Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile

The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.

A network-based approach to understanding gene-biological processes affecting economically important traits of Nelore cattle

This study aimed to build gene-biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene-biological process network analysis was performed with the differentially expressed genes in common. For production traits, 37 genes were found in common, of which 13 genes were enriched for six Gene Ontology (GO) terms; these terms were not functionally grouped. However, the enriched GO terms were related to homeostasis, the development of muscles and the immune system. For carcass traits, four genes were found in common. Thus, it was not possible to functionally group these genes into a network. For meat quality traits, the analysis revealed 222 genes in common. CSRP3 was the only gene differentially expressed in all three groups. Non-redundant biological terms for clusters of genes were functionally grouped networks, reflecting the cross-talk between all biological processes and genes involved. Many biological processes and pathways related to muscles, the immune system and lipid metabolism were enriched, such as striated muscle cell development and triglyceride metabolic processes. This study provides insights into the genetic mechanisms of production, carcass and meat quality traits of Nelore cattle. This information is fundamental for a better understanding of the complex traits and could help in planning strategies for the production and selection systems of Nelore cattle.

Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle

The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.

Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle

This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.

Candida species contamination in drinking groundwater from residence wells in three municipalities of midwestern Brazil and the potential human health risks

Groundwater represents one of the largest safe drinking water sources worldwide; however, it has been threatened by increased human activities in recent years. Candida species express virulence factors that contribute to the establishment and worsening of infections, although little is known about the virulence profiles of these species in potable groundwater. The aim of this study was to detect the presence of yeasts in groundwater from residential wells and to evaluate the antifungal susceptibility profile, hydrolytic enzyme production, adhesion capacity, and biofilm formation of Candida spp. Fifty yeasts representing nine genera were isolated: Candida (48%), Meyerozyma (20%), Pichia (8%), Exophiala (8%), Clavispora (4%), Kodamaea (4%), Rhodotorula (4%), Hanseniaspora (2%), and Kazachstania (2%). Candida parapsilosis was the most commonly isolated species, and approximately 29% of the Candida isolates were resistant to at least one azole. All Candida isolates were able to produce hydrolytic enzymes and adhere to polystyrene, and most were classified as hydrophobic. Candida spp. can establish and form biofilms when cultivated in different media such as Sabouraud broth, water, and calcium hypochlorite. The use of contaminated groundwater for human consumption represents a possible route for the transmission of clinically relevant yeasts that can cause fungal infections, especially in immunocompromised individuals. Therefore, it is important to evaluate and establish effective measures for groundwater treatment to ensure the quality and safety for consumption.

Genes and proteins associated with ribeye area and meat tenderness in a commercial Nellore cattle population

Despite several studies on genetic markers and differently expressed genes related to ribeye area (REA) and tenderness traits in beef cattle, there is divergence in the results regarding the genes associated with these traits. Thirteen genes that had been associated or have biological functions that may influence such phenotypes were included in this study. A total of five genes for REA (IGF-1, IGF-2, MSTN, NEDD4, and UBE4A) and eight genes for meat tenderness (CAPN1, CAPN2, CAST, HSPB1, DNAJA1, FABP4, SCD, and PRKAG3) were selected from previously studies in beef cattle. Genes and its respective proteins expression were validated in a commercial population of Nellore cattle using quantitative real-time PCR (RT-qPCR) and advanced mass spectrometry (LC / MS-MS) techniques, respectively. MSTN gene was upregulated in animals with low REA. CAPN1, CAPN2, CAST, HSPB1, and DNAJA1 genes were upregulated in animals with tougher meat. The proteins translated by these genes were not differentially expressed. Our results could confirm the potential of some studied genes as biomarkers for carcass and meat quality in Nellore cattle.

24 Structural variants affecting mRNAs isoforms splice sites associated with marbling in Nellore cattle

The mRNA identification and associated splice variants affecting meat marbling in Nellore cattle could contribute to a better understanding of the genetic architecture of this complex trait. Longissimus thoracis samples from the 20 most extreme bulls (out of 80 bulls set) for marbling [high (n=10) and low (n=10) groups] trait were used to perform transcriptomic analysis using RNA-Sequencing. The CLC Genomics Workbench software was used to align the fragments of each sample to the bovine reference genome (ARS-UCD1.2) and to perform differential expressed transcript analysis (DE). An average of 37,000 transcripts and 14 mRNA DE (P ≤ 0.001; FC &gt; 2) were detected in the muscle transcriptome. Among them, three transcripts were up-regulated (COL4A2-202, GHRH-201 and ENSBTAT00000070459.1) and 11 down-regulated (HBB-201, HBA-201, RPL14-202, CATHL1-201, CATHL4-201, MAPKAPK2-204, PCBD1-201, RPL30-203, NEURL1-202, PGLYRP1-201 and ENSBTAT00000038384.2) in high marbling group in relation to low group. Structural variants, including Single Nucleotide Variant (SNV), insertion or deletion were also found in the mRNA DE (4 in high and 6 in low marbling groups), causing possible splice site disruption. For high marbling group, in the COL4A2-202 transcript, three SNVs [one guanine (G) located on chromosome 12 at 85,104,867 bp, two cytosine (C), at the positions: 85,119,139 and 85,145,937 bp] were found. From these, one is a non-synonyms mutation [SNV (G) 85,145,937bp], causing an amino acid change (ENSBTAP00000005916.5: p.Glu1088Asp) in Collagen alpha-2(IV) chain protein (COL4A2). Interestingly, animals with low marbling presented also deletions (85,100,930 pb) in this same gene, causing an amino acid change (ENSBTAP00000005916.5:p.Pro113fs)in the COL4A2 protein. Functional enrichment analysis, using the DE mRNAs list, identified significant metabolic pathways (FDR &lt; 0.05), such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis and phenylalanine degradation. The results suggest potential key regulatory genes associated with marbling, an economically important trait for the beef industry and for the consumer.

Funding FAPESP (#2009/16118-5, #11/21241-0, #2017/02470-3, #2017/10630–2, #2018/ 20026–8, #2018/11154-2) and CAPES (#001).

Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle

The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies used to measure beef tenderness. Longissimus thoracis samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF (tender (n = 10) and tough (n = 10)) and MFI (high (n = 10) and low (n = 10)) traits were collected to perform transcriptomic analysis using RNA-Sequencing. All analysis were performed through CLC Genomics Workbench. A total of 39 and 27 transcripts for WBSF and MFI phenotypes were DE, respectively. The possible DE novel mRNA isoforms, for WBSF and MFI traits, are myosin encoders (e.g. MYL1 and MYL6). In addition, we identified potential mRNA isoforms related to genes affecting the speed fibers degradation during the meat aging process. The DE novel transcripts are transcripted by genes with biological functions related to oxidative process, energy production and striated muscle contraction. The results suggest that the identified mRNA isoforms could be used as potential candidate to select animals in order to improve meat tenderness.

Transcriptome profiling of muscle in Nelore cattle phenotypically divergent for the ribeye muscle area

This study aimed to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle of uncastrated Nelore males phenotypically divergent for ribeye muscle area (REA). A total of 80 animals were phenotyped for REA, and 15 animals each with the highest REA and the lowest REA were selected for analyses. DEGs found (N = 288) belonging to families related to muscle cell growth, development, motility and proteolysis, such as actin, myosin, collagen, integrin, solute carrier, ubiquitin and kelch-like. Functional analysis showed that many of the significantly enriched gene ontology terms were closely associated with muscle development, growth, and degradation. Through co-expression network analysis, we predicted three hub genes (PPP3R1, FAM129B and UBE2G1), these genes are involved in muscle growth, proteolysis and immune system. The genes expression levels and its biological process found this study may result in differences in muscle deposition, and therefore, Nelore animals with different REA proportions.

Prediction of meat quality traits in Nelore cattle by near-infrared reflectance spectroscopy

The main definition for meat quality should include factors that affect consumer appreciation of the product. Physical laboratory analyses are necessary to identify factors that affect meat quality and specific equipment is used for this purpose, which is expensive and destructive, and the analyses are usually time consuming. An alternative method to performing several beef analyses is near-infrared reflectance spectroscopy (NIRS), which permits to reduce costs and to obtain faster, simpler, and nondestructive measurements. The objective of this study was to evaluate the feasibility of NIRS to predict shear force [Warner-Bratzler shear force (WBSF)], marbling, and color (*a = redness; b* = yellowness; and L* = lightness) in meat samples of uncastrated male Nelore cattle, that were approximately 2-yr-old. Samples of longissimus thoracis (n = 644) were collected and spectra were obtained prior to meat quality analysis. Multivariate calibration was performed by partial least squares regression. Several preprocessing techniques were evaluated alone and in combination: raw data, reduction of spectral range, multiplicative scatter correction, and 1st derivative. Accuracies of the calibration models were evaluated using the root mean square error of calibration (RMSEC), root mean square error of prediction (RMSEP), coefficient of determination in the calibration (R2C), and prediction (R2P) groups. Among the different preprocessing techniques, the reduction of spectral range provided the best prediction accuracy for all traits. The NIRS showed a better performance to predict WBSF (RMSEP = 1.42 kg, R2P = 0.40) and b* color (RMSEP = 1.21, R2P = 0.44), while its ability to accurately predict L* (RMSEP = 1.98, R2P = 0.16) and a* (RMSEP = 1.42, R2P = 0.17) was limited. NIRS was unsuitable to predict subjective meat quality traits such as marbling in Nelore cattle.

Differences in global gene expression in muscle tissue of Nellore cattle with divergent meat tenderness

Background

Meat tenderness is the consumer’s most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the high percentage of Zebu genes in the Brazilian cattle population, mainly Nellore cattle, the improvement of meat tenderness is important since the increasing proportion of Zebu genes in the population reduces meat tenderness. However, the measurement of this trait is difficult once it can only be made after animal slaughtering. New technologies such as RNA-Seq have been used to increase our understanding of the genetic processes regulating quantitative traits phenotypes. The objective of this study was to identify differentially expressed genes related to meat tenderness, in Nellore cattle in order to elucidate the genetic factors associated with meat quality. Samples were collected 24 h postmortem and the meat was not aged.

Results

We found 40 differentially expressed genes related to meat tenderness, 17 with known functions. Fourteen genes were up-regulated and 3 were down-regulated in the tender meat group. Genes related to ubiquitin metabolism, transport of molecules such as calcium and oxygen, acid-base balance, collagen production, actin, myosin, and fat were identified. The PCP4L1 (Purkinje cell protein 4 like 1) and BoLA-DQB (major histocompatibility complex, class II, DQ beta) genes were validated by qRT-PCR. The results showed relative expression values similar to those obtained by RNA-Seq, with the same direction of expression (i.e., the two techniques revealed higher expression of PCP4L1 in tender meat samples and of BoLA-DQB in tough meat samples).

Conclusions

This study revealed the differential expression of genes and functions in Nellore cattle muscle tissue, which may contain potential biomarkers involved in meat tenderness.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4323-0) contains supplementary material, which is available to authorized users.

Molecular evidence of Borrelia burgdorferi sensu lato in patients in Brazilian central-western region

We aimed to detect DNA of Borrelia burgdorferi in whole blood and serum samples of patients with clinical symptoms and epidemiology compatible with Brazilian Lyme-like disease. Four patients with positive epidemiological histories were recruited for the study. Blood samples were collected, screened by serologic testing by ELISA and Western blotting and molecular identification of B. burgdorferi by amplifying a fragment of the conserved gene that synthesizes the hook flagellar flgE. The results showed positive serology and for the first time, the presence of B. burgdorferi sensu lato in humans in the Midwest region of Brazil. The resulting sequences were similar to GenBank corresponding sequences of B. burgdorferi flgE gene. By neighbor-joining the phylogenetic analysis, the flgE sequence of the Brazilian strain clustered in a monophyletic group with the sequence of B. burgdorferi sensu lato under 100% bootstrap support. This study opens up promising perspectives and reinforces the need for additional studies to determine the epidemiological characteristics of the disease, as well as the impact of the prevalence of Brazilian borreliosis in Mato Grosso do Sul State, Brazil.