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.

Morphology and motor behavior of endemic fishes in the upper reaches of the Yangtze River basin.

Dam construction alters the hydrodynamic conditions, consequently impacting the swimming behavior of fish. To explore the effect of flow hydrodynamics on fish swimming behavior, five endemic fish species in the upper Yangtze River basin were selected. Through high-speed video visualization and computer analysis, these species' swimming patterns under different flow velocities (0.1-1.2 m/s) were investigated. The kinematic and morphological characteristics of the fish were presented. The principal component analysis was used to analyse the main factors influencing the swimming ability of fish and to determine the correlation coefficients among fish behavior indicators. Fish exhibited three different swimming patterns under different flow velocities. Low velocity (0.1-0.3 m/s) corresponds to free motion, middle velocity (0.4-0.7 m/s) corresponds to cruising motion, and high velocity corresponds to stress motion (0.8-1.2 m/s). The fish kinematic index curves were obtained, and four of five fish species showed two extreme points, which means the optimal and adverse swimming strategies can be determined. With the increase in flow velocity, the tail-beat frequency showed an increasing trend, whereas the tail-beat angle and amplitude showed a decreasing trend. Morphological and kinematic parameters were the two main indexes that affect the swimming ability of fish, which accounts for 41.9% and 26.9%, respectively.

GmNF-YC4 delays soybean flowering and maturation by directly repressing GmFT2a and GmFT5a expression.

Flowering time and growth period are key agronomic traits which directly affect soybean (Glycine max (L.) Merr.) adaptation to diverse latitudes and farming systems. The FLOWERING LOCUS T (FT) homologs GmFT2a and GmFT5a integrate multiple flowering regulation pathways and significantly advance flowering and maturity in soybean. Pinpointing the genes responsible for regulating GmFT2a and GmFT5a will improve our understanding of the molecular mechanisms governing growth period in soybean. In this study, we identified the Nuclear Factor Y-C (NFY-C) protein GmNF-YC4 as a novel flowering suppressor in soybean under long-day (LD) conditions. GmNF-YC4 delays flowering and maturation by directly repressing the expression of GmFT2a and GmFT5a. In addition, we found that a strong selective sweep event occurred in the chromosomal region harboring the GmNF-YC4 gene during soybean domestication. The GmNF-YC4Hap3 allele was mainly found in wild soybean (Glycine soja Siebold & Zucc.) and has been eliminated from G. max landraces and improved cultivars, which predominantly contain the GmNF-YC4Hap1 allele. Furthermore, the Gmnf-yc4 mutants displayed notably accelerated flowering and maturation under LD conditions. These alleles may prove to be valuable genetic resources for enhancing soybean adaptability to higher latitudes.

Catalyst-Free Electrochemical Sulfonylation of Organoboronic Acids.

A simple and efficient electrochemical sulfonylation of organoboronic acids with sodium arylsulfinate salts has been reported for the first time. A variety of aryl, heteroaryl, and alkenylsulfones were obtained in good to excellent yields via a simple electrochemical sulfonylation of various arylboronic acids, heterocyclic boronic acids, or alkenylboronic acids with sodium arylsulfinate at room temperature in 5 h under the catalyst-free and additive-free conditions. A plausible mechanism has been proposed based on various radical-trapping and CV control experiments.

Scd1 Deficiency in Early Embryos Affects Blastocyst ICM Formation through RPs-Mdm2-p53 Pathway.

Embryos contain a large number of lipid droplets, and lipid metabolism is gradually activated during embryonic development to provide energy. However, the regulatory mechanisms remain to be investigated. Stearoyl-CoA desaturase 1 (Scd1) is a fatty acid desaturase gene that is mainly involved in intracellular monounsaturated fatty acid production, which takes part in many physiological processes. Analysis of transcripts at key stages of embryo development revealed that Scd1 was important and expressed at an increased level during the cleavage and blastocyst stages. Knockout Scd1 gene by CRISPR/Cas9 from zygotes revealed a decrease in lipid droplets (LDs) and damage in the inner cell mass (ICM) formation of blastocyst. Comparative analysis of normal and knockout embryo transcripts showed a suppression of ribosome protein (RPs) genes, leading to the arrest of ribosome biogenesis at the 2-cell stage. Notably, the P53-related pathway was further activated at the blastocyst stage, which eventually caused embryonic development arrest and apoptosis. In summary, Scd1 helps in providing energy for embryonic development by regulating intra-embryonic lipid droplet formation. Moreover, deficiency activates the RPs-Mdm2-P53 pathway due to ribosomal stress and ultimately leads to embryonic development arrest. The present results suggested that Scd1 gene is essential to maintain healthy development of embryos by regulating energy support.

Incipient Motion of Exposed Microplastics in an Open-Channel Flow.

The incipient motion threshold of microplastics (MPs), defined as the condition that is just sufficient to initiate MP movement, is key to assessing the transport and fate of MPs in water bodies, yet only a few studies have focused on its prediction. This study experimentally investigated the effects of bed roughness (smooth and rough beds) and MP properties (shapes, sizes, and densities) on the incipient velocity (Ui) and critical shear stress (τc) of exposed MPs in an open-channel flow. For a total of 19 types of MPs, Ui and τc were found to range from 0.06 to 0.21 m/s and 0.01 to 0.075 N/m2, respectively. The commonly used thresholds for sediment transport, for example, critical shield parameter Θc and movability number Λc, were established for MPs based on τc. Based on the experimental data of the literature and this study, it was found that predictions of Θc and Λc for sediments do not apply to MPs. A new explicit formula for Λc was proposed for predicting the incipient motion of MPs by introducing the dimensionless particle diameter (d*) and a new dimensionless parameter related to the particle size, density, and shape. The new formula has an absolute error of 12.3%, which is smaller than the existing formula for MPs (55.6%).

CRISPR/Cas9-Mediated Knockout of miR-130b Affects Mono- and Polyunsaturated Fatty Acid Content via PPARG-PGC1α Axis in Goat Mammary Epithelial Cells.

MicroRNA (miRNA)-130b, as a regulator of lipid metabolism in adipose and mammary gland tissues, is actively involved in lipogenesis, but its endogenous role in fatty acid synthesis remains unclear. Here, we aimed to explore the function and underlying mechanism of miR-130b in fatty acid synthesis using the CRISPR/Cas9 system in primary goat mammary epithelial cells (GMEC). A single clone with deletion of 43 nucleotides showed a significant decrease in miR-130b-5p and miR-130b-3p abundances and an increase of target genes PGC1α and PPARG. In addition, knockout of miR-130b promoted triacylglycerol (TAG) and cholesterol accumulation, and decreased the proportion of monounsaturated fatty acids (MUFA) C16:1, C18:1 and polyunsaturated fatty acids (PUFA) C18:2, C20:3, C20:4, C20:5, C22:6. Similarly, the abundance of fatty acid synthesis genes ACACA and FASN and transcription regulators SREBP1c and SREBP2 was elevated. Subsequently, interference with PPARG instead of PGC1α in knockout cells restored the effect of miR-130b knockout, suggesting that PPARG is responsible for miR-130b regulating fatty acid synthesis. Moreover, disrupting PPARG inhibits PGC1α transcription and translation. These results reveal that miR-130b directly targets the PPARG-PGC1α axis, to inhibit fatty acid synthesis in GMEC. In conclusion, miR-130b could be a potential molecular regulator for improving the beneficial fatty acids content in goat milk.

ZnBr2-Catalyzed Dehydrogenative Borylation of Terminal Alkynes.

The simple, commercially available ZnBr2 has been successfully employed as a highly efficient and chemoselective catalyst for the dehydrogenative borylation of terminal alkynes with HBpin under mild conditions. It shows a good tolerance toward various functional groups such as aryl, alkyl, heteroaryl, etc. The plausible reaction mechanism has been investigated based on the corresponding stoichiometric experiments and DFT calculations.

ELOVL6 promoter binding sites directly targeted by sterol regulatory element binding protein 1 in fatty acid synthesis of goat mammary epithelial cells.

The elongation of long-chain fatty acid family member 6 (ELOVL6) gene plays an important role in the synthesis of long-chain saturated and monounsaturated fatty acids. Although some studies have revealed that ELOVL6 is the target of sterol regulatory element binding protein 1 (SREBP1; gene name SREBF1) in rodents, the mechanism underlying ELOVL6 regulation during lactation in dairy goats remains unknown. The present study aimed to investigate the transcriptional regulation mechanism of ELOVL6 in goat mammary epithelial cells (GMEC). We used PCR to clone and sequenced a 2,370 bp fragment of the ELOVL6 5' flanking region from goat genomic DNA. Deletion analysis revealed a core promoter region located -105 to -40 bp upstream of the transcriptional start site. Mutant sterol regulatory elements (SRE) 1 and 3 significantly reduced the ELOVL6 promoter activities in GMEC. Both SRE1 and SRE3 binding sites were required for the basal transcriptional activity of ELOVL6. Luciferase reporter assays showed that SREBF1 knockdown decreased ELOVL6 promoter activities in GMEC. Furthermore, SRE1 and SRE3 sites were simultaneously mutated completely abolished the stimulatory effect of SREBF1 and the repressive effect of linoleic acid on ELOVL6 gene promoter activities. Furthermore, chromatin immunoprecipitation assays confirmed that SREBP1 directly bound to SRE sites in the ELOVL6 promoter. In conclusion, these results indicate that SREBP1 regulates ELOVL6 transcription via the SRE elements located in the ELOVL6 promoter in goat mammary gland.

Mutagenesis of GmFT2a and GmFT5a mediated by CRISPR/Cas9 contributes for expanding the regional adaptability of soybean.

Flowering time is a key agronomic trait that directly influences the successful adaptation of soybean (Glycine max) to diverse latitudes and farming systems. GmFT2a and GmFT5a have been extensively identified as flowering activators and integrators in soybean. Here, we identified two quantitative trait loci (QTLs) regions harbouring GmFT2a and GmFT5a, respectively, associated with different genetic effects on flowering under different photoperiods. We analysed the flowering time of transgenic plants overexpressing GmFT2a or GmFT5a, ft2a mutants, ft5a mutants and ft2aft5a double mutants under long-day (LD) and short-day (SD) conditions. We confirmed that GmFT2a and GmFT5a are not redundant, they collectively regulate flowering time, and the effect of GmFT2a is more prominent than that of GmFT5a under SD conditions whereas GmFT5a has more significant effects than GmFT2a under LD conditions. GmFT5a, not GmFT2a, was essential for soybean to adapt to high latitude regions. The ft2aft5a double mutants showed late flowering by about 31.3 days under SD conditions and produced significantly increased numbers of pods and seeds per plant compared to the wild type. We speculate that these mutants may have enormous yield potential for the tropics. In addition, we examined the sequences of these two loci in 202 soybean accessions and investigated the flowering phenotypes, geographical distributions and maturity groups within major haplotypes. These results will contribute to soybean breeding and regional adaptability.

Soybean adaption to high-latitude regions is associated with natural variations of GmFT2b, an ortholog of FLOWERING LOCUS T.

Day length has an important influence on flowering and growth habit in many plant species. In crops such as soybean, photoperiod sensitivity determines the geographical range over which a given cultivar can grow and flower. The soybean genome contains ~10 genes homologous to FT, a central regulator of flowering from Arabidopsis thaliana. However, the precise roles of these soybean FTs are not clearly. Here we show that one such gene, GmFT2b, promotes flowering under long-days (LDs). Overexpression of GmFT2b upregulates expression of flowering-related genes which are important in regulating flowering time. We propose a 'weight' model for soybean flowering under short-day (SD) and LD conditions. Furthermore, we examine GmFT2b sequences in 195 soybean cultivars, as well as flowering phenotypes, geographical distributions and maturity groups. We found that Hap3, a major GmFT2b haplotype, is associated with significantly earlier flowering at higher latitudes. We anticipate our assay to provide important resources for the genetic improvement of soybean, including new germplasm for soybean breeding, and also increase our understanding of functional diversity in the soybean FT gene family.

Two-Dimensional Immiscible Domain of Cholesterol in the Lipid Bilayer Membrane Promotes Early Stage Calcification by Inducing Oriented Nucleation of Hydroxyapatite.

Biomineralization is characterized by the fact that the crystallization of inorganic minerals is guided by an in vivo biological interface. However, the interfaces that direct calcification are widely debated up to date. In this paper, it was found that the two-dimensional (2D) immiscible domain of cholesterol in the lipid bilayer can induce the deposition of calcium phosphate by rapidly promoting the nucleation of the hydroxyapatite (001) plane. This promotion effect is related to the high lattice matching degree between the 2D cholesterol immiscible domain and the (001) plane of hydroxyapatite (HAP), which leads to the heteroepitaxy of HAP. The lipid bilayer derived from cells or vesicles is the largest biological interface in the body, thus revealing whether the lipid bilayer can induce the deposition of calcium phosphate will facilitate the understanding of the important role of cells or vesicles in calcification.

[Permeation mechanism of phenolic acid components from traditional Chinese medicine on PES membrane separation process].

To explore the permeation mechanism of micro-molecule medicinal ingredients of water extract of tradition Chinese medicine(TCM) in membrane separation process. With phenolic acid components as the model solute, five phenolic acids with similar molecular weight and structure, namely gallic acid, protocatechuate acid, 4-hydroxybenzoic acid, 3-hydroxybenzoic acid and salicylic acid, were selected in the PES membrane separation experiments. With the relative flux and the transmission rate as indexes, the scanning electron microscopy(SEM) and the electrochemical impedance spectroscopy(EIS) were used to analyze the permeation mechanism of different phenolic acid components. The results showed phenolic acids with similar molecular weight had different permeation behaviors, with decreased relative flux and increased solute permeation with the increase of solute concentration. According to the permeation behavior analyzed by the molecular structure of solute, the transmission rate of phenolic acids increased with the increase of the number of hydroxyl, and the order of substituent positions of phenolic acids based on the permeation rate as follows: para-substituted > meta-substitution > ortho-substitution. Electrochemical impedance spectroscopy reflected the role of charge repulsion in the membrane process; that is to say, the greater the resistance is, the less the solute permeation is. Therefore, the permeation phenomenon of the phenolic acid components in the PES membrane is not only the result of simple sieving mechanisms, but also has the effects of steric hindrance and charge repulsion during the membrane process.

Green hydroboration of carboxylic acids and mechanism investigation.

A catalyst-free and solvent-free method for the hydroboration of a variety of carboxylic acids with pinacolborane was developed. The hydroboration of various aromatic and aliphatic carboxylic acids as well as dicarboxylic acids with HBpin could be completed within 6 h at room temperature or within 1 h at 60 °C to give the products in quantitative yields under neat conditions without the need for any solvent or metal catalyst. The possible reaction mechanism was investigated in detail based on the corresponding DFT calculations and the stoichiometric reaction of acetic acid with different equivalents of HBpin (at room temperature and 0 °C) and it revealed the stepwise nature of the protocol.

Ytterbium-Catalyzed Hydroboration of Aldehydes and Ketones.

The well-defined heavy rare-earth ytterbium iodide complex 1 (L2YbI) has been successfully employed as an efficient catalyst for the hydroboration of a wide range of aldehydes and ketones with pinacolborane (HBpin) at room temperature. The protocol requires low catalyst loadings (0.1-0.5 mol %) and proceeds rapidly (>99% conversion in <10 min). Additionally, catalyst 1 shows a good functional group tolerance even toward the hydroxyl and amino moieties and displays chemoselective hydroboration of aldehydes over ketones under mild conditions.

Improvement of Soybean Agrobacterium-Mediated Transformation Efficiency by Adding Glutamine and Asparagine into the Culture Media.

As a genetically modified crop, transgenic soybean occupies the largest global scale with its food, nutritional, industrial, and pharmaceutical uses.Efficient transformation is a key factor for the improvement of genetically modified soybean. At present, the Agrobacterium-mediated method is primarily used for soybean transformation, but the efficiency of this method is still relatively low (below 5%) compared with rice (above 90%). In this study, we examined the influence of l-glutamine and/or l-asparagine on Agrobacterium-mediated transformation in soybean and explored the probable role in the process of Agrobacterium-mediated transformation. The results showed that when the amino acids l-glutamine and l-asparagine were added separately or together to the culture medium, the shoot induction frequency, elongation rate, and transformation frequency were improved. The combined effects of l-glutamine and l-asparagine were better than those of l-glutamine and l-asparagine alone. The 50 mg/L l-glutamine and 50 mg/L l-asparagine together can enhance the transformation frequency of soybean by attenuating the expression level of GmPRs (GmPR1, GmPR4, GmPR5, and GmPR10) and suppression of the plant defense response. The transgene was successfully transmitted to the T1 generation. This study will be useful in genetic engineering of soybean.

CRISPR/Cas9-Mediated Deletion of Large Genomic Fragments in Soybean.

At present, the application of CRISPR/Cas9 in soybean (Glycine max (L.) Merr.) has been mainly focused on knocking out target genes, and most site-directed mutagenesis has occurred at single cleavage sites and resulted in short deletions and/or insertions. However, the use of multiple guide RNAs for complex genome editing, especially the deletion of large DNA fragments in soybean, has not been systematically explored. In this study, we employed CRISPR/Cas9 technology to specifically induce targeted deletions of DNA fragments in GmFT2a (Glyma16g26660) and GmFT5a (Glyma16g04830) in soybean using a dual-sgRNA/Cas9 design. We achieved a deletion frequency of 15.6% for target fragments ranging from 599 to 1618 bp in GmFT2a. We also achieved deletion frequencies of 12.1% for target fragments exceeding 4.5 kb in GmFT2a and 15.8% for target fragments ranging from 1069 to 1161 bp in GmFT5a. In addition, we demonstrated that these CRISPR/Cas9-induced large fragment deletions can be inherited. The T2 'transgene-free' homozygous ft2a mutants with a 1618 bp deletion exhibited the late-flowering phenotype. In this study, we developed an efficient system for deleting large fragments in soybean using CRISPR/Cas9; this system could benefit future research on gene function and improve agriculture via chromosome engineering or customized genetic breeding in soybean.

[Study on essential oil separation from Forsythia suspensa oil-bearing water body based on vapor permeation membrane separation technology].

To investigate the feasibility of vapor permeation membrane technology in separating essential oil from oil-water extract by taking the Forsythia suspensa as an example. The polydimethylsiloxane/polyvinylidene fluoride (PDMS/PVDF) composite flat membrane and a polyvinylidene fluoride (PVDF) flat membrane was collected as the membrane material respectively. Two kinds of membrane osmotic liquids were collected by self-made vapor permeation device. The yield of essential oil separated and enriched from two kinds of membrane materials was calculated, and the microscopic changes of membrane materials were analyzed and compared. Meanwhile, gas chromatography-mass spectrometry (GC-MS) was used to compare and analyze the differences in chemical compositions of essential oil between traditional steam distillation, PVDF membrane enriched method and PDMS/PVDF membrane enriched method. The results showed that the yield of essential oil enriched by PVDF membrane was significantly higher than that of PDMS/PVDF membrane, and the GC-MS spectrum showed that the content of main compositions was higher than that of PDMS/PVDF membrane; The GC-MS spectra showed that the components of essential oil enriched by PVDF membrane were basically the same as those obtained by traditional steam distillation. The above results showed that vapor permeation membrane separation technology shall be feasible for the separation of Forsythia essential oil-bearing water body, and PVDF membrane was more suitable for separation and enrichment of Forsythia essential oil than PDMS/PVDF membrane.