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Background Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. Results We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. Conclusions Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.

The aim of this trial was to compare some meat physical quality traits and the expression of some tenderness-related genes between Goudali (G, Bos indicus) breed and Italian Simmental × Goudali (SimGoud, SG, Bos taurus x Bos indicus) crossbreed. Ten G and 12 SG bulls, aged 31 ± 0.49 months, bred in the same farm and conditions in Western Highland Plateau Savannah of Cameroon were considered. Physical quality traits of longissimus thoracis (LT) muscle such as water losses, colour parameters and rheological properties were determined together with ultimate pH (pHu). The mRNA early post-mortem abundance of calpain-1 (Capn1), calpain-2 (Capn2), calpastatin (Cast), caspase 3 (Casp3), caspase 9 (Casp9), αB-crystallin (Cryab), heat shock proteins 27 (Hsp27), 40 (Hsp40) and 70 (Hsp70) was detected by qPCR. The Capn1, Cast, Hsp27 and Hsp70, early post-mortem protein content was determined by ELISA. The meat of G bulls had greater values of lightness (p < .05) and cooking loss (p < .05) than SG. The expression of Hsp70 in G was greater at mRNA (p < .05) level than SG. None of the other variables considered was significantly different between G and SG breeds. Whereas crossbreeding with Italian Simmental breed changed the colour and ameliorated the water retention capacity of G meat, tenderness and the expression of tenderness-related genes, both at mRNA and at protein level, were not significantly different between the pure local breed and the crossbreed. In comparison with pure Goudali, crossbreeding Goudali with Italian Simmental breed has a limited impact on meat traits in tropical conditions.

Background Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers’ profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle ( Bos taurus indicus ); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated. Results A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF. Conclusions A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

In this study, 105 bacterial colonies were isolated from the feces of newborn healthy Bos indicus calves and 37 isolates were confirmed using morphological, biochemical tests, and genus-specific PCR as lactobacilli. 11 isolates were then short-listed for in vitro probiotic testing based on their ability to dwell under acid and bile stress. Species-level identification using 16S rRNA gene sequencing revealed that they were Ligilactobacillus salivarius. These isolates flourished in 0.4% phenol, depicting resistance in adverse conditions encountered in the gastrointestinal tract. The results of cell surface hydrophobicity were found to be 74.50% for RBL12 and 62.62% for RBL09 in hexadecane and xylene, respectively, and that of auto-aggregation was highest in RBL26 (58.92%). These isolates also produced digestive enzymes like amylase, protease, and β-galactosidase. Further assays reiterated their antimicrobial and coaggregation potential against diarrhea-causing pathogens like Escherichia coli ATCC-25922 and Salmonella arizonae ATCC-13314. Biosafety assessment revealed that none of the tested isolates were hemolytic and mucinolytic in nature. Furthermore, the antioxidant potential of the isolates was also confirmed using 1,1‑diphenyl‑2‑picrylhydrazyl (DPPH) and ferric ion-reducing antioxidant power (FRAP) assay. Along with efficient utilization of inulin, isolates showed promising adhesion ability to the HT-29 cell line. The current findings hence conclude that these Lactobacillus isolates can be exploited as animal probiotics for potential application in young calves to foster gut health and immunity.

This study was conducted in Badri cattle using a double digest restriction-site associated DNA sequencing approach. The study aimed to identify and annotate high confidence single nucleotide polymorphisms (SNPs) and their mapping in candidate genes related to production and fertility in dairy cattle. A total of 7,168,552 genome-wide SNPs were initially identified in Badri cattle by alignment with the Bos indicus reference genome. After filtration of SNPs, 65,483 high confidence SNPs were retained and further used for downstream analysis. Annotation of high confidence SNPs revealed 99.197% SNPs had modifier impact, 0.326% SNPs were low impact, 0.036% were high impact, and 0.441% were moderate impact SNPs. Most SNPs in Badri cattle were found in intergenic, transcript and intronic regions. The candidate genes for milk production PRKCE, ABCG2, GHR, EPS8, CAST and NRXN1 were found to harbour maximum high confidence variants. Among candidate genes for fertility in cattle, ATP2B1, SOX5, WDR27, ARHGAP12, CACNA1D, ANKRD6, GRIA3, ZNF521 and CAST822 have maximum high confidence variants mapped in them. The SNPs found mapped in the candidate genes will be important genetic tools in the search for phenotype-modifying nucleotide changes and will aid in formulating relevant genetic improvement programmes for dairy cattle.

Abstract We hypothesized that the inclusion of calcium salts of fatty acid (CSFA) into the diets and the fatty acid (FA) profile of the supplements would impact performance and meat characteristics of Bos indicus bulls. Hence, the objective was to evaluate the effects of CSFA profiles on intake, body weight (BW), carcass, and meat characteristics of feedlot-finished B indicus bulls. Fifty-three Nellore bulls [initial BW 315 ± 5.9 kg and 20 ± 2 mo] were used. At the beginning, 6 bulls were randomly chosen and slaughtered for determination of their BW composition, and the remaining 47 bulls were evaluated during a 140-d experimental period. The bulls were placed in individual pens, blocked according to initial BW and randomly allocated to 1 of the 3 following treatments: (1) control diet containing sugarcane bagasse, ground corn, citrus pulp, peanut meal, and mineral–vitamin mix (CON), (2) CON with the addition of 3.3% of CSFA from soybean oil (CSO), or (3) CON with the addition of a mixture of 3.3% of CSFA from palm, soybean, and cottonseed oils (CPSCO). Diets were offered ad libitum and formulated to be isonitrogenous. Bulls supplemented with CSFA had a greater (P < 0.01) final BW, dry matter intake, average daily gain (ADG), feed efficiency (FE), and FA intake vs. CON. Among carcass parameters, CSFA-supplemented bulls had greater (P < 0.01) carcass ether extract concentration vs. CON bulls. When the CSFA profile was evaluated (CSO vs. CPSCO), CPSCO bulls had a better (P ≤ 0.03) FE, carcass ADG, and hot carcass weight (HCW) vs. CSO bulls. The FA intakes differed among CSFA treatments, as the total saturated, palmitic, and oleic FA intakes were greater for CPSCO (P < 0.01), whereas lower intakes of total unsaturated and polyunsaturated FA (P < 0.01) were observed for CPSCO vs. CSO. Samples from the Longissimus muscle contained greater palmitoleic (P = 0.01) and reduced linoleic (P = 0.02) FA concentrations in CSFA-supplemented bulls vs. CON bulls. In agreement with the FA intakes, CPSCO-supplemented bulls had a greater (P ≤ 0.05) unsaturated FA concentration vs. CSO in Longissimus muscle. In summary, CSFA supplementation improved the performance of finishing B. indicus bulls vs. CON. Moreover, the inclusion of CSFA from palm, soybean, and cottonseed oil benefited the FE, carcass ADG, and HCW compared with the inclusion of CSFA from soybean oil, demonstrating the potential of specific FA for improving the performance and meat quality of B. indicus bulls.

The placenta is a major driver of prenatal growth and involved in programming of postnatal performance. We therefore determined placental and embryo-fetal ultrasonographic parameters in early pregnancy and their relationships with birth weight and postnatal weights in a Bos indicus-Bos taurus composite beef cattle population. Pregnancies were generated in 2-yr-old Droughtmaster heifers by artificial insemination after estrus synchronization in 2 consecutive years (2009, n = 36 and 2010, n = 57), with a subset of 2010 heifers used again as lactating 3-yr-old cows in 2011 (n = 24). Each cohort was managed as 1 contemporary group for measurements of Corpus luteum diameter, amnion length and width, placentome width and thickness, and embryo-fetal crown-rump length, at 7 and 8 wk of gestation. This was followed by recordings of birth weight, branding weight at 5 to 6 mo of age and weaning weight 2 mo later. At a significance threshold of P < 0.05, placentome thickness at week 7 was negatively correlated with weights at birth (r = -0.23), branding (r = -0.25), and weaning (r = -0.35), whereas placentome width at week 7 (r = 0.24) and thickness at week 8 (r = 0.29) were positively correlated with birth weight. Thicker placentomes in males at week 7 (7%) difference mirrored sex differences in weights at birth (7%), branding (10%), and weaning (6%). The sex difference trend for birth weight was not consistent across sire-year combinations, ranging from -3.2 to +4.7 kg (birth weight of males - females per sire). These results support the hypothesis that placental parameters at the transition from embryo to fetal stage are major predictors of fetal and postnatal growth, albeit with significant environmentally induced plasticity, in stabilized B. indicus-B. taurus composite populations, and suggest that elements of B. indicus-B. taurus reciprocal differences in birth weight persist in composite populations.

Abstract This 2-yr study evaluated the growth and puberty attainment of Bos indicus-influenced beef heifers offered 2 different postweaning concentrate supplementation amounts and delivery frequencies. On day 0 of each year, 64 Brangus crossbred heifers were stratified by initial body weight (BW) and age (mean = 244 ± 22 kg; 314 ± 17 d) and assigned into 1 of 16 bahiagrass pastures (4 heifers/pasture/yr). Treatments were randomly assigned to pastures in a 2 × 2 factorial design (4 pastures/treatment/yr) and consisted of concentrate dry matter (DM) supplementation at 1.25% or 1.75% of BW which were offered either daily (7×) or 3 times weekly (3×) for 168 d. On day 56 of each year, heifers were assigned to an estrus synchronization protocol consisting of intravaginal controlled internal drug release (CIDR) insertion on day 56, CIDR removal on day 70, i.m. injection of 25 mg of prostaglandin F2α (PGF2α) on day 86, and i.m. injection of 100 µg of gonadotropin-releasing hormone and timed-AI at 66 h after PGF2α injection (day 89). Heifers were exposed to Angus bulls from day 89 to 168 (1 bull/pasture). Pregnancy diagnosis was assessed on day 213 of each year. Supplementation amount × frequency effects were not detected (P ≥ 0.12) for any variable, except for plasma concentrations of glucose (P = 0.10) and urea nitrogen (PUN; P = 0.01). Herbage mass, herbage allowance, and nutritive value did not differ (P ≥ 0.12) among treatments. Increasing supplementation DM amount from 1.25% to 1.75% of BW increased (P ≤ 0.05) plasma concentrations of insulin-like growth factor 1 (IGF-1), overall average daily gain (ADG), final BW, percentage of pubertal heifers on day 89, pregnancy and calving percentages, and percentage of heifers calving within the first 21 d of the calving season. However, reducing the supplementation frequency from daily to 3× weekly, regardless of supplementation amount, did not impact overall pregnancy and calving percentages (P ≥ 0.42), but caused (P ≤ 0.05) fluctuations in plasma concentrations of insulin and IGF-1 and decreased (P ≤ 0.03) overall ADG, final BW, puberty attainment on days 56, 89, and 168, and percentage of heifers calving during the first 21 d of the calving season. Hence, increasing the supplement DM amount did not prevent the negative effects of reducing the frequency of supplementation (3× vs. 7× weekly) on growth and reproduction of replacement Bos indicus-influenced beef heifers.

Abstract Bos indicus typically perform better than Bos taurus when consuming a low-quality diet; however, the response to supplementation is generally greater in B. taurus. The underlying mechanisms supporting these responses have not been fully elucidated. Characterization of differences in rumen prokaryotic populations and their functional role in the two subspecies may provide additional insight. Ten cannulated steers (5 Angus and 5 Brahman) were used in concurrent 5 × 5 Latin squares. Animals were offered ad libitum access to rice straw (4.7% CP). Treatments consisted of an unsupplemented control diet and two levels (50 or 120 mg N/kg BW) of isonitrogenous supplements (30% CP), that were either high (H; 74%) or low (L; 26%) in undegradable intake protein. Rumen samples were collected at 0 and 4 h postfeeding and separated into liquid and solid fractions. Rumen bacterial taxa were sequenced utilizing a Roche 454 platform based on the 16s rRNA gene. At 97% sequence similarity, 97,826 operational taxonomic units were identified, which included 24 phyla, 108 families, and 255 genera. Analysis included SAS PROC mixed model, QIIME, and PICRUSt. Across all samples, Bacteroidetes and Firmicutes accounted for 65% and 28% of total bacterial abundance, respectively. The families Prevotellaceae (P = 0.05) and Ruminococcaceae (P = 0.004) and the genera Prevotellaceae (family; P = 0.003) within the phyla Bacteroidetes differed significantly in relative abundance with added protein when compared to the control. Consistent differences in the relative abundance of family and genus taxa between B. indicus and B. taurus suggest roles the symbiotic rumen microbiome may have in the capacity of B. indicus to utilize low-quality forage over a range of supplement types and levels including (Prevotella, Ruminococcus [family], Sphingobacteriaceae [family], Bacteroidales [order], Pontibacter, Bacteroides, Succiclasticum, Barnesiella, and Xylanibacter). Overall bacterial community diversity differences across parameters were limited. Rice straw is recalcitrant to bacterial digestion because of high levels of silica in the epidermis making this straw more resistant to bacterial attachment. Thus, this analysis represents the bacterial diversity and function of the rumen under conditions depleted CP, recalcitrant fiber matrix and restricted digestibility which appear to limit the microbial population to those capable of attaching and digesting complexed structural carbohydrates, resulting in reduced plasticity, and more evenness in diversity across parameters.

Objective: As one of the most valuable genetic resources of Ongole beef cattle globally, the Sumba Ongole (SO) cattle population is being studied in this investigation of myostatin (MSTN) gene polymorphism and its association with growth traits. Materials and Methods: Blood samples from 161 SO cattle were collected and analyzed. Deoxyribonucleic acid (DNA) was isolated. The DNA was electrophoresed and extracted, and finally, the annealing temperature was optimized, followed by amplification and sequencing. Next, we used a Basic local alignment search tool to assess the sequencing data. Results: The analysis revealed 22 single nucleotide polymorphisms (SNPs) in the MSTN gene in this region that showed genetic variation. Two SNPs, c.424 G > A, and c.467 G > C, were found to be significantly associated with SO cattle phenotypes of wither height, heart girth, and hip height (p < 0.05) but not with body weight or body length (p > 0.05). Conclusion: As a result of our findings, the MSTN gene polymorphism and its correlation with growth traits in SO cattle may be employed as a candidate marker in SO cattle and other beef cattle breeds.