restriction enzyme polymorphisms, located 149 bp apart in the cattle genome, as possible markers of the production potential of Canchim crossbreed cattle, a 5/8 Charolais (Bos taurus) and 3/8 Nelore (Bos indicus) breed developed in Brazil, by evaluating the birth weight, weaning weight, yearling weight and plasma insulin-like growth factor-1 (IGF-1) concentration of 7 month to 10 months old Canchim calves (n = 204) of known genealogy and which had been genotyped for the AluI and DdeI markers. Our results showed significant effect (p < 0.05) between the homozygous DdeI+/DdeI+ polymorphism and the estimated breeding value for weaning weight (ESB-WW), while the AluI leucine homozygous (L/L) and leucine/valine (L/V) heterozygous polymorphisms showed no significant effect on the traits studied. The restriction sites of the two enzymes led to the formation of haplotypes which also exerted a significant effect (p < 0.05) on the ESB-WW, with the largest difference being 8.5 kg in favor of the homozygous L plus DdeI+/L plus DdeI+ genotype over the heterozygous L plus DdeI-/V plus DdeI+ genotype.

This study assesses the respiratory dynamics related to stress parameters and resting time before slaughter, in the quality of surubim (Pseudopatystoma spp.) fillets. A completely randomized design was conducted using five treatments: resting time before slaughter of 0, 2, 4, 8 and 24 hours, with 15 fish sampled per treatment. Time 0 corresponded to the treatment without resting time, where the fish were slaughtered immediately after arriving at the processing plant. The resting time did not affect the electrolyte balance, hemoglobin, plasma, hepatic glycogen, myofibrillar fragmentation index (MFI) and water holding capacity (WHC) of surubins. However, with increased resting time, there was a significant decrease in muscle glycogen and an increase in blood pH and blood bicarbonate levels. Additionally, respiratory parameters showed an increase in pO 2 and, consequently, in O 2 saturation and a decrease in pCO 2 .The hematocrit and MCV values of the surubins after 24 hours of resting decreased significantly. In the first hours of resting, the highest values of erythrocytes and CHCM were observed. The lowest level of stress was observed for fish having 24 hours of resting. Fish having longer resting periods (8 and 24 hours) presented fillets with a higher pH (P <0.05) and the rigor mortis establishment time was shorter for the first 2 hours and 24 hours of resting time. There was a linear decrease in fillet lightness and an increase in the intensity of red (CIE a*) color up to 24 hours when resting was increased. In CIE b*, a linear decrease (P <0.05) of the yellow intensity of the fillets was observed as the surubim resting time increased. A resting time of 4 to 8 hours before slaughter is effective in reestablishing homeostasis after transporting surubim, providing fillets with higher quality and a greater length of the pre-rigor mortis period.