Search Results (158)

Breeding programs often overlook the use of root traits. Therefore, we investigated the relevance of sorghum root traits in explaining its adaptation to combined drought and heat stress (CDHS). Six (i.e., three pre-release lines + three checks) sorghum genotypes were established at two low-altitude (i.e., <600 masl) locations with a long-term history of averagely very high temperatures in the beginning of the summer season, under two management (i.e., CDHS and well-watered (WW)) regimes. At each location, the genotypes were laid out in the field using a randomized complete block design (RCBD) replicated two times. Root trait data, namely root diameter (RD), number of roots (NR), number of root tips (NRT), total root length (TRL), root depth (RDP), root width (RW), width–depth ratio (WDR), root network area (RNA), root solidity (RS), lower root area (LRA), root perimeter (RP), root volume (RV), surface area (SA), root holes (RH) and root angle (RA) were gathered using the RhizoVision Explorer software during the pre- and post-flowering stage of growth. RSA traits differentially showed significant (p < 0.05) correlations with grain yield (GY) at pre- and post-flowering growth stages and under CDHS and WW conditions also revealing genotypic variation estimates exceeding 50% for all the traits. Regression models varied between pre-flowering (p = 0.013, R² = 47.15%, R² Predicted = 29.32%) and post-flowering (p = 0.000, R² = 85.64%, R² Predicted = 73.30%) growth stages, indicating post-flowering as the optimal stage to relate root traits to yield performance. RD contributed most to the regression model at post-flowering, explaining 51.79% of the 85.64% total variation. The Smith–Hazel index identified ICSV111IN and ASAREACA12-3-1 as superior pre-release lines, suitable for commercialization as new varieties. The study demonstrated that root traits (in particular, RD, RW, and RP) are linked to crop performance under CDHS conditions and should be incorporated in breeding programs. This approach may accelerate genetic gains not only in sorghum breeding programs, but for other crops, while offering a nature-based breeding strategy for stress adaptation in crops. Full article

The mismatch between the rapid expansion of breeding scale and outdated techniques has hindered the development of the sea cucumber (A. japonicus) industry. Our previous work revealed that ecological seedling breeding can produce red-colored A. japonicus, a phenotype not observed in traditional artificial breeding, where individuals are typically green. To investigate the molecular and genetic basis of this novel red coloration, we compared the growth conditions of red sea cucumbers and green sea cucumbers, as well as the differences in the pigment composition, gene expression and metabolites of their body walls. Red individuals showed higher body length and weight, and elevated levels of astaxanthin, lutein, canthaxanthin, and β-carotene in the body wall. Transcriptomic and metabolomic analyses identified differentially expressed genes and metabolites associated with pigmentation. In particular, FMO2 and WDR18, involved in the cytochrome P450 drug metabolism pathway, were significantly upregulated in red individuals and are known to play roles in pigment biosynthesis and light signal perception. Key metabolites such as astaxanthin and fucoxanthin were implicated in body color formation. Moreover, genes in the arachidonic acid metabolism pathway were highly expressed, suggesting that dietary factors may contribute to pigment synthesis and accumulation. These findings provide novel insights into the mechanisms underlying body color variation in A. japonicus and offer potential for improved breeding strategies. Full article

Floral pigmentation contributes directly to reproductive strategies and fitness by shaping pollinator behaviour, and its regulation therefore represents a critical aspect of flower development. Additionally, it is a major determinant of aesthetic and economic value in the ornamental plant industry. This review explores the genetic, biochemical, and ecological bases of floral colour change, focusing on the biosynthesis and regulation of the three major classes of plant pigments: carotenoids, flavonoids (particularly anthocyanins), and betalains. These pigments, derived from primary metabolism through distinct biosynthetic pathways, define the spatial and temporal variability of floral colouration. We discuss the molecular mechanisms underlying flower colour change from opening to senescence, highlighting pigment biosynthesis and degradation, pH shifts, metal complexation, and co-pigmentation. Additionally, we address the regulatory networks, including transcription factors (MYB, bHLH, and WDR) and post-transcriptional control, that influence pigment production. Finally, we provide a comprehensive survey of angiosperm species exhibiting dynamic petal colour changes, emphasizing how these mechanisms are regulated. Full article

Sensenbrenner syndrome, or cranioectodermal dysplasia (CED), is a rare autosomal recessive ciliopathy characterized by craniofacial, skeletal, ectodermal, and renal abnormalities. Ocular involvement, though infrequent, can include retinal dystrophy with early-onset visual impairment. We report a case of a 2-year-old boy with classic clinical features of CED and significant ocular findings. Genetic testing revealed two novel compound heterozygous variants in the WDR19 gene—c.1778G>T and c.3536T>G—expanding the known mutational spectrum associated with this condition. Ophthalmologic evaluation demonstrated bilateral optic nerve hypoplasia, high hyperopia, and severely reduced ERG responses, consistent with global retinal dysfunction. Fundoscopy revealed optic disk pallor, vessel attenuation, and peripheral pigment changes. Multisystem findings included postaxial polydactyly, brachydactyly, short stature, hypotonia, and stage 2 chronic kidney disease. This case highlights the importance of early ophthalmologic screening in suspected CED and underscores the utility of ERG in detecting early retinal involvement. The identification of two previously undescribed WDR19 variants contributes to genotype–phenotype correlation in CED and emphasizes the need for ongoing documentation to guide diagnosis, management, and genetic counseling. Full article

Autism spectrum disorder (ASD) is a neurodevelopmental impairment that occurs due to mutations related to the formation of the nervous system, combined with the impact of various epigenetic and environmental factors. This necessitates the identification of the genetic variations involved in ASD pathogenesis. We performed whole exome sequencing (WES) in a cohort of 22 Bulgarian male and female individuals showing ASD features alongside segregation analyses of their families. A targeted panel of genes was chosen and analyzed for each case, based on a detailed examination of clinical data. Gene analyses revealed that specific variants concern key neurobiological processes involving neuronal architecture, development, and function. These variants occur in a number of genes, including SHANK3, DLG3, NALCN, and PACS2 which are critical for synaptic signaling imbalance, CEP120 and BBS5 for ciliopathies, SPTAN1 for spectrins structure, SPATA5, TRAK1, and VPS13B for neuronal organelles trafficking and integrity, TAF6, SMARCB1, DDX3X, MECP2, and SETD1A for gene expression, CDK13 for cell cycle control, ALDH5A1, DPYD, FH, and PDHX for mitochondrial function, and PQBP1, HUWE1, and WDR45 for neuron homeostasis. Novel single nucleotide variants in the SPATA5, CEP120, BBS5, SETD1A, TRAK1, VPS13B, and DDX3X genes have been identified and proposed for use in ASD diagnostics. Our data contribute to a better understanding of the complex neurobiological features of autism and are applicable in the diagnosis and development of personalized therapeutic approaches. Full article

Sheep have evolved remarkable phenotypic diversity through artificial and natural selection, with reproductive traits being pivotal for breeding economics. As a unique genetic resource, Pishan red sheep exhibit exceptional advantages, including perennial estrus, high fecundity, and stable hereditary characteristics, establishing them as an optimal model for investigating reproductive genetics. In this study, we performed whole-genome resequencing of Pishan red sheep, generating 9084.81 Gb of raw data and identifying 53,968,686 high-quality single-nucleotide polymorphisms (SNPs). Through selective sweep analysis, 92 genomic regions under selection were detected, containing 90 positional candidate genes significantly associated with growth, reproduction, and immune functions. Notably, we revealed BMPRIB, UNC5C, PDLIM5, GRID2, and HPGDS as core positional candidate genes influencing litter size, operating through the TGF-beta and Thyroid hormone signaling pathways. A genome-wide association study (GWAS) further identified 59 trait-related SNPs, including 39 loci linked to growth traits (affecting positional candidate genes such as PROM1, TAPT1, LDB2, and KIF16B) and 20 loci of positional candidate genes associated with reproductive traits (involving ASPA, RAP1GAP2, PHIP, and WDR82).These findings not only elucidate the molecular basis of superior reproductive performance in Pishan red sheep, but also provide functional markers for precision breeding. Full article

Congenital hypogonadotropic hypogonadism (CHH) is a rare and heterogeneous genetic disorder with variable penetrance caused by GnRH deficiency, leading to delayed puberty and infertility. In 50–60% of cases, CHH is associated with non-reproductive abnormalities, most commonly anosmia/hyposmia (Kallmann syndrome, KS). Over 60 genes have been implicated in CHH pathogenesis. We aimed to perform genetic screening in a cohort of 14 patients (10 males, 4 females; mean age 22 ± 7.72 years) with suspected or diagnosed HH/KS. Genetic analysis was conducted using next-generation sequencing (NGS) with a custom panel of 46 candidate genes. Variant interpretation followed ACMG standards and guidelines. Multiple tools were used to predict the structural effects of variants on tertiary protein structure, assessing their pathogenicity. Novel variants were functionally characterized by qRT-PCR on mRNA extracted from peripheral leukocytes. NGS identified nine rare variants and four novel variants in genes previously associated with normosmic isolated HH (nHH) and/or KS (FGFR1, PROK2, TAC3R, DCC, WDR11, IL17RD, DUSP6, KAL1, FGF8, IL17RD and DCC). The variant in TAC3R (p.Trp275Ter) was pathogenic; variants in ANOS1 (c.541+1G>A), IL17RD (c.1303_1304dup, p.Lys436ThrfsTer58), and TAC3R (p.Lys361Ter) were likely pathogenic. Nine variants were classified as variants of uncertain significance (VUS). Our study identified a possible genetic cause in 71% of the CHH/KS cohort, emphasizing the importance of genetic screening and functional characterization of genetic variants in patients with a phenotypically and genetically heterogeneous disorder like CHH. Full article

Background: As one of the most important poultry species worldwide, chickens provide substantial amounts of meat, eggs, and other products for human consumption. With continuous improvements in living standards, consumer demand for high-quality animal products is increasing, making it essential to understand the genetic basis of key traits such as egg production, meat quality, and disease resistance for targeted genetic improvement. Methods: In this study, a number of the candidate genes associated with important traits in chickens were screened by various comparative genomics analysis methods. To further clarify the relationship between these candidate genes and important traits in chickens, they were functionally annotated through the KOG, GO, and KEGG databases. Results: These candidate genes are mainly concentrated in the functional categories of transcription and signal transduction mechanisms and are involved in biological processes such as cyclic nucleotide biosynthesis and intracellular signaling, which involve signaling pathways such as ECM–receptor interactions and calcium signaling. Conclusions: Based on the annotation results from various databases, a functional search of the candidate genes and related literature reports, the following results were obtained: genes such as TBX22, LCORL, and GH were associated with chicken growth traits; genes such as A-FABP, H-FABP, and PRKAB2 were associated with chicken meat quality; genes such as IGF-1, SLC25A29, and WDR25 were associated with chicken reproductive traits; and genes such as C1QBP, VAV2 and IL12B were associated with chicken disease resistance traits. Overall, the findings of this study provide novel insights and candidate genes for genetic improvements in chickens, laying a foundation for future research and breeding strategies targeting key economic traits. Full article

Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim of this systematic review was to summarize genetic determinants of colonic diverticulosis. Methods: The PubMed^® database was searched for original studies in humans. The inclusion criteria were named genetic factor and confirmed diverticulosis. Patients with diverticulitis and diverticular diseases were excluded from this review. Results: Out of 137 publications, 10 articles met the inclusion criteria: six large association studies (GWAS) and four cross-sectional studies. The genes regulating ECM turnover, including TIMP1, MMP3, and MMP9, are involved in diverticulosis development. The TIMP1 (rs4898) T allele has been associated with increased susceptibility, potentially due to its role in ECM remodeling. Similarly, MMP3 (rs3025058) and MMP9 (rs3918242) polymorphisms contribute to altered collagen degradation. The COL3A1 (rs3134646) variant coding modified collagen type III may promote diverticular formation. Other genes, such as ARHGAP15 (rs4662344, rs6736741), affect cytoskeletal dynamics. Identified in GWAS studies, gene candidates may be grouped into blood group and immune system-related genes (ABO, HLA-DQA1, HLA-H, OAS1, TNFSF13, FADD), extracellular matrix and connective tissue genes (COL6A1, COLQ, EFEMP1, ELN, HAS2, TIMP2), signaling and cell communication (BMPR1B, WNT4, RHOU, PHGR1, PCSK5), nervous system and neurodevelopment (BDNF, CACNB2, GPR158, SIRT1, SCAPER, TRPS1), metabolism and transporters (SLC25A28, SLC35F3, RBKS, PPP1R14A, PPP1R16B), lipids and cholesterol (LDAH, LYPLAL1, STARD13), transcription and gene regulation (ZBTB4, UBTF, TNRC6B), apoptosis (FADD, PIAS1), and poorly characterized genes (C1TNF7, ENSG00000224849, ENSG00000251283, LINC01082, DISP2, SNX24, THEM4, UBL4B, UNC50, WDR70, SREK1IP1). Conclusions: There are a number of gene variants that probably predispose to colonic diverticulosis. Detailed characterization of the multigene background of diverticulosis will enable appropriate therapeutic or preventive interventions in the future. Full article

The hydrodynamic processes in estuarine regions play a crucial role in the morphological and ecological stability of coastal zones. As a key hydrodynamic characteristic of bifurcated rivers, the water diversion ratio (WDR) influences flow distribution, sediment transport, and shoreline changes in estuaries. This study focuses on the lower Minjiang River and employs a MIKE 21-based two-dimensional hydrodynamic model to quantify the WDR variations between the South and North Ports on the scale of a tidal cycle during the wet season and to reveal the regulatory effects of diversion dyke length and angle. The results indicate that the WDR of the North Port exhibits significant variation with tidal stages. The WDR of the North Port increases with the length of the diversion dyke. The current 110 m-long dyke has little effect on regulating water flow between the North and South Ports, and its WDR remains unaffected by changes in angle. In contrast, a 450 m-long dyke is highly sensitive to angle variations. This study not only provides scientific support for channel regulation in the lower Minjiang River but also offers indirect insights into shoreline stability and ecological management under the combined influence of human activities and natural processes in estuarine environments. Full article

Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale. Methods: Here, we analyzed high-depth genomes of 210 sheep from 20 worldwide breeds to identify the pattern and distribution of genome-wide runs of homozygosity (ROH) and detect candidate selected genes in ROH islands for agronomic and phenotypic traits. Results: Leveraging whole-genome sequencing data, we found a large number of short ROH (e.g., <1.0 Mb) in all breeds and observed the overall higher values of ROH statistics and inbreeding coefficient in European breeds than in Asian breeds and Dorper sheep. We identified some well-known candidate genes (e.g., CAMK4, HOXA gene family, ALOX12, FGF11, and MTOR) and 40 novel genes (e.g., KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, and PAX1) that are functionally associated with fecundity, body size, and wool-related traits in sheep. Based on the candidate genes, we revealed different genetic bases for the fecundity traits of European and Asian sheep. Conclusions: This study improves the resolution of ROH detection and provides new insights into genomic inbreeding and trait architecture in sheep as well as useful markers for future breeding practice. Full article

In the past three years, the stereo matching method based on 3D CNNs has achieved surprising results and has received more and more attention. However, most stereo matching approaches aim to improve prediction accuracy by constructing and aggregating cost volumes through extensive 3D convolutions, which not only does not fully utilize the geometric information, but also overlooks the computational speed. Thus, achieving high-accuracy, high-efficiency stereo matching has become challenging. In this paper, we present a rapid and precise stereo matching network named CGW based on 3D CNNs, which simultaneously achieves real-time functioning, considerable accuracy, and a strong generalization capability. The network is divided into two parts. The first part constructs the geometric attention cube through a lightweight feature extraction network and a lightweight 3D regularization network. The second part filters the context features using the geometric attention cube to obtain the context geometric cube, and finally, the disparity is predicted and refined to obtain the final disparity. We adopted MobileNetV3 as an efficient backbone for feature extraction and designed 3D depthwise separable convolutions with residual structures to replace traditional 3D convolutions for constructing the cost volume and performing cost aggregation, aiming to reduce the model size and improve the computational speed. Additionally, we designed the context geometric attention (CGA) module and embedded it into the lightweight 3D regularization network, as well as designed the Warped Disparity Refinement (WDR) network to further improve the disparity prediction accuracy. CGA effectively guides cost aggregation by integrating rich contextual and geometric information, while also providing feedback for feature learning to guide more efficient context feature extraction. WDR constructs a warping cost volume using the obtained initial disparity, combined with image features, the initial disparity map, and reconstruction errors, to optimize the disparity. According to the initial disparity, it searches for the accurate disparity within a refined range. By narrowing the search range, WDR simplifies the task for the network to locate the correct disparity (residual), while simultaneously improving the computational efficiency. Experiments conducted on multiple benchmark datasets showed that, compared to other fast methods, CGW has advantages in both speed and accuracy and exhibits better generalization performance. Full article

This study presented a comprehensive analysis of the microbial ecology in water diversion rivers (WDRs) in the source area of the East Route of the South-to-North Water Diversion Project (ER-SNWDP) in China across various water periods. Proteobacteria, Chloroflexi, Acidobacteriota, and Bacteroidota were identified as the dominant microbial phyla in river sediment. During the wet period, microbial communities exhibited the highest richness, biodiversity, and the most intense antagonistic relationships compared to those in the dry and normal water periods. Generally, the microbial network predominantly existed in symbiotic models characterized by mutual benefit and symbiosis throughout all periods. During the dry period, the microbial co-occurrence network was found to be the most complex, with microbial OTUs showing the closest interconnections. The dominant mechanisms governing community diversity, succession, and biogeography were spatial turnover of species and stochastic processes. A more pronounced impact of stochastic processes on microbial community assemblages was observed during normal or wet periods than the dry period. Functional prediction of metabolic pathways indicated that the main ecological functions of microbial communities encompassed carbohydrate metabolism, amino acid metabolism, energy metabolism, etc. This study could provide essential scientific data for ecological regulation, ecological protection, and water resources management in WDRs. Full article

While the modulation of the excitatory and inhibitory neuronal transmission by the phytochemical flavonoid, myricetin (MYR), has been noted in the nervous system, the way in which MYR affects the excitability of nociceptive sensory neurons in vivo remains to be established. This study aimed to explore whether administering MYR intravenously, in acute doses, to rats, diminishes the excitability of SpVc wide-dynamic range (WDR) spinal trigeminal nucleus caudalis (SpVc) neurons in response to nociceptive and non-nociceptive mechanical stimulation in vivo. Recordings of extracellular single units were obtained from SpVc neurons when orofacial mechanical stimulation was applied to anesthetized rats. The average firing rate of SpVc WDR neurons, to both non-noxious and noxious mechanical stimuli, was significantly and dose-dependently inhibited by MYR (1–5 mM, intravenously), and the maximum reversible inhibition of the discharge frequency, for both non-noxious and noxious mechanical stimuli, occurred within 5–10 min. The suppressive effects of MYR continued for about 20 min. These findings indicate that an acute, intravenous administration of MYR reduces the SpVc nociceptive transmission, likely through the inhibition of the CaV channels and by activating the Kv channels. Therefore, MYR might be utilized as a treatment for trigeminal nociceptive pain, without causing side effects. Full article

Garden dahlias (Dahlia pinnata) are popular for their rich flower color variations that have produced many typical bicolor cultivars. Previous studies on the anthocyanin biosynthetic pathway (ABP) observed that the miR156-SPL9 module contributes to the formation of white tips on dahlia petals by repressing the MYB-bHLH-WDR complex. In this study, we further detected the potential post-transcriptional regulation involved in the bicolor petal formation by the small RNA sequencing of red bases and white tips. Compared with red bases, 89 differentially expressed miRNAs and 6349 target genes were identified. And 78 up-regulated miRNAs with their 249 down-regulated target genes were involved in the formation process of white petal tips. The target genes of differentially expressed miRNAs significantly enriched in the ABPs and miRNAs of six conserved families (MIR 156, 164, 167, 169, 482 and 6114) targeted to four transcription factor families (ARF, HD-ZIP, SBP and NAC) were involved in the post-transcriptional gene silencing (PTGS) of the ABP. Transcription sequencing and quantitative reverse transcription PCR analysis demonstrated that the MIR167-ARF8 module and the MIR6114-ANL2 module were the candidate regulators of the inactive ABP in the white tips by depressing the transcription of multiple structure genes. The findings gave new insights into the post-transcriptional regulation of the ABP and would be valuable for further studies of the PTGS mechanisms of bicolor petal formation. Full article