Integrated analysis of genomics and transcriptomics revealed the genetic basis for goaty flavor formation in goat milk.

Goat milk exhibits a robust and distinctive "goaty" flavor. However, the underlying genetic basis of goaty flavor remains elusive and requires further elucidation at the genomic level. Through comparative genomics analysis, we identified divergent signatures of certain proteins in goat, sheep, and cow. MMUT has undergone a goat-specific mutation in the B12 binding domain. We observed the goat FASN exhibits nonsynonymous mutations in the acyltransferase domain. Structural variations in these key proteins may enhance the capacity for synthesizing goaty flavor compounds in goat. Integrated omics analysis revealed the catabolism of branched-chain amino acids contributed to the goat milk flavor. Furthermore, we uncovered a regulatory mechanism in which the transcription factor ZNF281 suppresses the expression of the ECHDC1 gene may play a pivotal role in the accumulation of flavor substances in goat milk. These findings provide insights into the genetic basis underlying the formation of goaty flavor in goat milk. STATEMENT OF SIGNIFICANCE: Branched-chain fatty acids (BCFAs) play a crucial role in generating the distinctive "goaty" flavor of goat milk. Whether there is an underlying genetic basis associated with goaty flavor is unknown. To begin deciphering mechanisms of goat milk flavor development, we collected transcriptomic data from mammary tissue of goat, sheep, cow, and buffalo at peak lactation for cross-species transcriptome analysis and downloaded nine publicly available genomes for comparative genomic analysis. Our data indicate that the catabolic pathway of branched-chain amino acids (BCAAs) is under positive selection in the goat genome, and most genes involved in this pathway exhibit significantly higher expression levels in goat mammary tissue compared to other species, which contributes to the development of flavor in goat milk. Furthermore, we have elucidated the regulatory mechanism by which the transcription factor ZNF281 suppresses ECHDC1 gene expression, thereby exerting an important influence on the accumulation of flavor compounds in goat milk. These findings provide insights into the genetic mechanisms underlying flavor formation in goat milk and suggest further research to manipulate the flavor of animal products.

Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats.

BACKGROUND: Breeding polled goats is a welfare-friendly approach for horn removal in comparison to invasive methods. To gain a comprehensive understanding of the genetic basis underlying polledness in goats, we conducted whole-genome sequencing of 106 Xinong Saanen dairy goats, including 33 horned individuals, 70 polled individuals, and 3 polled intersexuality syndrome (PIS) individuals. METHODS: The present study employed a genome-wide association study (GWAS) and linkage disequilibrium (LD) analysis to precisely map the genetic locus underlying the polled phenotype in goats. RESULTS: The analysis conducted in our study revealed a total of 320 genome-wide significant single nucleotide polymorphisms (SNPs) associated with the horned/polled phenotype in goats. These SNPs exhibited two distinct peaks on chromosome 1, spanning from 128,817,052 to 133,005,441 bp and from 150,336,143 to 150,808,639 bp. The present study identified three genome-wide significant SNPs, namely Chr1:129789816, Chr1:129791507, and Chr1:129791577, as potential markers of PIS-affected goats. The results of our LD analysis suggested a potential association between MRPS22 and infertile intersex individuals, as well as a potential association between ERG and the polled trait in goats. CONCLUSION: We have successfully identified three marker SNPs closely linked to PIS, as well as several candidate genes associated with the polled trait in goats. These results may contribute to the development of SNP chips for early prediction of PIS in goats, thereby facilitating breeding programs aimed at producing fertile herds with polled traits.

Phase Error Reduction for a Structured-Light 3D System Based on a Texture-Modulated Reprojection Method.

Fringe projection profilometry (FPP), with benefits such as high precision and a large depth of field, is a popular 3D optical measurement method widely used in precision reconstruction scenarios. However, the pixel brightness at reflective edges does not satisfy the conditions of the ideal pixel-wise phase-shifting model due to the influence of scene texture and system defocus, resulting in severe phase errors. To address this problem, we theoretically analyze the non-pixel-wise phase propagation model for texture edges and propose a reprojection strategy based on scene texture modulation. The strategy first obtains the reprojection weight mask by projecting typical FPP patterns and calculating the scene texture reflection ratio, then reprojects stripe patterns modulated by the weight mask to eliminate texture edge effects, and finally fuses coarse and refined phase maps to generate an accurate phase map. We validated the proposed method on various texture scenes, including a smooth plane, depth surface, and curved surface. Experimental results show that the root mean square error (RMSE) of the phase at the texture edge decreased by 53.32%, proving the effectiveness of the reprojection strategy in eliminating depth errors at texture edges.

SEpi-3D: soft epipolar 3D shape measurement with an event camera for multipath elimination.

Multipath in 3D imaging happens when one pixel receives light from multiple reflections, which causes errors in the measured point cloud. In this paper, we propose the soft epipolar 3D(SEpi-3D) method to eliminate multipath in temporal space with an event camera and a laser projector. Specifically, we align the projector and event camera row onto the same epipolar plane with stereo rectification; we capture event flow synchronized with the projector frame to construct a mapping relationship between event timestamp and projector pixel; we develop a multipath eliminating method that utilizes the temporal information from the event data together with the epipolar geometry. Experiments show that the RMSE decreases by 6.55mm on average in the tested multipath scenes, and the percentage of error points decreases by 7.04%.

Fatty Acid Desaturation Is Suppressed in Mir-26a/b Knockout Goat Mammary Epithelial Cells by Upregulating INSIG1.

MicroRNA-26 (miR-26a and miR-26b) plays a critical role in lipid metabolism, but its endogenous regulatory mechanism in fatty acid metabolism is not clear in goat mammary epithelial cells (GMECs). GMECs with the simultaneous knockout of miR-26a and miR-26b were obtained using the CRISPR/Cas9 system with four sgRNAs. In knockout GMECs, the contents of triglyceride, cholesterol, lipid droplets, and unsaturated fatty acid (UFA) were significantly reduced, and the expression of genes related to fatty acid metabolism was decreased, but the expression level of miR-26 target insulin-induced gene 1 (INSIG1) was significantly increased. Interestingly, the content of UFA in miR-26a and miR-26b simultaneous knockout GMECs was significantly lower than that in wild-type GMECs and miR-26a- and miR-26b-alone knockout cells. After decreasing INSIG1 expression in knockout cells, the contents of triglycerides, cholesterol, lipid droplets, and UFAs were restored, respectively. Our studies demonstrate that the knockout of miR-26a/b suppressed fatty acid desaturation by upregulating the target INSIG1. This provides reference methods and data for studying the functions of miRNA families and using miRNAs to regulate mammary fatty acid synthesis.

LncRNA LOC102176306 plays important roles in goat testicular development.

Long ncRNAs regulate a complex array of fundamental biological processes, while its molecular regulatory mechanism in Leydig cells (LCs) remains unclear. In the present study, we established the lncRNA LOC102176306/miR-1197-3p/peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) regulatory network by bioinformatic prediction, and investigated its roles in goat LCs. We found that lncRNA LOC102176306 could efficiently bind to miR-1197-3p and regulate PPARGC1A expression in goat LCs. Downregulation of lncRNA LOC102176306 significantly supressed testosterone (T) synthesis and ATP production, decreased the activities of antioxidant enzymes and mitochondrial complex I and complex III, caused the loss of mitochondrial membrane potential, and inhibited the proliferation of goat LCs by decreasing PPARGC1A expression, while these effects could be restored by miR-1197-3p inhibitor treatment. In addition, miR-1197-3p mimics treatment significantly alleviated the positive effects of lncRNA LOC102176306 overexpression on T and ATP production, antioxidant capacity and proliferation of goat LCs. Taken together, lncRNA LOC102176306 functioned as a sponge for miR-1197-3p to maintain PPARGC1A expression, thereby affecting the steroidogenesis, cell proliferation and oxidative stress of goat LCs. These findings extend our understanding of the molecular mechanisms of T synthesis, cell proliferation and oxidative stress of LCs.

Guided, Fusion-Based, Large Depth-of-field 3D Imaging Using a Focal Stack.

Three dimensional (3D) imaging technology has been widely used for many applications, such as human-computer interactions, making industrial measurements, and dealing with cultural relics. However, existing active methods often require both large apertures of projector and camera to maximize light throughput, resulting in a shallow working volume in which projector and camera are simultaneously in focus. In this paper, we propose a novel method to extend the working range of the structured light 3D imaging system based on the focal stack. Specifically in the case of large depth variation scenes, we first adopted the gray code method for local, 3D shape measurement with multiple focal distance settings. Then we extracted the texture map of each focus position into a focal stack to generate a global coarse depth map. Under the guidance of the global coarse depth map, the high-quality 3D shape measurement of the overall scene was obtained by local, 3D shape-measurement fusion. To validate the method, we developed a prototype system that can perform high-quality measurements in the depth range of 400 mm with a measurement error of 0.08%.

MiR-103-5p deficiency suppresses lipid accumulation via upregulating PLSCR4 and its host gene PANK3 in goat mammary epithelial cells.

Lipids are intimately related to the unique flavor and nutritional values of goat milk. MicroRNAs (miRNA) participate in the regulation of various biological functions, including the synthesis and degradation of lipids. Several studies have shown that miR-103 is involved in the regulation of lipid metabolism, however, the molecular mechanism by which miR-103 regulates lipid metabolism in goat mammary gland is poorly understood. In this study, miR-103 was knocked out in goat mammary epithelial cells (GMECs) by CRISPR/Cas9, and the accumulation of lipid droplets, triglycerides, and cholesterol in the cells was suppressed subsequently. Overexpression or knockdown of miR-103-5p and miR-103-3p in GMECs revealed that it was miR-103-5p that promoted lipid accumulation but not miR-103-3p. In addition, Pantothenate Kinase 3 (PANK3), the host gene of miR-103, and Phospholipid Scramblase 4 (PLSCR4) were identified as the target genes of miR-103-5p by dual fluorescein and miRNA pulldown. Furthermore, we identified that cellular lipid levels were negatively regulated by PANK3 and PLSCR4. Lastly, in miR-103 knockout GMECs, the knockdown of PANK and PLSCR4 rescued the lipid accumulation. These findings suggest that miR-103-5p promotes lipid accumulation by targeting PLSCR4 and the host gene PANK3 in GMECs, providing new insights for the regulation of goat milk lipids via miRNAs.

Whole-genome resequencing of native and imported dairy goat identifies genes associated with productivity and immunity.

Understanding the differences in genetic variation between local Chinese dairy goat breeds and imported breeds can help germplasm innovation and molecular breeding. However, the research is limited in this area. In this study, whole-genome resequencing data from 134 individuals of both local and imported dairy goat breeds were analyzed, and their differences in genomic genetic variation, genetic diversity, and population structure were subsequently identified. We also screened candidate genes associated with important traits of dairy goats such as milk production (STK3, GHR, PRELID3B), reproduction (ATP5E), growth and development (CTSZ, GHR), and immune function (CTSZ, NELFCD). Furthermore, we examined allele frequency distributions for the genes of interest and found significant differences between the two populations. This study provides valuable resources for the study of genetic diversity in dairy goats and lays the foundation for the selective breeding of dairy goats in the future.

Widely Targeted Metabolomic Analysis Revealed the Diversity in Milk from Goats, Sheep, Cows, and Buffaloes and Its Association with Flavor Profiles.

The milk flavor can be attributed to the presence of numerous flavor molecules and precursors. In this study, we employed widely targeted metabolomic analysis techniques to analyze the metabolic profiles of various milk samples obtained from goats, sheep, dairy cows, and buffaloes. A total of 631 metabolites were identified in the milk samples, which were further categorized into 16 distinct classes. Principal component analysis (PCA) suggested that the metabolite profiles of samples from the same species exhibit clustering, while separated patterns of metabolite profiles are observed across goat, sheep, cow, and buffalo species. The differential metabolites between the groups of each species were screened based on fold change and variable importance in projection (VIP) values. Five core differential metabolites were subsequently identified, including 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid, inosine 5'-triphosphate, methylcysteine, N-cinnamylglycine, and small peptide (L-tyrosine-L-aspartate). Through multiple comparisons, we also screened biomarkers of each type of milk. Our metabolomic data showed significant inter-species differences in the composition and concentration of some compounds, such as organic acids, amino acids, sugars, nucleotides, and their derivatives, which may affect the overall flavor properties of the milk sample. These findings provided insights into the molecular basis underlying inter-species variations in milk flavor.

Depth estimation for speckle projection system using progressive reliable points growing matching.

In this paper, we propose a progressive reliable points growing matching scheme to estimate the depth from the speckle projection image. First a self-adapting binarization is introduced to reduce the influence of inconsistent intensity. Then we apply local window-based correlation matching to get the initial disparity map. After the initialization, we formulate a progressive updating scheme to update the disparity estimation. There are two main steps in each round of updation. At first new reliable points are progressively selected based on three aspects of criterion including matching degree, confidence, and left-right consistency; then prediction-based growing matching is adopted to recalculate the disparity map from the reliable points. Finally, the more accurate depth map can be obtained by subpixel interpolation and transformation. The experimental results well demonstrate the effectiveness and low computational cost of our scheme.

Genome-wide analysis of the acyl-coenzyme A synthetase family and their association with the formation of goat milk flavour.

Goat milk is rich in fat and protein, thus, has high nutritional values and benefits human health. However, goaty flavour is a major concern that interferes with consumer acceptability of goat milk and the 4-alkyl-branched-chain fatty acids (vBCFAs) are the major substances relevant to the goaty flavour in goat milk. Previous research reported that the acyl-coenzyme A synthetases (ACSs) play a key role in the activation of fatty acids, which is a prerequisite for fatty acids entering anabolic and catabolic processes and highly involved in the regulation of vBCFAs metabolism. Although ACS genes have been identified in humans and mice, they have not been systematically characterized in goats. In this research, we performed genome-wide characterization of the ACS genes in goats, identifying that a total of 25 ACS genes (without ACSM2A) were obtained in the Capra hircus and each ACS protein contained the conserved AMP-binding domain. Phylogenetic analysis showed that out of the 25 genes, 21 belonged to the ACSS, ACSM, ACSL, ACSVL, and ACSBG subfamilies. However, AACS, AASDH, ACSF, and ACSF3 genes were not classified in the common evolutionary branch and belonged to the ACS superfamily. The genes in the same clade had similar conserved structures, motifs and protein domains. The expression analysis showed that the majority of ACS genes were expressed in multi tissues. The comparative analysis of expression patterns in non-lactation and lactation mammary glands of goat, sheep and cow indicated that ACSS2 and ACSF3 genes may participate in the formation mechanisms of goaty flavour in goat milk. In conclusion, current research provides important genomic resources and expression information for ACSs in goats, which will support further research on investigating the formation mechanisms of the goaty flavour in goat milk.

Pulsed thrust measurements using electromagnetic calibration techniques.

A thrust stand for accurately measuring impulse bits, which ranged from 10-1000 µN s using a noncontact electromagnetic calibration technique is described. In particular, a permanent magnet structure was designed to produce a uniform magnetic field, and a multiturn coil was made to produce a calibration force less than 10 mN. The electromagnetic calibration force for pulsed thrust measurements was linear to the coil current and changed less than 2.5% when the distance between the coil and magnet changed 6 mm. A pulsed plasma thruster was first tested on the thrust stand, and afterward five single impulse bits were measured to give a 310 µN s average impulse bit. Uncertainty of the measured impulse bit was analyzed to evaluate the quality of the measurement and was found to be 10 µN s with 95% credibility.