Production systems and breeding practices of Begaria cattle breed as input for a community-based breeding program
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ABSTRACT:
SUBMITTER: Aseged T
PROVIDER: S-EPMC10685181 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from -0.009 to 0.029. A low (-0.12-0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5-1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.
| S-EPMC9341487 | biostudies-literature
Project description:Understanding antibiotic use in livestock systems is key in combating antimicrobial resistance (AMR) and developing effective interventions. Using a standardised questionnaire, we investigated the patterns and drivers of antibiotic use in 165 cattle farms across the three major cattle production systems in Kenya: intensive, extensive, and semi-intensive systems across in three counties: Machakos, Makueni and Narok in Kenya. We used a causal diagram to inform regression models to explore the drivers of antibiotic use in the study farms. Antibiotic use was reported in 92.7% of farms, primarily for prophylactic purposes. Oxytetracycline, penicillin, and streptomycin were the most used antibiotics to treat and control the most reported diseases including mastitis, diarrhoea and East Coast fever (ECF). Regression analysis indicated a positive association between the frequency of antibiotic use at the farm level and both disease incidence and herd size. Conversely, farms that provided cattle with appropriate housing were less likely to use antibiotics, and there was no difference in antibiotic use between those who consulted with veterinarians or sourced antibiotics directly from animal health providers. Our study highlights the complexities around understanding the interplay between practices and drivers of antibiotic use. It also underscores the necessity to enhance education regarding the appropriate usage of antibiotics among cattle farmers, encourage the adoption of proper herd management practices which may reduce disease burden, and reinforce veterinary services and supportive legislation to promote the prudent use of antimicrobials.
| S-EPMC10665206 | biostudies-literature
Project description:Purpose: calculate genetic diversity in lentil
2021-09-29 | GSE184819 | GEO
Project description:BackgroundThe genome-wide association study (GWAS) is a useful approach to identify genes affecting economically important traits in dairy cattle. Here, we report the results from a GWAS based on high-density SNP genotype data and estimated breeding values for nine production, fertility, body conformation, udder health and workability traits in the Brown Swiss cattle population that is part of the international genomic evaluation program.ResultGWASs were performed using 50 k SNP chip data and deregressed estimated breeding values (DEBVs) for nine traits from between 2061 and 5043 bulls that were part of the international genomic evaluation program coordinated by Interbull Center. The nine traits were milk yield (MY), fat yield (FY), protein yield (PY), lactating cow's ability to recycle after calving (CRC), angularity (ANG), body depth (BDE), stature (STA), milk somatic cell score (SCS) and milk speed (MSP). Analyses were performed using a linear mixed model correcting for population confounding. A total of 74 SNPs were detected to be genome-wide significantly associated with one or several of the nine analyzed traits. The strongest signal was identified on chromosome 25 for milk production traits, stature and body depth. Other signals were on chromosome 11 for angularity, chromosome 24 for somatic cell score, and chromosome 6 for milking speed. Some signals overlapped with earlier reported QTL for similar traits in other cattle populations and were located close to interesting candidate genes worthy of further investigations.ConclusionsOur study shows that international genetic evaluation data is a useful resource for identifying genetic factors influencing complex traits in livestock. Several genome wide significant association signals could be identified in the Brown Swiss population, including a major signal on BTA25. Our findings report several associations and plausible candidate genes that deserve further exploration in other populations and molecular dissection to explore the potential economic impact and the genetic mechanisms underlying these production traits in cattle.
| S-EPMC3548702 | biostudies-literature
Project description:Consumer and community engagement (CCE) in the implementation of genomics into health services and associated research is needed to ensure that changes benefit the affected patients. Queensland Genomics was a program to implement genomics into a public health service. We describe its Community Advisory Group's (CAG) structure and function and provide recommendations based on the CAG members' perspectives. The CAG provided advice to the Queensland Genomics program and its projects in an advisory capacity. The CAG was also resourced to develop and lead community-focused activities. Key enablers for CAG included; diversity of CAG members' skills and experience, adequate resourcing, and the CAG's ability to self-determine their direction. The CAG experienced limitations due to a lack of mechanisms to implement CCE in the Program's projects. Here, we provide insights and commentary on this CAG, which will be useful for other initiatives seeking to undertake CCE in genomic research and health care.
| S-EPMC9355292 | biostudies-literature
Project description:Understanding the relationship of foot angle and claw set to beef cattle structural soundness will be critical to the selection of animals that fit forage-based production systems. In an effort to address concerns about foot and leg structure, the American Angus Association's foot angle and foot claw set expected progeny differences (EPD) were developed in 2019. As a result, these relatively new EPD and associated guidelines have limited phenotypic data submitted thus far. While ample research has evaluated lameness and foot issues in the dairy breeds, less is known about the factors that affect foot structure in beef cattle. This review focuses on beef cattle foot and leg structure, selection factors that may have led to increased problems with feet and legs, and the importance of foot and leg structure in forage-based grazing production systems. Specifically, the importance of locomotion and freedom of movement in extensive rangeland environments is discussed relative to the current literature. In addition, environmental factors that may influence foot and leg structure are addressed as well as heritability of various aspects of foot and leg traits. Where possible, information gaps and research needs are identified to enhance further investigation and the improvement of foot and leg selection tools.
| S-EPMC9913362 | biostudies-literature
Project description:Life Cycle Assessment (LCA) of livestock production systems is often based on inventory data for farms typical of a study region. As information on individual animals is often unavailable, livestock data may already be aggregated at the time of inventory analysis, both across individual animals and across seasons. Even though various computational tools exist to consider the effect of genetic and seasonal variabilities in livestock-originated emissions intensity, the degree to which these methods can address the bias suffered by representative animal approaches is not well-understood. Using detailed on-farm data collected on the North Wyke Farm Platform (NWFP) in Devon, UK, this paper proposes a novel approach of life cycle impact assessment that complements the existing LCA methodology. Field data, such as forage quality and animal performance, were measured at high spatial and temporal resolutions and directly transferred into LCA processes. This approach has enabled derivation of emissions intensity for each individual animal and, by extension, its intra-farm distribution, providing a step towards reducing uncertainty related to agricultural production inherent in LCA studies for food. Depending on pasture management strategies, the total emissions intensity estimated by the proposed method was higher than the equivalent value recalculated using a representative animal approach by 0.9-1.7 kg CO2-eq/kg liveweight gain, or up to 10% of system-wide emissions. This finding suggests that emissions intensity values derived by the latter technique may be underestimated due to insufficient consideration given to poorly performing animals, whose emissions becomes exponentially greater as average daily gain decreases. Strategies to mitigate life-cycle environmental impacts of pasture-based beef productions systems are also discussed.
| S-EPMC5738973 | biostudies-literature
Project description:The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (FROH), % of homozygosis (FSNP), and inbreeding coefficient (Fx). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (FROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.
| S-EPMC6313910 | biostudies-other
Project description:The objective of this study was to evaluate growth and reproductive performance of highland Dawuro sheep population managed under a community-based breeding program in Ethiopia. Records used in the study were collected over 6 years (2017-2022). In the current study, 3554 records were considered. Studied traits were birth weight (BWT), 3-month weight (WWT), 6-month weight (SMWT), daily gain from birth to weaning (ADG0-3), daily gains from weaning to 6-month age(ADG3-6), litter size(LS), lambing interval (LI), and annual reproductive rates(ARR). The data were analyzed using general linear models of SAS software. The overall least squares mean (LSM± SE) for BWT, WWT, SMWT, ADG0-3, and ADG3-6 were 2.69±0.02; 14.6±0.49, 22.8±0.22 kg, 128.05±2.27 gram (g), and 71.5±0.23 gram respectively. Site difference exerted significantly on BWT, WWT, and SMWT. The result of WWT and SMWT results of Dawuro sheep were comparable with previously reported known Ethiopian sheep breeds. The overall least squares mean ± standard error of LS, LI and, ARR were 1.67±0.04 lambs, 239±31.91 days, and 2.19±0.06 lambs, respectively. WWT and SMWT traits showed good responses to selection. The general implication of the result to future improvement program was continue selection, strengthening the existing breeder cooperatives, integration of full animal health, feed packages, conservation of prolific flocks, improving the management of animals, expanding the current CBBP to adjacent potential kebele, create market linkage and scaling out the existing best practice to a new sites.
| S-EPMC10174558 | biostudies-literature
Project description:This paper addresses knowledge gaps in the biomass, productivity and value of livestock for the pastoral, mixed crop-livestock and specialized dairy systems in Ethiopia. Population size, reproductive performance, mortality, offtake and productivity of cattle were calculated from official statistics and a meta-analysis of data available in the published literature. This information was then used to estimate biomass and output value for 2020 using a herd dynamics model. The mixed-crop livestock system dominates the Ethiopian cattle sector, with 55 million cattle (78% total population) and contributing 8.52 billion USD to the economy through the provision of meat, milk, hides and draft power in 2021. By comparison, the pastoral (13.4 million head) and specialized dairy (1.8 million head) systems are much smaller. Productivity varied between different production systems, with differences in live body weight, productivity and prices from different sources. The estimated total cattle biomass was 14.8 billion kg in 2021, i.e., 11.3 billion kg in the mixed crop-livestock system, 2.60 billion kg in the pastoral system and 0.87 billion kg in the specialized dairy system. The total economic asset values of cattle in the mixed crop-livestock, pastoral and specialized dairy systems were estimated as 24.8, 5.28 and 1.37 billion USD, respectively. The total combined output value (e.g., beef, milk and draft power) of cattle production was 11.9 billion USD, which was 11.2% of the GDP in Ethiopia in 2021. This work quantifies the importance of cattle in the Ethiopian economy. These estimates of herd structure, reproductive performance, productivity, biomass, and economic value for cattle production systems in Ethiopia can be used to inform high-level policy, revealing under-performance and areas to prioritize and provide a basis for further technical analysis, such as disease burden.
| S-EPMC10598381 | biostudies-literature