Utilizing 3D Point Cloud Technology with Deep Learning for Automated Measurement and Analysis of Dairy Cows

This paper introduces an approach to the automated measurement and analysis of dairy cows using 3D point cloud technology. The integration of advanced sensing techniques enables the collection of non-intrusive, precise data, facilitating comprehensive monitoring of key parameters related to the health, well-being, and productivity of dairy cows. The proposed system employs 3D imaging sensors to capture detailed information about various parts of dairy cows, generating accurate, high-resolution point clouds. A robust automated algorithm has been developed to process these point clouds and extract relevant metrics such as dairy cow stature height, rump width, rump angle, and front teat length. Based on the measured data combined with expert assessments of dairy cows, the quality indices of dairy cows are automatically evaluated and extracted. By leveraging this technology, dairy farmers can gain real-time insights into the health status of individual cows and the overall herd. Additionally, the automated analysis facilitates efficient management practices and optimizes feeding strategies and resource allocation. The results of field trials and validation studies demonstrate the effectiveness and reliability of the automated 3D point cloud approach in dairy farm environments. The errors between manually measured values of dairy cow height, rump angle, and front teat length, and those calculated by the auto-measurement algorithm were within 0.7 cm, with no observed exceedance of errors in comparison to manual measurements. This research contributes to the burgeoning field of precision livestock farming, offering a technological solution that not only enhances productivity but also aligns with contemporary standards for sustainable and ethical animal husbandry practices.

Korean Cattle 3D Reconstruction from Multi-View 3D-Camera System in Real Environment

The rapid evolution of 3D technology in recent years has brought about significant change in the field of agriculture, including precision livestock management. From 3D geometry information, the weight and characteristics of body parts of Korean cattle can be analyzed to improve cow growth. In this paper, a system of cameras is built to synchronously capture 3D data and then reconstruct a 3D mesh representation. In general, to reconstruct non-rigid objects, a system of cameras is synchronized and calibrated, and then the data of each camera are transformed to global coordinates. However, when reconstructing cattle in a real environment, difficulties including fences and the vibration of cameras can lead to the failure of the process of reconstruction. A new scheme is proposed that automatically removes environmental fences and noise. An optimization method is proposed that interweaves camera pose updates, and the distances between the camera pose and the initial camera position are added as part of the objective function. The difference between the camera's point clouds to the mesh output is reduced from 7.5 mm to 5.5 mm. The experimental results showed that our scheme can automatically generate a high-quality mesh in a real environment. This scheme provides data that can be used for other research on Korean cattle.

Profiling of differentially expressed proteins between fresh and frozen-thawed Duroc boar semen using ProteinChip CM10

Many studies have been conducted to improve technology for semen cryopreservation in pigs. However, computer-assisted analysis of sperm motility and morphology is insufficient to predict the molecular function of frozen-thawed semen. More accurate expression patterns of boar sperm proteins may be derived using the isobaric tags for relative and absolute quantification (iTRAQ) technique. In this study, the iTRAQ-labeling system was coupled with liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis to identify differentially expressed CM10-fractionated proteins between fresh and frozen-thawed boar semen. A total of 76 protein types were identified to be differentially expressed, among which 9 and 67 proteins showed higher and lower expression in frozen-thawed than in fresh sperm samples, respectively. The classified functions of these proteins included oxidative phosphorylation, mitochondrial inner membrane and matrix, and pyruvate metabolic processes, which are involved in adenosine triphosphate (ATP) synthesis; and sperm flagellum and motile cilium, which are involved in sperm tail structure. These results suggest a possible network of biomarkers associated with survival after the cryopreservation of Duroc boar semen.

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip

BACKGROUND

Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome.

OBJECTIVE

This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level.

METHODS

Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure.

RESULTS

KWB showed the lowest average expected heterozygosity (H_E = 0.1904), while KWH showed the highest genetic diversity (H_E = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations.

CONCLUSION

This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC.

Whole-genome resequencing analysis of 20 Micro-pigs

BACKGROUND

Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs.

OBJECTIVE

In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics.

RESULTS

Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11.

CONCLUSION

In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.

Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse

BACKGROUND

The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds.

OBJECTIVE

The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse).

RESULTS

Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function.

CONCLUSION

We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.