Search Results (113)

Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems. Full article

Vertebrate molecular genetic research methods typically employ single genetic loci (monolocus markers) and those involving a variable number of loci (multilocus markers). The former often employ microsatellites that ensure accuracy in establishing inbreeding, tracking pan-generational dynamics of genetic parameters, assessing genetic purity, and facilitating genotype/phenotype correlations. They also enable the determination and identification of unique alleles by studying and managing marker-assisted breeding regimes to control the artificial selection of agriculturally important traits. Microsatellites consist of 2–6 nucleotides that repeat numerous times and are widely distributed throughout genomes. Their main advantages lie in their ease of use for PCR amplification, their known genome localization, and their incredible polymorphism (variability) levels. Robust lab-based molecular technologies are supplemented by high-quality statistics and bioinformatics and have been widely employed, especially in those instances when more costly, high throughput techniques are not available. Here, we consider that human and livestock microsatellite studies have been a “roadmap” for the genetics, breeding, and conservation of wildlife and rare animal breeds. In this context, we examine humans and other primates, cattle and other artiodactyls, chickens and other birds, carnivores (cats and dogs), elephants, reptiles, amphibians, and fish. Studies originally designed for mass animal production have thus been adapted to save less abundant species, highlighting the need for molecular scientists to consider where research may be applied in different disciplines. Full article

Rarámuri Criollo (RC) cattle have been raised by the isolated Tarahumara communities of Chihuahua, Mexico, for nearly 500 years, mostly under natural selection and minimal management. RC cattle were introduced to the United States Department of Agriculture-Agricultural Research Service Jornada Experimental Range (RCJER) in 2005 to begin evaluations of beef production performance and their adaptation to the harsh ecological and climatic conditions of the Northern Chihuahuan Desert. While this research unveiled crucial information on their phenotypic plasticity and adaptation, the genetic diversity and structure of the RCJER population remains poorly understood. This study analyzed the genetic diversity, population structure, ancestral composition, and selection signatures of the RCJER herd using a ~64 K SNP array. The RCJER herd exhibits moderate genetic diversity and low population stratification with no evident clustering, suggesting a shared genetic background among different subfamilies. Admixture analysis revealed the RCJER herd represents a distinctive genetic pool within the Criollo cattle breeds, with significant Iberian ancestry. Selection signatures identified candidate genes and quantitative trait loci (QTL) for traits associated with milk composition, growth, meat and carcass, reproduction, metabolic homeostasis, health, and coat color. The RCJER population represents a distinctive genetic resource adapted to harsh environmental conditions while maintaining productive and reproductive attributes. These findings are crucial to ensuring the long-term genetic conservation of the RCJER and their strategic expansion into locally adapted beef production systems in the USA. Full article

The yak (Bos grunniens), the only large domesticated species endemic to the Qinghai–Tibet Plateau, is a vital resource for local livelihoods and regional economic sustainability. However, yak breeding faces significant challenges, including limited understanding of the genetic architecture underlying quantitative traits, inadequate advanced breeding strategies, and the sterility of hybrid offspring from yak–cattle crosses. These constraints have hindered genetic progress in key production traits. To address these issues, integrating modern genomic tools into yak breeding programs is imperative. This review explores the application and potential of molecular marker-assisted selection (MAS) and genomic prediction (GP) in yak genetic improvement. We systematically evaluate critical components of genomic breeding pipelines, including: (1) phenotypic trait assessment, (2) sample collection strategies, (3) reference population design, (4) high-throughput genotyping (via genome sequencing and SNP arrays), (5) predictive model development, and (6) heritability estimation. By synthesizing current advances and methodologies, this work aims to provide a framework for leveraging genomic technologies to enhance breeding efficiency, preserve genetic diversity, and accelerate genetic gains in yak populations. Full article

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective genotyping platform essential for molecular breeding of livestock. In this study, we developed a liquid SNP capture chip suitable for five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. The panel consisted of 42,686 SNPs (~40 K). These SNPs were evenly distributed on each bovine chromosome, with the majority of SNPs having minor allele frequencies >0.05 and located within intergenic regions. The performance evaluation of this SNP chip panel was proceeded by genotyping 200 individuals, revealing that this panel has a high SNP call rate of 99.48%. The SNP chip panel was further used to examine the population structure of a beef cattle population with 205 individuals and demonstrated the ability to differentiate between foreign and indigenous cattle breeds. The SNP chip was also used to determine the runs of homozygosity (ROH) within a local Hubei beef cattle population of 195 individuals. We identified 2547 ROH and several genes associated with economically important traits in the study population. Our findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. Full article

The aim of this paper is to review the literature on the environmental impacts of pasture-based dairy cattle systems, focusing on the factors affecting the main impact categories. This paper also aimed at comparing data of the literature on environmental impacts in pasture-based vs. confined systems. The environmental impact of pasture-based dairy cattle systems appears to be highly influenced by several input factors. Life cycle assessments have shown significant variability in methodological approaches, which complicates the comparison of results across studies. The different variables affecting environmental impacts make it challenging to draw universally valid conclusions regarding the comparison of pasture-based and confined dairy systems on a global scale. In addition, the analysis of the variables highlights the considerable potential to reduce the environmental impact of milk production in both systems by adopting productivity-enhancing activities, low inputs and best management practices. Further aspects such as geographical factors, carbon sequestration, animal health and welfare, toxicological aspects due to the use of drugs and antimicrobials in animals and the maintenance of local animal breeds should be incorporated into LCAs for a full comprehensive understanding of the environmental impacts of dairy farms. Full article

The Russian Black Pied (RBP) is one of Russia’s most popular dairy cattle breeds. It was developed in the USSR during the 1930s by crossing Russian native cattle with Dutch cattle. Since the mid-1970s, the RBP has been cross-bred with Holstein cattle to enhance milk production. To trace haplotypes and selection signatures in the RBP genomes formed during cross-breeding and selection, we conducted local ancestry inference and scans for selection signatures in 12 resequenced RBP animals. Scans for selection using hapFLK and window-based F_ST identified 65 putatively selected regions across the genome, with 4 identified by both methods. Candidate missense variants were detected within these regions, including KIAA1755, CNBD1, and MPZL3, which may be related to milk traits, pathogen resistance, and climate adaptation. Local ancestry inference and functional annotation analyses suggest that regions with a higher fraction of native haplotypes are enriched for genes associated with keratin filaments, antimicrobial defence, the immune system, protein digestion, and amino acid transporters. The results of our study could be utilised for conservation purposes and the improvement of this and other breeds. Full article

In Europe, intensive agriculture threatens species-rich semi-natural communities that have emerged from traditional agricultural activities. To protect these communities, subsidies are given to farmers through agri-environmental schemes (AESs). However, after nearly twenty years in operation, the uniform support system for farmers has not produced the expected results. Therefore, we conducted 15 semi-structured, in-depth qualitative interviews with beef cattle farmers in Estonia and identified the socio-ecological aspects of their activities. We found that small-scale farmers cannot compete with intensive farmers in the meat market because many breeds with slower weight gain and smaller body weights are grazed in semi-natural grasslands. Although two food quality schemes have been created in Estonia to value extensively grown meat, the permanent agricultural grasslands are under-supported, and the family farmers managing these areas feel the unfair distribution of subsidies. Moreover, family farms cannot compete with large farms, as the availability of pastures on family farms limits the number of livestock, and European Union animal welfare requirements and extreme weather conditions in 2023 have limited the number of herds. Since AESs have a large impact on farmers, we recommend that they be more flexible and consider the socio-cultural background of farmers and their impact on local communities when defining support. Full article

In view of the threat to local breeds resulting from intensive animal production, many studies are conducted in search of arguments confirming their importance in food production. In the case of milk production, not only is its quantity important, but its quality is as well, including its chemical composition. Particular focus has recently been placed on the casein proteins beta-casein (CSN2) and kappa-casein (CSN3), due to their potential impact on human health or on the suitability of milk for cheese production. The present study analysed the polymorphism of these proteins in 1777 cows belonging to two local cattle breeds, Polish Red and Polish White-Backed, using Illumina Infinium XT SNP technology on a EuroGenomics MD chip. The results indicate that the Polish White-Backed breed is predisposed to produce ‘A2 milk’, as the frequency of the CSN2 A2 allele in the population was 61.2%. The Polish Red breed was characterised by a higher frequency of the CNS3 B allele (35%), which according to extensive scientific literature is associated with better coagulation properties, and increased whey expulsion. The highest yield of milk and its constituents, confirmed at p ≤ 0.01, was obtained for Polish White-Backed cows with the A2A2 genotype in CSN2 and cows with the AA genotype in CSN3. In the Polish Red breed, no statistically significant differences were obtained between means for milk production traits. Full article

Understanding how breeders of local breeds view different social actors can be of great importance to the process of local breed conservation. The same goes for the motives in farming local breeds. However, there is little research that provides insight into these perspectives. The aim of this study was to investigate motives for farming and attitudes of Croatian breeders of two local cattle breeds (Istrian cattle and Buša), two local donkey breeds (Istrian donkey and Littoral Dinaric donkey), and one local horse breed (Croatian Posavina horse) towards consumers, the local population and the regional and national administration. In addition, the influence of motives, attitudes, and the socio-economic characteristics of the breeders on the planned scope of breeding over the next five years was investigated. The study was conducted on a sample of 204 breeders of selected local breeds. The results of the study show that the most important motive for keeping a local breed is the attractiveness (beauty) of the breed followed by its emotional and sentimental value. Around one-third of farmers have a relatively positive attitude towards all stakeholders, with the role of the local population and consumers being viewed most positively. Almost half of the farmers (49%) plan to increase the size of their herd and only 8% plan to reduce it or to stop farming. The planned farming volume over the next five years is significantly influenced by the importance of economic and traditional motives and the change in the number of animals over the last five years. This study represents a valuable contribution to understanding the views of farmers of local breeds towards key societal stakeholders, and the findings can be used in campaigns to promote the keeping of these valuable breeds. Full article

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. F_ST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). F_ST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point F_ST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions. Full article

Animal biodiversity is essential for maintaining the functionality of local food systems and ensuring sustainable livelihoods. Starting in 2000, the Food and Agriculture Organization of the United Nations (F.A.O.) has drawn attention to the decline in cattle populations, including the Transylvanian Pinzgau breed from Romania. Renowned for its hardiness, adaptability, and enhanced resistance to diseases and climate change, the Transylvanian Pinzgau is regarded as an important genetic asset for advancing livestock production. As a result, tracking genetic diversity has become a key focus in breeding programs, particularly for small, endangered local populations that play a vital role in regional agro-ecological systems. This research paper sought to assess the genetic diversity of a group of 24 head of cattle from the Transylvania region by analyzing two mtDNA markers, cytochrome b and D-loop sequences, both widely recognized for their relevance and importance in the analysis of genetic diversity of cattle and phylogenetic studies. The findings, derived through statistical analysis of nucleotide sequences using specialized software, indicated that the analyzed cattle are part of the ancestral T haplogroup, with a direct lineage tracing back to Bos taurus. This information can aid in developing crossbreeding programs focused on conserving essential genetic resources, improving other cattle breeds, and protecting biodiversity. Full article

Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, θπ, F_ST, and XP-EHH methods, genes associated with immunity (ITGB3, CD55, OTUD1, and PRLH) and heat tolerance (COX4I2, DNAJC18, DNAJC1, EIF2AK4, and ASIC2) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources. Full article

Dung beetles mostly feed on mammal dung. Throughout the European Alps, the dung produced by local domestic ungulates attracts many species of dung beetles, giving rise to rich and diversified communities that play an important role in the Alpine agricultural ecosystem. There is, therefore, understandable concern about the introduction of exotic livestock, such as alpacas (Vicugna pacos (Linnaeus, 1758)), into the region. This research studied dung beetle assemblages in an Alpine valley where both cattle and alpacas are raised. We used standardized pitfall traps baited with alpaca or cow dung along altitudinal transects to assess the “attractiveness” of the two resources to dung beetles. Most species entered both trap types. The average number of species per trap did not vary significantly and the nMDS trap ordination largely overlapped, but the total number of individuals and the average number of individuals per trap were higher in traps baited with alpaca dung. This difference was largely due to the preference of the dominant species Euheptaulacus carinatus (Germar, 1824) for alpaca dung-baited traps. Moreover, both the abundance and specific richness changed with altitude, being greatest in alpaca traps during July at intermediate altitudes. IndVal analyses showed that eight out of nine species (all Aphodiinae) showed a preference for alpaca traps. Since the microclimatic conditions (i.e., temperature) of the two trap types were virtually the same, it is reasonable to consider trophic preferences as the source of the observed differences. Finally, we also sampled the beetles present in the alpaca latrines and cow dung pats deposited on pastures, providing confirmation that dung beetles do indeed visit the dung of both species. Our results emphasize the usefulness of polyphagia and the trophic flexibility of dung beetles, providing evidence that the long history of pastoralism in the Alps has not led local species to adapt to the dung of domestic ungulates. The results also suggest that alpaca breeding could be a sustainable activity since, thanks to the work of dung beetles which feed upon and move the dung into their tunnels (as occurs with cattle dung), there is less need for farmers to remove the dung from pastures. Full article

Cattle farming is an important part of the global livestock industry, and cattle body size is the key indicator of livestock growth. However, traditional manual methods for measuring body sizes are not only time-consuming and labor-intensive but also incur significant costs. Meanwhile, automatic measurement techniques are prone to being affected by environmental conditions and the standing postures of livestock. To overcome these challenges, this study proposes a multi-view fusion-driven automatic measurement system for full-attitude cattle body measurements. Outdoors in natural light, three Zed2 cameras were installed covering different views of the channel. Multiple images, including RGB images, depth images, and point clouds, were automatically acquired from multiple views using the YOLOv8n algorithm. The point clouds from different views undergo multiple denoising to become local point clouds of the cattle body. The local point clouds are coarsely and finely aligned to become a complete point cloud of the cattle body. After detecting the 2D key points on the RGB image created by the YOLOv8x-pose algorithm, the 2D key points are mapped onto the 3D cattle body by combining the internal parameters of the camera and the depth values of the corresponding pixels of the depth map. Based on the mapped 3D key points, the body sizes of cows in different poses are automatically measured, including height, length, abdominal circumference, and chest circumference. In addition, support vector machines and Bézier curves are employed to rectify the missing and deformed circumference body sizes caused by environmental effects. The automatic body measurement system measured the height, length, abdominal circumference, and chest circumference of 47 Huaxi Beef Cattle, a breed native to China, and compared the results with manual measurements. The average relative errors were 2.32%, 2.27%, 3.67%, and 5.22%, respectively, when compared with manual measurements, demonstrating the feasibility and accuracy of the system. Full article