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Genome-wide scan for run of homozygosity (ROH) stretches, effective population size (N e ) and selection signatures can help to elucidate mechanisms of selection and pinpoint genomic regions linked with phenotypic traits. This study aimed to identify the genomic patterns of ROH, N e and selection signatures in two Iranian main sheep breeds including Afshari and Qezel (known as meat and dairy sheep, respectively) using 49,017 single nucleotide polymorphisms (SNPs) generated using the ovine 50K SNP BeadChips. Analysis of ROH in Iranian sheep breeds revealed the differences in the pattern of ROH length and burden in these breeds. Inbreeding estimated based on ROH stretches showed very low amount of inbreeding in these indigenous sheep breeds. The Qezel breed displayed a higher N e than Afshari breed. Furthermore, the potential selection was detected in genomic regions using three complementary approaches including F ST (fixation index), XP-EHH (cross-population extended haplotype homozygosity), and hapFLK (haplotype differentiation). Our results identified the genomic regions that were enriched with the genes associated with immune response (e.g., IL23A, STAT2 and DOCK5 ), milk traits (e.g., PCCA , ACAP3 , TTK and BTG3 ), energy metabolisms (e.g., GLS2 ), reproduction (e.g., ANGPT2 ), fecundity (e.g., BMP5 ), nervous system (e.g., DLG2 , PCDH9 , and FRMPD4 ), growth traits and muscle formation ( NPY , MYF5 and PPP1R12A ), and sweat gland development ( SCNN1D ). Some regions were also detected for the first time and overlapped with no genes suggesting novel loci associated with traits that differentiate these breeds. Overall, the finding of this study may shed light on the genomic regions linked to economically important traits in sheep as well as for developing the conservation and selection breeding programs.

Neuroticism is a relatively stable personality trait characterized by negative emotionality (for example, worry and guilt) 1 ; heritability estimated from twin studies ranges from 30 to 50% 2 , and SNP-based heritability ranges from 6 to 15% 3 – 6 . Increased neuroticism is associated with poorer mental and physical health 7 , 8 , translating to high economic burden 9 . Genome-wide association studies (GWAS) of neuroticism have identified up to 11 associated genetic loci 3 , 4 . Here we report 116 significant independent loci from a GWAS of neuroticism in 329,821 UK Biobank participants; 15 of these loci replicated at P  < 0.00045 in an unrelated cohort ( N  = 122,867). Genetic signals were enriched in neuronal genesis and differentiation pathways, and substantial genetic correlations were found between neuroticism and depressive symptoms ( r g  = 0.82, standard error (s.e.) = 0.03), major depressive disorder (MDD; r g  = 0.69, s.e. = 0.07) and subjective well-being ( r g  = –0.68, s.e. = 0.03) alongside other mental health traits. These discoveries significantly advance understanding of neuroticism and its association with MDD. Analysis of 329,000 individuals in the UK Biobank identifies 116 loci associated with neuroticism. Genes implicated are enriched in neuronal differentiation pathways, and genetic correlations between neuroticism and other mental health traits are elucidated.

Methane (CH4) emissions present a significant challenge to both environmental sustainability and energy efficiency in ruminants, including beef cattle that are born in dairy herds. Although numerous approaches, including alterations in feed and the use of additives, are under investigation to mitigate these emissions, the genetic selection of animals that produce lower levels of methane offers the potential for enduring and cumulative advantages. Transcriptome analysis represents a crucial advancement in elucidating the networks and mechanisms through which the ruminant genome influences methane emissions. In the present study, methane emissions were measured using a GreenFeed system in beef-on-dairy cattle (n = 11). High-throughput RNA sequencing was conducted on animal blood samples, followed by differential gene expression analysis using methane production (g/d) as a continuous trait. The analysis identified eleven differentially expressed genes (DEGs), including six downregulated (KIAA1211L, LOC107131224, OSCP1, IL12B, LOC618859, FREM1) and five upregulated (DSCAML1, OSBP2, ACAN, PRSS16, CD1B) genes (Padj < 0.05) with one gene exhibiting potential biomarker characteristics. Gene and cell enrichment, as well as pathway analysis, suggested that nervous, immune, and endocrine systems may be involved in ruminal methane production by beef-on-dairy cattle. These findings highlight the potential of transcriptomic biomarkers to guide genetic selection strategies, offering a sustainable pathway to reduce methane emissions and enhance both environmental and agricultural efficiency.

The anti-cancer vinblastine and vincristine alkaloids can only be naturally found in periwinkle ( Catharanthus roseus ). Both of these alkaloids' accumulations are known to be influenced by salicylic acid (SA). The transcriptome data to reveal the induction effect (s) of SA, however, seem restricted at this time. In this study, the de novo approach of transcriptome assembly was performed on the RNA-Sequencing (RNA-Seq) data in C. roseus . The outcome demonstrated that SA treatment boosted the expression of all the genes in the Terpenoid Indole Alkaloids (TIAs) pathway that produces the vinblastine and vincristine alkaloids. These outcomes supported the time-course measurements of vincristine alkaloid, the end product of the TIAs pathway, and demonstrated that SA spray had a positive impact on transcription and alkaloid synthesis. Additionally, the abundance of transcription factor families including bHLH, C3H, C2H2, MYB, MYB-related, AP2/ ERF, NAC, bZIP, and WRKY suggests a role for a variety of transcription families in response to the SA stimuli. Di-nucleotide and tri-nucleotide SSRs were the most prevalent SSR markers in microsatellite analyses, making up 39% and 34% of all SSR markers, respectively, out of the 77,192 total SSRs discovered.

Duchenne muscular dystrophy (DMD) manifests as a hereditary condition that diminishes muscular strength through the progressive degeneration of structural muscle tissue, which is brought about by deficiencies in the dystrophin protein required for the integrity of muscle cells. DMD is among four different types of dystrophinopathy disorders. Current studies have established that long non-coding RNAs (lncRNAs) play a significant role in determining the trajectory and overall prognosis of chronic musculoskeletal conditions. LncRNAs are different in terms of their lengths, production mechanisms, and operational modes, but they do not produce proteins, as their primary activity is the regulation of gene expression. This research synthesizes current literature on the role of lncRNAs in the regulation of myogenesis with a specific focus on certain lncRNAs leading to DMD increments or suppressing muscle biological functions. LncRNAs modulate skeletal myogenesis gene expression, yet pathological lncRNA function is linked to various muscular diseases. Some lncRNAs directly control genes or indirectly control miRNAs with positive or negative effects on muscle cells or the development of DMD. The research findings have significantly advanced our knowledge about the regulatory function of lncRNAs on muscle growth and regeneration processes and DMD diseases.

Vinblastine and vincristine are two important anti-cancer drugs that are synthesized by the Terpenoid Indole Alkaloids (TIAs) pathway in periwinkle ( Catharanthus roseus ). The major challenge in the pharmaceutical industry is the low production rate of these Alkaloids. TIA pathway is affected by elicitors, such as salicylic acid (SA). This study aimed to investigate the expression pattern of some key genes in TIAs pathway under SA treatment. Foliar application of SA (0.01 and 0.1 mM) was used and leaves samples were taken at 0, 12, 18, 24 and 48 h after the treatment. qRT-PCR was used to investigate the expression pattern of Chorismate mutase ( Cm ), tryptophan decarboxylase ( Tdc ), Geraniol-10-hydroxylase ( G10h ), Secologanin synthase ( Sls ), Strictosidine synthase ( Str ), Desacetoxyvindoline-4-hydroxylase ( D4h ) and Deacetylvindoline-4-O-acetyltransferase ( Dat ) genes, following the SA treatment. The results of this experiment showed that transcript levels of Tdc , G10h , Sls , Str , D4h and Dat genes were significantly up-regulated in both SA concentration treatments. Furthermore, the highest transcript levels of Dat was observed after 48 h of the SA treatments. qRT-PCR results suggests that SA induces transcription of major genes involved in Alkaloids biosynthesis in Catharanthus roseus. It can be concluded that up-regulation of Tdc , G10h , Sls, Str , D4h and Dat genes can result in a higher production rate of Vinblastine and vincristine Alkaloids.

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

Groundwater storage refers to the water stored in the pore spaces of underground aquifers, which has been increasingly affected by both climate change and anthropogenic activities in recent decades. Therefore, monitoring their changes and the factors that affect it is of great importance. Although the influence of natural factors on groundwater is well-recognized, the impact of human activities, despite being a major contributor to its change, has been less explored due to the challenges in measuring such effects. To address this gap, our study employed an integrated approach using remote sensing and the Google Earth Engine (GEE) cloud-free platform to analyze the effects of various anthropogenic factors such as built-up areas, cropland, and surface water on groundwater storage in the Lake Urmia Basin (LUB), Iran. Key anthropogenic variables and groundwater data were pre-processed and analyzed in GEE for the period from 2000 to 2022. The processes linking these variables to groundwater storage were considered. Built-up area expansion often increases groundwater extraction and reduces recharge due to impervious surfaces. Cropland growth raises irrigation demand, especially in semi-arid areas like the LUB, leading to higher groundwater use. In contrast, surface water bodies can supplement water supply or enhance recharge. The results were then exported to XLSTAT software2019, and statistical analysis was conducted using the Mann–Kendall (MK) non-parametric trend test on the variables to investigate their potential relationships with groundwater storage. In this study, groundwater storage refers to variations in groundwater storage anomalies, estimated using outputs from the Global Land Data Assimilation System (GLDAS) model. Specifically, these anomalies are derived as the residual component of the terrestrial water budget, after accounting for soil moisture, snow water equivalent, and canopy water storage. The results revealed a strong negative correlation between built-up areas and groundwater storage, with a correlation coefficient of −1.00. Similarly, a notable negative correlation was found between the cropland area and groundwater storage (correlation coefficient: −0.85). Conversely, surface water availability showed a strong positive correlation with groundwater storage, with a correlation coefficient of 0.87, highlighting the direct impact of surface water reduction on groundwater storage. Furthermore, our findings demonstrated a reduction of 168.21 mm (millimeters) in groundwater storage from 2003 to 2022. GLDAS represents storage components, including groundwater storage, in units of water depth (mm) over each grid cell, employing a unit-area, mass balance approach. Although storage is conceptually a volumetric quantity, expressing it as depth allows for spatial comparison and enables conversion to volume by multiplying by the corresponding surface area.

Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.

Background With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows. Methods Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes. Results Values are reported as mean ± SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7% ± 2.8%, P  = 0.032; HC: 54.5% ± 3.4%, P  = 0.048) compared to the Control (48.2% ± 3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81 ± 0.06 (Control) to 0.58 ± 0.05 for AP ( P  = 0.012) and 0.64 ± 0.05 for HC ( P  = 0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P  < 0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways ( P  = 0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P  = 0.0075) and methane emissions per unit of dry matter intake (CH 4 /DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P  = 0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P  = 0.035), alongside a significant reduction in methane intensity (CH 4 /DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments ( P  > 0.05). Conclusions In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H 2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.