Assessing Bos taurus introgression in the UOA Bos indicus assembly

Background Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus—B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus—B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. Results The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. Conclusions We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle.

PSIV-6 Differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality

The amount of intramuscular fat directly influences the meat quality. However, significant differences in the ability to accumulate intramuscular fat are present among different beef cattle breeds. While Wagyu, a cattle breed that originated from Japan, is renowned for abundant intramuscular fat, Brahman cattle generally have very little intramuscular fat accumulation and produce tougher meat. We identified that bovine intramuscular fat is derived from a group of bipotent progenitor cells named fibro/adipogenic progenitors (FAPs) which also give rise to fibroblasts. Thus, the variation in intramuscular fat development between Wagyu and Brahman is likely attributed to the difference in FAPs between these two breeds. In order to understand the gene expression difference between FAPs of the two breeds, single-cell RNA-seq was performed using total single-nucleated cells isolated from the longissimus muscle of young purebred Wagyu, purebred Brahman, and Wagyu-Brahman cross cattle. FAPs constitute the largest single-nucleated cell population in both Wagyu and Brahman skeletal muscle. Multiple subpopulations of FAPs with different gene expression profiles were identified, suggesting that FAP is a heterogeneous population. A unique FAP cluster expressing lower levels of fibrillar collagen and extracellular remodeling enzyme genes but higher levels of select proadipogenic genes was identified exclusively in Wagyu skeletal muscle, which likely contributes to the robust intramuscular adipogenic efficiency of Wagyu FAPs. In conclusion, the difference in the cellular composition and gene expression of FAPs between Wagyu and Brahman cattle likely contribute to their distinct meat quality.

PSXVI-18 Heifers are from Venus, steers are from mars: Sex differences in social behaviors in drylot housed brahman cattle exposed to a cattle brush

Sex differences in cattle productivity and efficiency have been established, yet an empirical examination of how sex influences cattle social behavior in dry lots is absent. Our objective was to evaluate the impact of sex on the performance of social behaviors and brush use in drylot-housed Brahman yearling steers (n = 2 pens; 19 steers/pen) and heifers (n = 2 pens; 15 heifers/pen). Cattle were video recorded from 8:00 to 20:00 for 71 d, and to date, d 1 has been decoded using continuous observations. Video was decoded for social behavior for 15 minutes of every 30 minutes using continuous observations. Average bout duration (sec), total duration per day (sec), and bout frequency of allogrooming, bar licking, tongue rolling, and brush utilization were recorded for each pen. Frequency was recorded for headbutting and mounting. Data were normalized, and the differences between sexes for each behavior were evaluated with a t-test (PROC TTEST). Average bout duration, bout frequency, and total duration for allogrooming (P > 0.15), bar licking (P > 0.63), and brush use (P > 0.78) and bout frequency for brush displacement (P > 0.78) and headbutt (P > 0.76) did not differ between sexes. Heifers tended (P = 0.09) to perform more bunk displacements than steers (heifers: 94.5 ± 64.5 count/pen/d; steers: 29 ± 3 count/pen/d). Steers performed more mounts than heifers (P < 0.0001; steers: 2.5 ± 0.5 mounts/pen/d; heifers: 0 ± 0 mounts/pen/d). This preliminary evaluation suggests that sexes may differ in the prevalence and type of social behaviors performed while housed in drylots, yet inclusion of more data will confirm these early observations.

Molecular detection of Theileria species, Anaplasma species, Candidatus Mycoplasma haemobos, Trypanosoma evansi and first evidence of Theileria sinensis-associated bovine anaemia in crossbred Kedah-Kelantan x Brahman cattle

Background Serious disease outbreaks in cattle are usually associated with blood pathogens. This study aims to detect blood pathogens namely Theileria species, Anaplasma species, Candidatus Mycoplasma haemobos and Trypanosoma evansi, and determine their phylogenetic relationships and haemato-biochemical abnormalities in naturally infected cattle. Methods Molecular analysis was achieved by PCR amplification and sequencing of PCR amplicons of 18SrRNA gene of Theileria species, 16SrRNA genes of Anaplasma and Mycoplasma species, MPSP genes of T. orientalis and T. sinensis, MSP4 gene of A. marginale, 16SrRNA gene of Candidatus Mycoplasma haemobos, and RoTat1.2 VSG gene of Trypanosoma evansi, in sixty-one (61) clinically ill Kedah-Kelantan x Brahman cattle in Pahang, Malaysia. Results A total of 44 (72.13%) cattle were infected with more than one blood pathogen. Theileria species was the blood pathogen with the highest molecular detection rate (72.13, 95% CI 59.83–81.81%). Nucleotide blast analyses of all sequences demonstrated high degree of molecular similarity (98–100%) in comparison with their respective reference sequences. Analysis of 18SrRNA gene sequences of Theileria species and 16SrRNA gene sequences of Anaplasma species revealed Theileria sinensis and Anaplasma platys respectively as additional species detected in these cattle. MPSP-PCR analysis was conducted for further confirmation of T. sinensis. The blood picture of eight infected cattle groups revealed poikilocytosis, anisocytosis, rouleaux formation and degenerative left shift. High mean erythrocyte fragility values were common in infected cattle groups. Anaemia of the macrocytic normochromic type and spherocytes were observed in the T. evansi and Anaplasma platys + Theileria sinensis double species co-infected cattle group. Normocytic normochromic anaemia was observed in the T. sinensis infected cattle group. Significant (p < 0.05) increases in serum liver and kidney parameters, total protein, globulin, total and unconjugated bilirubin and decreased albumin values were observed in the T. evansi infected cattle when compared to clinically healthy cattle. Conclusion We present the first evidence of Theileria sinensis-associated bovine anaemia (TSABA) in Malaysian cattle. Because of the high occurrence of bovine theileriosis and detection of A. platys, there is an urgent need for appropriate preventive and control measures against these blood pathogens.

Reproductive Performance Of Bali Cattle Cross Breed Brahman Cattle Through Improving The Genetic Quality Of Local Livestock In Special Effort for Cows to be Pregnant Program

One of the problems that exist in the community is the lack of identification of the reproductive performance of prospective brooders of Bali cattle that are artificially inseminated. The researcher conducted a research to determine the reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP (Special Effort for Cows to be Pregnant Program) Program in Kolaka Regency. The parameters observed in this study were; artificial insemination's first age (Years), How many times the artificial insemination (AI) was pregnant (S/C), Length of pregnancy (months), Calving Interval (CI) (months), Birth weight (Kilograms), Correlation of AI's first age with birth weight. Sources of date used in this study are primary and secondary data. Data collection techniques carried out in this study were observation and interviews. The date obtained was analyzed descriptively, analysis of variance, average, and to calculate the relationship between variables was analyzed by correlation. Reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP Program in Kolaka district include; first age AI 23.63±1.99 months, Service per Conception (S/C) 1.56±0.55, gestational age 9.03±0.38 months, Calving Interval (CI) 12.24±0 .52 months, birth weight 27.85 ± 2.96 and the correlation between AI prime age and birth spacing was 0.77.

Reproductive Performance Of Bali Cattle Cross Breed Brahman Cattle Through Improving The Genetic Quality Of Local Livestock In Special Effort for Cows to be Pregnant Program

One of the problems that exist in the community is the lack of identification of the reproductive performance of prospective brooders of Bali cattle that are artificially inseminated. The researcher conducted a research to determine the reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP (Special Effort for Cows to be Pregnant Program) Program in Kolaka Regency. The parameters observed in this study were; artificial insemination's first age (Years), How many times the artificial insemination (AI) was pregnant (S/C), Length of pregnancy (months), Calving Interval (CI) (months), Birth weight (Kilograms), Correlation of AI's first age with birth weight. Sources of date used in this study are primary and secondary data. Data collection techniques carried out in this study were observation and interviews. The date obtained was analyzed descriptively, analysis of variance, average, and to calculate the relationship between variables was analyzed by correlation. Reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP Program in Kolaka district include; first age AI 23.63±1.99 months, Service per Conception (S/C) 1.56±0.55, gestational age 9.03±0.38 months, Calving Interval (CI) 12.24±0 .52 months, birth weight 27.85 ± 2.96 and the correlation between AI prime age and birth spacing was 0.77.

Reproductive Performance Of Bali Cattle Cross Breed Brahman Cattle Through Improving the Genetic Quality of Local Livestock in Special Effort for Cows to be Pregnant Program

One of the problems that exist in the community is the lack of identification of the reproductive performance of prospective brooders of Bali cattle that are artificially inseminated. The researcher conducted a research to determine the reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP (Special Effort for Cows to be Pregnant Program) Program in Kolaka Regency. The parameters observed in this study were; artificial insemination's first age (Years), How many times the artificial insemination (AI) was pregnant (S/C), Length of pregnancy (months), Calving Interval (CI) (months), Birth weight (Kilograms), Correlation of AI's first age with birth weight. Sources of date used in this study are primary and secondary data. Data collection techniques carried out in this study were observation and interviews. The date obtained was analyzed descriptively, analysis of variance, average, and to calculate the relationship between variables was analyzed by correlation. Reproductive performance of Bali Cattle inseminated with Brahman Cattle Semen in SECP Program in Kolaka district include; first age AI 23.63±1.99 months, Service per Conception (S/C) 1.56±0.55, gestational age 9.03±0.38 months, Calving Interval (CI) 12.24±0 .52 months, birth weight 27.85 ± 2.96 and the correlation between AI prime age and birth spacing was 0.77.

Title: Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75–0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10−6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes—BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3—are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus–pituitary–ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.