Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing

Abstract Brahman cattle (Bos indicus) are well adapted to thrive in tropical environments. Since their introduction to Australia in 1933, Brahman’s ability to grow and reproduce on marginal lands has proven their value in the tropical beef industry. The poll phenotype, which describes the absence of horns, has become desirable in the cattle industry for animal welfare and handler safety concerns. The poll locus has been mapped to chromosome one. Four alleles, each a copy number variant, have been reported across this locus in B. indicus and Bos taurus. However, the causative mutation in Brahman cattle has not been fully characterized. Oxford Nanopore Technologies’ minION sequencer was used to sequence four homozygous poll (PcPc), four homozygous horned (pp), and three heterozygous (Pcp) Brahmans to characterize the poll allele in Brahman cattle. A total of 98 Gb were sequenced and an average coverage of 3.33X was achieved. Read N50 scores ranged from 9.9 to 19 kb. Examination of the mapped reads across the poll locus revealed insertions approximately 200 bp in length in the poll animals that were absent in the horned animals. These results are consistent with the Celtic poll allele, a 212-bp duplication that replaces 10 bp. This provides direct evidence that the Celtic poll allele is segregating in the Australian Brahman population.

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Differences in copper and selenium metabolism between Angus (Bos taurus) and Brahman (Bos indicus) cattle

Journal of Animal Science ◽

10.1093/jas/skab048 ◽

2021 ◽

Author(s):

J Ranches ◽

R Alves ◽

M Vedovatto ◽

E Anne Palmer ◽

P Moriel ◽

...

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

First Trimester ◽

Beef Cows ◽

Experimental Unit ◽

University Of Florida ◽

Brahman Cattle ◽

Research And Education ◽

The University ◽

Se Status

Abstract A two-year study was conducted at the University of Florida – IFAS, Range Cattle Research and Education Center (Ona, FL) to evaluate differences in the metabolism of Cu and Se of Angus (Bos taurus) and Brahman (Bos indicus) cattle. Thirty-two pregnant beef cows (n = 8 Brahman and 8 Angus/year) were enrolled in the study in the first trimester of gestation. The study consisted of 3 phases: (1) restriction (d 0 to d 90); (2) supplementation (d 91 to 150), and (3) calving. During all 3 phases, cows were individually fed and housed in partially covered drylot pens. During the restriction and supplementation phases cows were provided a 1.5 kg/d of a grain-based concentrate supplement, which was fortified with flowers of S (50 g of supplemental S/cow daily; restriction phase) or Cu and Se (100 and 3 mg/d of Cu and Se, respectively; supplementation phase). Blood and liver samples were collected from all cows on 30 d intervals and from both cows and calves within 24 h of calving. Colostrum and milk samples were collected at calving and 7 d after birth. All data were analyzed using the MIXED procedure of SAS, where cow and calf were the experimental unit. During the restriction phase, a breed × day effect (P = 0.03) was observed where Brahman had greater liver Cu concentration than Angus cows in all sampling days. For liver Se concentration, a tendency (P = 0.07) for a breed effect was observed where Angus cows tended to have greater liver Se concentration than Brahman. During the supplementation phase, breed (P < 0.001) and day (P < 0.01) effects were observed, where Brahman cows had greater liver Cu concentration than Angus. For liver Se concentration, a day effect (P < 0.001) was observed, where liver Se concentration increased (P < 0.001) from d 90 to 120 and remained unchanged (P = 0.86) until d 150. At calving no effects of breed (P = 0.34) were observed for liver Cu concentration of cows, however, Brahman calves tended (P = 0.09) to have greater liver Cu concentration than Angus calves. For Se liver concentration at calving, Angus cows tended (P = 0.07) to have greater liver Se concentration than Brahman cows, however no breed differences (P = 0.70) were observed for liver Se concentration of calves at birth. In summary substantial differences in multiple indicators of Cu and Se status were observed between Angus and Brahman cattle, implying that Angus and Brahman cattle possibly have different mechanisms to maintain adequate Cu and Se status.

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Bos indicus and Bos taurus crossbred dairy cattle in Australia. IV.* Progeny testing and expected rate of genetic improvement

Australian Journal of Agricultural Research ◽

10.1071/ar9760309 ◽

1976 ◽

Vol 27 (2) ◽

pp. 309 ◽

Cited By ~ 4

Author(s):

IR Franklin ◽

RH Hayman ◽

RO Hewetson

Keyword(s):

Dairy Cattle ◽

Heat Tolerance ◽

Genetic Improvement ◽

Bos Taurus ◽

Bos Indicus ◽

Progeny Testing ◽

Dairy Farmers ◽

Improvement Program ◽

Tropical Environments ◽

Tick Resistance

A dairy improvement program designed to develop a breed of cattle adapted to tropical environments is described. Each year young crossbred (Bos indicus x Bos taurus) bulls are screened for heat tolerance and tick resistance, and then progeny-tested in the herds of cooperating dairy farmers. Estimates of phenotypic and genetic means, variances and correlations are presented for production of milk and milk components, and the rate of genetic improvement is discussed. In particular the heritability of milk yield in the crossbred progeny is 0.27, and the theoretical rate of improvement is 2.6% per year. ____________________ *Part III, Aust. J. Agric. Res., 25: 1023 (1974).

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Identificación de ADN mitocondrial Bos taurus en poblaciones de ganado Cebú Brahman colombiano

Ciencia y Tecnología Agropecuaria ◽

10.21930/rcta.vol7_num2_art:66 ◽

2007 ◽

Vol 7 (2) ◽

pp. 21

Author(s):

Gloria Patricia Barrera ◽

Rodrigo Alfredo Martínez ◽

Manuel Fernando Ariza

Keyword(s):

Mitochondrial Dna ◽

Genetic Divergence ◽

Bos Taurus ◽

Consensus Sequence ◽

Bos Indicus ◽

Zebu Cattle ◽

American Continent ◽

Brahman Cattle ◽

D Loop ◽

Dna Fragment

El continente americano fue colonizado en el siglo XVI por los europeos quienes introdujeron por primera vez el ganado bovino de origen Bos taurus. La introducción de ganado Bos indicus ocurrió muchos años después, con las primeras importaciones desde la India, las cuales incluyeron principalmente machos. Con el fin de estudiar la participación de hembras Bos taurus en el origen del ganado Cebú colombiano, se secuenció un fragmento del ADN mitocondrial de 374 pb (D-Loop) en seis animales de la raza Cebú Brahman colombiano y 20 individuos representativos de las cinco razas criollas colombianas: seis de Blanco Orejinegro (BON), cinco de Costeño con Cuernos (CCC), tres de Romosinuano (ROMO), cuatro de Casanareño (CAS) y dos de San Martinero (SM). Adicionalmente, para el mismo fragmento se secuenciaron dos individuos de la raza española Pirenaica, como referente Bos taurus. La comparación de las secuencias reveló que los animales de la raza Cebú Brahman colombiano analizados presentaron ADN mitocondrial de origen taurino con mayor cercanía respecto de las razas criollas de origen Bos taurus europeo que con relación a las secuencias consenso Bos indicus, frente a las que se hallaron mayores divergencias. Adicionalmente, las divergencias de las razas criollas colombianas con respecto al consenso Bos taurus europeo variaron entre 0,005 y 0,014, resultado que sugiere la participación de matrilineajes Bos taurus en el origen del Cebú Brahman colombiano. Identification of mitochondrial DNA of Bos taurus origin in Colombian Zebu Brahman cattle The American continent was colonised in the XVI century by the Europeans who introduced the Bos taurus cattle. The introduction of Bos indicus cattle was done a few years later with cattle from India, mainly males. In order to study the participation of Bos Taurus females in the origin of the Colombian Zebu cattle, a 374 bp mitochondrial DNA fragment was sequenced (D-Loop) in six animals belonging to Colombian Zebu Brahman breed and 20 individuals representative of he five Colombian native breeds: 6 of Blanco Orejinegro (BON), five of Costeño Con Cuernos (CCC), three of Romosinuano (ROMO), four of Casanareño (CAS) and two of San Martinero (SM). As a reference to Bos taurus, two individuals of the Spanish Pirenaica breed were also sequenced for the same fragment. Comparison between sequences revealed that the Zebu Brahman cattle has mitochondrial DNA of Bos Taurus origin and closer to the native breeds of Spanish origin. Although described as Bos indicus, it showed the lowest genetic divergence when compared with the consensus sequence of European Bos taurus. The genetic divergences of the Colombian native breeds compared with the European Bos Taurus ranged between 0.005 and 0.014. This suggests the participation of Bos taurus matrilineages in the origin of the Colombian Zebu Brahman cattle.

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The impact of two different hormonal growth promotants (HGPs) on the eating quality of feedlot-finished steer carcasses

Animal Production Science ◽

10.1071/an17121 ◽

2019 ◽

Vol 59 (2) ◽

pp. 384 ◽

Cited By ~ 2

Author(s):

D. T. Packer ◽

G. H. Geesink ◽

R. Polkinghorne ◽

J. M. Thompson ◽

A. J. Ball

Keyword(s):

Bos Taurus ◽

Bos Indicus ◽

Gluteus Medius ◽

Eating Quality ◽

Beef Industry ◽

Muscle Area ◽

Eye Muscle ◽

Longissimus Lumborum ◽

The Impact

The Meat Standards Australia beef-grading model applies a variable adjustment for different cuts of hormonal growth promotant (HGP)-treated carcasses, but does not differentiate between different HGP types. Using 300 non-implanted Bos indicus–Bos taurus composite steers, an experiment was conducted to compare the effects of an oestradiol only (OES) and a combination trenbolone acetate and oestradiol (TBA+OES) implant with non-implanted animals (CON) fed a concentrate ration for 73 days before slaughter, on eating quality of the mm. longissimus lumborum (LL) and gluteus medius (GM) muscles. Sensory and objective LL and GM samples were aged for either 5 or 35 days before freezing at −20°C. Carcass weights from each group were significantly (P < 0.05) different. Corrected for carcass weight, HGP treatment had a significant effect on hump height, ossification score, marble score, P8 fat depth and eye-muscle area. The TBA+OES treatment resulted in significantly (P < 0.05) tougher meat than the OES and CON treatments as assessed by shear force, although this difference was reduced with aging. Sensory scores (tenderness, juiciness, like flavour, overall liking and a composite MQ4 score) confirmed a negative HGP treatment effect, whereby TBA+OES was significantly lower than the CON and OES treatments after 5 days of aging, and these differences were reduced through aging. TBA+OES had a greater impact on sensory scores in the LL when compared to the GM. Both HGP treatments increased calpastatin activity, and the TBA+OES treatment was significantly (P < 0.05) different from the CON and OES treatments. It was concluded that OES and TBA+OES implants have different impacts on meat eating-quality measurements, which could have important implications for the Australian and international beef industry.

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BeefSpecs fat calculator to assist decision making to increase compliance rates with beef carcass specifications: evaluation of inputs and outputs

Animal Production Science ◽

10.1071/an14614 ◽

2014 ◽

Vol 54 (12) ◽

pp. 2011 ◽

Cited By ~ 2

Author(s):

M. J. McPhee ◽

B. J. Walmsley ◽

D. G. Mayer ◽

V. H. Oddy

Keyword(s):

Sensitivity Analysis ◽

Mean Square Error ◽

Bos Taurus ◽

Bos Indicus ◽

Mean Square ◽

Beef Industry ◽

Factorial Matrix ◽

The Mean ◽

Input Variables ◽

Inputs And Outputs

This study evaluated the BeefSpecs fat calculator, a decision-support system developed to assist the beef industry to increase compliance rates with carcass specifications (weight and fat specifications). A challenge to the BeefSpecs calculator and a sensitivity analysis were used to evaluate the inputs and outputs of BeefSpecs. Five industry datasets (n = 80, 97, 68, 25, and 13 for Datasets 1–5, respectively) of Bos taurus, Bos indicus, and Bos taurus × Bos indicus breeds for steers and heifers were collated to challenge BeefSpecs, and a nine-way factorial matrix (n = 57 600) of input variables was created for the sensitivity analysis. There were no significant (P > 0.05) differences in the mean bias between observed and predicted values in any of the datasets but there were significant (P < 0.01) differences in the unity of slope for Datasets 2, 3, and 5. The root-mean-square error was 1.72, 2.61, 2.87, 2.68, and 2.00 mm for Datasets 1–5. The decomposition of the mean-square error of prediction indicated that most of the error contained in the predictions of all models was of a random nature (94%, 85%, 85%, 95% for Datasets 1–4), except in Dataset 5, which had a 47% proportion of error in the slope component. All datasets indicated little bias (0.13%, 12.19%, 12.69%, 0.60%, and 0.12% for Datasets 1–5) in the model predictions. An analysis of variance with the nine-way factorial matrix on the predicted output of final P8 fat was conducted for the sensitivity analysis. A significant (P < 0.01) four-way interaction of days on feed × frame score × initial liveweight × sex was detected. Final P8 fat was sensitive to measurement error in the inputs of frame score when animals had longer feeding periods (e.g. 180 days) and to initial P8 fat when animals had lower initial liveweights (e.g. 200 kg) and higher frame scores (e.g. 7). For each unit of error in estimating frame score, BeefSpecs predicts final P8 with an error of up to 2.3 mm in heifers and up to 1.7 mm in steers. Error in the estimation of initial P8 fat of 2 mm will result in an error of up to 3 mm in the prediction of final P8 fat. The sensitivity analysis of BeefSpecs input variables (frame score and initial P8 fat) on the prediction of final P8 fat indicates that increasing the accuracy of estimating frame score and P8 fat is an issue that needs addressing.

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Bovine embryo transfer recipient synchronisation and management in tropical environments

Reproduction Fertility and Development ◽

10.1071/rd09214 ◽

2010 ◽

Vol 22 (1) ◽

pp. 67 ◽

Cited By ~ 39

Author(s):

Pietro S. Baruselli ◽

Roberta M. Ferreira ◽

Manoel F. Sá Filho ◽

Luiz F. T. Nasser ◽

Carlos A. Rodrigues ◽

...

Keyword(s):

Embryo Transfer ◽

Bos Taurus ◽

Bos Indicus ◽

Fixed Time ◽

Pregnancy Rates ◽

Bovine Embryo ◽

Tropical Environments ◽

Gonadotrophin Releasing Hormone ◽

Animal Handling ◽

Repeat Breeder

Numerous studies have shown that it is possible to manipulate follicular and luteal dynamics, thereby eliminating the need for oestrus detection in embryo transfer (ET) programmes. Fixed-time ET (FTET) protocols are based on the use of gonadotrophin-releasing hormone (GnRH) and prostaglandin (PG) F or progesterone/progestogen (P4)-releasing devices and oestradiol. The FTET protocols increases the proportion of recipients transferred, and therefore pregnancy rates, compared with the use of PGF followed by ET 7 days after oestrus. Furthermore, the addition of equine chorionic gonadotrophin (eCG) to the P4 and oestradiol-based FTET protocols results in an even higher proportion of recipients transferred, and thus higher pregnancy rates. The beneficial effect of eCG treatment may be related to increased growth of the dominant follicle and increased plasma P4 concentrations during the subsequent luteal phase. In Bos taurus × Bos indicus recipients, pregnancy rates were positively correlated with the diameter of the corpus luteum (CL) and the number of CL at ET. When repeat-breeder Holstein cows were used as recipients, FTET protocols increased number of recipients transferred and pregnancy rates compared with the traditional PGF-based synchronisation protocols. In conclusion, the use of FTET protocols eliminates the need for the detection of oestrus and results in a greater proportion of recipients transferred and satisfactory pregnancy rates. Thus, FTET optimises the use of recipients, reducing labour and animal handling and facilitating the use of ET.

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Treatments to Optimize the Use of Artificial Insemination and Reproductive Efficiency in Beef Cattle under Tropical Environments

Veterinary Medicine International ◽

10.4061/2011/923053 ◽

2011 ◽

Vol 2011 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Ocilon Gomes de Sá Filho ◽

José Luiz Moraes Vasconcelos

Keyword(s):

Body Weight ◽

Beef Cattle ◽

Artificial Insemination ◽

Bos Taurus ◽

Bos Indicus ◽

Reproductive Efficiency ◽

Tropical Environments ◽

Final Maturation ◽

Tropical Areas ◽

Tropical Climates

Bos indicuscattle, the preferred genetic group in tropical climates, are characterized by having a lower reproductive efficiency thanBos taurus. The reasons for the poorer reproductive efficiency of theBos indicuscows include longer lengths of gestation and postpartum anestrus, a short length of estrous behavior with a high incidence of estrus occurring during the dark hours, and puberty at older age and at a higher percentage of body weight relative to mature body weight. Moreover, geography, environment, economics, and social traditions are factors contributing for a lower use of reproductive biotechnologies in tropical environments. Hormonal protocols have been developed to resolve some of the reproductive challenges of theBos indicuscattle and allow artificial insemination, which is the main strategy to hasten genetic improvement in commercial beef ranches. Most of these treatments use exogenous sources of progesterone associated with strategies to improve the final maturation of the dominant follicle, such as temporary weaning and exogenous gonadotropins. These treatments have caused large impacts on reproductive performance of beef cattle reared under tropical areas.

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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab029 ◽

2021 ◽

Vol 11 (4) ◽

Author(s):

Yury A Barbitoff ◽

Andrew G Matveenko ◽

Anton B Matiiv ◽

Evgeniia M Maksiutenko ◽

Svetlana E Moskalenko ◽

...

Keyword(s):

Chromosomal Rearrangements ◽

Structural Features ◽

Multiple Observations ◽

Yeast Strains ◽

Trace Back ◽

Oxford Nanopore ◽

Long Read ◽

History Of ◽

Variant Analysis ◽

Yeast Genomes

Abstract Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.

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