Development Of Markers Research Articles

Development of immune-derived molecular markers for preeclampsia based on multiple machine learning algorithms

Preeclampsia (PE) is a major pregnancy-specific cardiovascular complication posing latent life-threatening risks to mothers and neonates. The contribution of immune dysregulation to PE is not fully understood, highlighting the need to explore molecular markers and their relationship with immune infiltration to potentially inform therapeutic strategies. We used bioinformatics tools to analyze gene expression data from the Gene Expression Omnibus (GEO) database using the GEOquery package in R. Differential expression analysis was performed using the DESeq2 and limma packages, followed by analysis of variance to identify immune-related differentially expressed genes (DEGs). Several machine learning algorithms, including least absolute shrinkage and selection operator (LASSO), bagged trees, and random forest (RF), were used to select immune-related signaling genes closely associated with the occurrence of PE. Our analysis identified 34 immune source–related DEGs. Using the identified PE- and immune source–related genes, we constructed a diagnostic forecasting model employing several ML algorithms. We identified six types of statistically significant immune cells in patients with PE and discovered a strong relationship between biomarkers and immune cells. Moreover, the immune-derived hub genes for PE exhibited strong binding capabilities with drugs, such as alitretinoin, tretinoin, and acitretin. This study presents a robust prediction model for PE that integrates multiple machine learning–derived immune-related biomarkers. Our results indicate that these biomarkers may outperform previously reported molecular signatures in predicting PE and provide insights into the mechanisms underlying immune dysregulation in PE. Further validation in larger cohorts could lead to their clinical application in PE prediction and treatment.

The role of oxidative stress and antioxidants in older individuals with osteoporotic hip fractures.

Osteoporosis is characteristically defined as a decrease in bone density and mass, accompanied by the deterioration of bone structure, which increases bone fragility and the risk of fractures. Osteoporosis frequently develops with age. In high-risk populations, oxidative damage is a common pathological condition. Oxidative stress plays a critical role in the development of osteoporosis and the formation of osteoporosis-related fractures. This study aimed to investigate the role of oxidative stress and antioxidants in bone tissue metabolism among elderly individuals with osteoporotic hip fractures, specifically intertrochanteric femur fractures and femoral neck fractures, who presented to our department. Based on power analysis, 24 patients over the age of 65 who presented with hip pain following a fall, were diagnosed with hip fractures (intertrochanteric or femoral neck fractures) on X-ray, were hospitalized in the Orthopedics and Traumatology Department, and underwent surgery were included in the study. A control group consisting of 24 healthy individuals matched for age and gender, with no history of fractures and meeting the same exclusion criteria, was also included. Levels of oxidative stress and antioxidant parameters, including total antioxidant status (TAS), total oxidant status (TOS), oxidative stress index (OSI), and paraoxonase-1 (PON-1), were measured in serum samples using spectrophotometric methods. The TAS (p=0.189) and OSI (p=0.110) levels in the patient group were significantly lower compared to the control group. Conversely, the TOS (p=0.002) and PON-1 (p=0.013) levels in the patient group were significantly higher than those in the control group. The data indicate that oxidative balance is disrupted due to increased oxidative load and the resulting antioxidant deficiency. A better understanding of the pathophysiology of the disease, along with the development of alternative treatment approaches and disease markers, will contribute to the literature.

Advancements in organic fluorescent materials: unveiling the potential of peripheral group modification in dithienyl-diketopyrrolopyrrole derivatives for one- and two-photon bioimaging.

The quest for novel organic fluorescent materials capable of two-photon absorption (2PA) has intensified in recent years due to their promising applications in biological imaging. Two-photon fluorescence microscopy (2PFM) offers high spatial-temporal resolution, reduced photodamage, and deeper tissue penetration compared to conventional techniques. However, the development of bright two-photon molecular markers remains a challenge, necessitating compounds with high fluorescence quantum yield and 2PA cross-section (σ2PA). Strategies such as increasing π-conjugation have shown promise but are hindered by synthesis complexities and limited biocompatibility. Alternatively, incorporating electron-donating (ED) or electron-withdrawing (EW) peripheral groups in a main structure has emerged as a viable approach, leading to significant enhancements in σ2PA. This study highlights the advantages and challenges of these strategies, emphasizing the importance of exploring new organic compounds and evaluating the efficacy of peripheral groups for advanced two-photon bioimaging applications.

Mitochondrial Dysfunction in Diabetic Periodontitis: Mechanisms and Therapeutic Potential.

Diabetic periodontitis is a common oral complication of diabetes characterized by progressive destruction of periodontal tissues. Recent evidence suggests that mitochondrial dysfunction plays a crucial role in the pathogenesis and progression of this condition. This review aims to systematically summarize the role and potential mechanisms of mitochondrial dysfunction in diabetic periodontitis. We first explore the relationship between diabetes and mitochondrial dysfunction, then analyze the specific manifestations of mitochondrial dysfunction in diabetic periodontitis, including morphological changes, energy metabolism disorders, increased oxidative stress, and enhanced apoptosis. We further delve into the connections between mitochondrial dysfunction and the pathogenic mechanisms of diabetic periodontitis, such as exacerbated inflammatory responses, decreased tissue repair capacity, and autophagy dysregulation. Finally, we discuss potential therapeutic targets based on mitochondrial function, including antioxidant strategies, mitochondria-targeted drugs, and autophagy regulators. We also propose future research directions, emphasizing the need for in-depth exploration of molecular mechanisms, development of new diagnostic markers and therapeutic strategies, and personalized treatment approaches. This review provides new insights into understanding the pathogenic mechanisms of diabetic periodontitis and offers a theoretical basis for developing targeted prevention and treatment strategies to improve oral health in diabetic patients.

Association between maternal usage of volatile organic compounds and West syndrome, the Japan Environment and Children’s study

Multiple etiologies of West syndrome have been reported; however, there are cases of unknown etiologies. Exposure to volatile organic compounds (VOCs) increases the risk of epilepsy; however, their effects on children remain unknown. This study aimed to investigate the association between maternal occupational usage of VOCs and West syndrome development in children. Using data from a cohort of 88,280 children, we extracted children born to mothers who had used VOCs during pregnancy. Based on an epilepsy diagnosis by the age of 2 years, the frequency of usage of VOCs was comparatively analyzed among the following groups: never diagnosed with epilepsy, West syndrome, and other epileptic syndromes. A total of 15, 154, and 88,111 children were categorized into the West syndrome, other epileptic syndrome, and never diagnosed with epilepsy groups, respectively. The odds ratio (OR) for West syndrome development increased with the frequency of permanent marker usage (one to three times a month: OR = 2.58, 95% confidence interval [CI] 0.75–8.90; one or more times a week: OR = 4.34, 95% CI 1.23–15.26). These results suggested an association between maternal occupational frequent usage of permanent marker and West syndrome development in children.

Development of Genomic SSR Markers for Assessing Genetic Diversity in Korean Native Fallopia multiflora

Fallopia multiflora, a perennial herb in the Polygonaceae family belonging to the genus Fallopia Adanson, is traditionally used as a Chinese herbal medicine. However, there is still confusion about the botanical origin of the species and the phylogenetic relationship between the cultivars and the wild relatives. To develop an efficient identification method, a molecular analysis was performed using SSR markers. The genetic diversity of the F. multiflora genetic resources has been assessed by using 10 locally collected accessions, including varieties and landraces. We screened 100 pairs of SSR primers and selected 71 successfully amplified SSR markers, in which one SSR was found to be a monomorphic marker. The results indicated that the number of alleles (NA) ranged from 2 to 10, with an average of 4.1 alleles. The major allele frequency (MAF) spanned from 0.20 to 0.90, the observed heterozygosity (HO) ranged from 0 to 0.80, and the polymorphic information content (PIC) varied between 0.16 and 0.86. Clustering analysis using an unweighted pair group mean algorithm (UPGMA) with all 70 SSR markers revealed three clusters among the F. multiflora accessions. Furthermore, seven minimum marker set combinations were identified and proved useful for variety identification. Therefore, these SSR markers could be valuable for various applications, including cultivar identification and assessing the purity of F. multiflora populations. Three genetic groups of F. multiflora should be considered as independent units for conservation and germplasm management of the species.

Single- and multi-locus genome-wide association study reveals genomic regions of thirteen yield-related traits in common wheat

Genetic dissection of yield-related traits can be used to improve wheat yield through molecular design breeding. In this study, we genotyped 245 wheat varieties and measured 13 yield-related plant height-, grain-, and spike-related traits, in seven environments, and identified 778 loci for these traits by genome-wide association study (GWAS) using single- and multi-locus models. Among these loci, nine were major, of which seven were novel, including Qph/lph.ahau-7A for plant height (PH) and leaf pillow height (LPH), Qngps/sps.ahau-1A for number of grains per spike (NGPS) and spikelet number per spike (SPS), Qsd.ahau-2B.1 and Qsd.ahau-5A.2 for spikelet density (SD), Qlph.ahau-7B.2 for LPH, Qgl.ahau-7B.3 for grain length (GL), and Qsl.ahau-3A.3 for spike length (SL). Through marker development, re-GWAS, gene annotation and cloning, and sequence variation, haplotype, and expression analyses, we confirmed two novel major loci and identified potential candidate genes, TraesCS7A02G118000 (named TaF-box-7A) and TraesCS1A02G190200 (named TaBSK2-1A) underlying Qph/lph.ahau-7A for PH-related traits and Qngps/sps.ahau-1A for spike-related traits. We also reported two favorable haplotypes, including TaF-box-Hap1 associated with low PH and LPH and TaBSK2-Hap3 associated with high NGPS and SPS. In summary, these findings can be applied to improve wheat yield and enrich our understanding of the complex genetic mechanisms of yield-related traits.

Silkless1 gene in maize: development and validation of the gene-based markers for breeding silkless baby corn.

The role of the silkless1 (sk1) gene in developing silkless baby corn, a distinctive trait in maize has been investigated. So far, no sk1 gene-specific marker has been available for accelerated development of silkless baby corn hybrids. We developed sk1 gene-based markers and validated them in backcross (BC) and F2 segregating generations, revealing a polymorphic marker corresponding to a silkless phenotype. Among all the developed markers, the MGU_sk1-1 marker (141bp size in sk1-mutant allele) validated its association with the silkless trait. The chi square (χ2) analysis revealed that the segregation of alleles Sk1Sk1 (219): Sk1sk1 (414): sk1sk1 (188) is as per the Mendelian ratio (1:2:1) in the F2 population. In 821 F2 plants, we found a 3:1 phenotypic ratio among the population with silked (633) and silkless (188) plants. We studied 349 BC plants and found a 1:1 phenotypic ratio between silked and silkless plants, as well as a genotypic ratio (1:1) between heterozygotes (Sk1sk1) and homozygous recessives (sk1sk1). Additionally, double mutants (sk1sk1/ts1ts1 and sk1sk1/ts2ts2) were identified using the sk1-based marker. This study is the first to show the practical use of sk1 gene in marker-assisted selection (MAS). This research also reports the development of novel genetic resources for innovative silkless baby corn breeding.

Complex auditory regularity processing across levels of consciousness in coma: Stage 1 Registered Report

Abstract A key question for the scientific study of consciousness is whether it is possible to identify specific features in brain activity that are uniquely linked to conscious experience. This question has important implications for the development of markers to detect covert consciousness in unresponsive patients. In this regard, many studies have focused on investigating the neural response to complex auditory regularities. One noteworthy example is the local global paradigm, which allows for the investigation of auditory regularity encoding at the ‘global’ level, based on the repetition of groups of sounds. The inference of global regularities is thought to depend on conscious access to such complex auditory stimuli as mostly shown in chronic stages of disorders of consciousness patients. However, whether global regularity encoding can identify covert consciousness along the consciousness spectrum including earlier stages of these disorders remains controversial. Here, we aim to fill this gap by investigating whether the inference of global auditory regularities can occur in acute coma, in the absence of consciousness, and how this may be modulated by the severity of the patients’ clinical condition and consciousness level measured using the Full Outline of UnResponsiveness (FOUR) score. We will acquire 63-channel continuous electroencephalography to measure the neural response to global auditory regularity in comatose patients (N=30) during the first day after cardiac arrest, when patients are unconscious, sedated and under normothermia, and during the second day (with reduced or absent sedation and body temperature control). We hypothesize that global regularity encoding will persist in the absence of consciousness independent of patient outcome, observed as above chance decoding of the neural response to global regularities using multivariate decoding analyses. We further hypothesize that decoding performance will positively correlate with the FOUR score, which indexes consciousness level, and typically improves between the first and second day after coma onset following cardiac arrest in patients with favourable outcome. In an exploratory analysis, we will also evaluate whether global regularity encoding may be influenced by the patients’ clinical management, specifically sedation, also shown to affect global deviance detection. Our results will shed light on the neurophysiological correlates of complex auditory regularity processing in unconscious patients and on the link to residual levels of consciousness during the underexplored state of coma upon the first days after cardiac arrest.

Development of sex-specific molecular markers for early sex identification in Hippophae gyantsensis based on whole-genome resequencing

Hippophae gyantsensis is a dioecious plant endemic to the Qinghai-Tibet Plateau and is significant for ecological restoration and sand stabilization. Its fruit is rich in bioactive compounds that offer economic potential. However, the inability to distinguish sexes before flowering and prolonged maturation hinder breeding and cultivation. We performed whole-genome resequencing on male and female plants, identified large insertion/deletion (InDel) variants, and developed two sex-specific primers (Higy_04 and Higy_06). These primers enable rapid, accurate PCR-based sex identification. All sex-specific sites were located on chromosome 2, suggesting its potential role as the sex chromosome. Additionally, we found a 1:1 sex ratio among offspring from the same mother plant, consistent with Mendelian inheritance, indicating that sex segregation is mainly genetically controlled. This work lays the foundation for developing molecular markers applicable across the entire genus Hippophae and contributes to understanding sex chromosome formation and adaptive evolution within the genus.

Whole slide image based prognosis prediction in rectal cancer using unsupervised artificial intelligence

BackgroundRectal cancer is a common cancer worldwide and lacks effective prognostic markers. The development of prognostic markers by computational pathology methods has attracted increasing attention. This paper aims to construct a prognostic signature from whole slide images for predicting progression-free survival (PFS) of rectal cancer through an unsupervised artificial intelligence algorithm.MethodsA total of 238 patients with rectal cancer from two datasets were collected for the development and validation of the prognostic signature. A tumor detection model was built by transfer learning. Then, on the basis of the tumor patches recognized by the tumor detection model, a convolutional autoencoder model was built for decoding the tumor patches into deep latent features. Next, on the basis of the deep latent features, the tumor patches were divided into different clusters. The cluster number and other hyperparameters were optimized by a nested cross-validation method. The percentage of each cluster from the patient’s tumor patches, which is hereafter called PCF, was calculated for prognostic signature construction. The prognostic signature was constructed by Cox proportional hazard regression with L2 regularization. Finally, bioinformatic analysis was performed to explore the underlying biological mechanisms of the PCFs.ResultsThe accuracy of the tumor detection model in distinguishing tumor patches from non-tumor patches achieved 99.3%. The optimal cluster number was determined to be 9. Therfore, 9 PCFs were calculated to construct the prognostic signature. The prognostic signature achieved a concordance index of 0.701 in the validation cohort. The Kaplan-Meier survival curves showed the prognostic signature had good risk stratification ability. Through the bioinformatic analysis, several PCF-associated genes were identified. These genes were enriched in various gene ontology terms.ConclusionThe developed prognostic signature can effectively predict PFS in patients with rectal cancer and exploration of the underlying biological mechanisms may help to promote its clinical translation.

Updates implemented in version 4 of the GlyCosmos Glycoscience Portal.

Glycosylation, characterized by its complexity and diversity, is a common system across all domains of life. The glycosylation of proteins or lipids imparts them with structural and functional roles, ranging from development to infectious or Mendelian disease. The high-throughput-based omics data has revealed that glycans are involved in important cellular processes. Comprehensive knowledge of glycosylation has contributed not only to the fundamental concepts in glycoscience but also to its applications, including the development of molecular markers for diagnosis and therapeutic tools for treating diseases. The GlyCosmos Glycoscience Portal (GlyCosmos) has undergone significant updates to better support the scientific community in studying glycosylation-related phenomena. Key enhancements include the integration of expanded datasets linking glycans to other omics fields, improved tools for glycan structure prediction and analysis, and upgraded visualization capabilities to streamline data interpretation. A strengthened focus on data standardization has also been introduced, fostering interoperability between glycoscience resources and external databases. Since its release in 2019, the portal has seen a fivefold increase in user engagement, reflecting its growing relevance. These recent advancements aim to provide researchers with a more comprehensive and user-friendly platform, enabling deeper insights into glycan roles in cellular processes and disease mechanisms. GlyCosmos will continue to evolve, prioritizing community needs and advancing the integration of glycoscience with broader biological and biomedical research.

The complexity of kodo millet: genomic analysis and implications in crop improvement.

This article explores possible future initiatives, such as the development of targeted breeding and integrated omics approach to boost kodo millet production, nutritional value, and environmental adaptation. Kodo millet is grouped under the genus Paspalum and family Gramineae. It is a tropical African crop that was initially domesticated in India approximately 3000years ago. It is predominantly cultivated in India as well as in various south-east Asian countries. Recent years have witnessed a resurgence of interest in kodo millet breeding, particularly owing to its outstanding nutritional profile. Kodo millet's ability to adapt to different marginal environments makes it promising to be grown as a part of sustainable agriculture. Availability of a plethora of diverse genetic resources in kodo millet has been instrumental in development of various improved cultivars through conventional breeding. Additionally, functional genomics has been instrumental in decoding the complex genetic architecture of kodo millet, thus enabling identification of key genes associated with drought tolerance, disease resistance, and improved nutritional profiling. Additionally, transcriptomics has deepened the insights into gene expression pattern in response to various stresses, offering valuable information for developing resistant genotypes. The expressed sequence tags (ESTs) available will surely benefit the scientists working on molecular breeding of millets through development and use of SSRs and SNPs markers under the marker assisted selection (MAS) scheme. This article examines potential directions for future research, including the advancement of genomics and targeted breeding approaches for holistic development of the kodo millet.

Single-Cell Multiomics Reveals TCR Clonotype-Specific Phenotype and Stemness Heterogeneity of T-ALL Cells.

T-cell acute lymphoblastic leukaemia (T-ALL) is a heterogeneous malignant disease with high relapse and mortality rates. To characterise the multiomics features of T-ALL, we conducted integrative analyses using single-cell RNA, TCR and chromatin accessibility sequencing on pre- and post-treatment peripheral blood and bone marrow samples of the same patients. We found that there is transcriptional rewiring of gene regulatory networks in T-ALL cells. Some transcription factors, such as TCF3 and KLF3, showed differences in activity and expression levels between T-ALL and normal T cells and were associated with the prognosis of T-ALL patients. Furthermore, we identified multiple malignant TCR clonotypes among the T-ALL cells, where the clonotypes consisted of distinct combinations of the same TCR α and β chain per patient. The T-ALL cells displayed clonotype-specific immature thymocyte cellular characteristics and response to chemotherapy. Remarkably, T-ALL cells with an orphan TCRβ chain displayed the strongest stemness and resistance to chemotherapy. Our study provided transcriptome and epigenome characterisation of T-ALL cells categorised by TCR clonotypes, which may be helpful for the development of novel predictive markers to evaluate treatment effectiveness for T-ALL.

Mining of Candidate Genes and Developing Molecular Markers Associated with Pokkah Boeng Resistance in Sugarcane (Saccharum spp.).

Sugarcane Pokkah Boeng (PB), a fungal disease caused by Fusarium spp., poses a significant threat to sugar industries globally. Breeding sugarcane varieties resistant to PB has become a priority, and the mining of PB resistance genes and the development of molecular markers provide a solid foundation for this purpose. This work comprehensively analyzes the genetic components of sugarcane's resistance to PB using transcriptome sequencing. A segregating population was created by crossing the susceptible parent ROC25 with the resistant parent Yunzhe89-7, which is a traditional cultivar known for its PB resistance. Transcriptome analysis uncovered many differentially expressed genes (DEGs) associated with PB resistance. Utilizing weighted gene co-expression network analysis (WGCNA), we identified gene modules closely related to disease phenotypes. We annotated their functions with bioinformatics tools, particularly focusing on genes enriched in the plant immune response's MAPK signaling pathway and ABC transporter synthesis pathways. In addition, by integrating whole-genome resequencing data of parental lines and transcriptome data of progeny, we identified a series of putative molecular markers that potentially effectively differentiate between highly resistant and susceptible materials. Our study provides crucial genetic resources and molecular methodologies that are essential for the advancement of sugarcane varieties with improved resistance to PB. These innovations are expected to accelerate the breeding process greatly.

Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean.

Seed protein content is a critical trait in soybean breeding, as it provides a primary source of high-quality protein for both human consumption and animal feed. This study aimed to enhance molecular marker-assisted selection for high-protein soybean varieties by developing Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers targeted at loci associated with seed protein content. Nineteen markers with high genotyping efficacy were identified through screening. Utilizing SN76 (a high-protein line) as the male parent and SN49 and DS1 (both low-protein lines) as female parents, 484 F6 generation individuals from these hybrid combinations were selected to validate the predictive accuracy of the 19 KASP markers. Notably, KASP-Pro-1, KASP-Pro-2, and KASP-Pro-3 effectively distinguished genotypes associated with high and low protein content, with prediction accuracies of 68.4%, 75.0%, and 83.3%, respectively. These results underscore the reliability and practical utility of the selected molecular markers, which are located within the genes Glyma.03G219900, Glyma.14G119000, and Glyma.17G074400, respectively. Haplotype analysis and gene pyramiding indicate that these three genes may influence seed protein content. Consequently, these KASP markers can be effectively integrated into genetic and genomic research on soybean seed protein content as well as into marker-assisted breeding.

Fine Mapping of Bush Gene and Development of Molecular Marker for Bush Type in Pumpkin (Cucurbita maxima Duch.)

Fine Mapping of Bush Gene and Development of Molecular Marker for Bush Type in Pumpkin (Cucurbita maxima Duch.)

Fine-Mapping of Tomato male sterile-24 Locus and Marker Development for ms-24 and Its Alleles, ms-10, ms-35, and ms-36

Male sterility is an essential trait for minimizing costs and ensuring seed purity in the production of tomato hybrid seeds. However, its application in commercial breeding faces challenges such as instability, low stigma exsertion rates, and the lack of molecular markers to facilitate the efficient backcrossing of male sterile loci into elite tomato lines. This study characterized the male sterile-24 (ms-24) mutant, which demonstrated exserted stigmas and complete male sterility. Our histological examination revealed that ms-24 anthers displayed dysfunctional development of the tetrads and tapetum. The ms-24 locus was finely mapped to a 149 kb interval containing 22 putative genes. Among these, Solyc02g079810, also known as MS-10, encodes a basic helix–loop–helix (bHLH) transcription factor essential for tapetum and pollen development. A sequencing analysis revealed an approximately 4.9 kb retrotransposon insertion in the first exon of the MS-10 gene in ms-24. Allelism tests confirmed that ms-24 was allelic to ms-10, which is also allelic to ms-35 and ms-36. The same retrotransposon insertion was also identified in the ms-10 mutant, and a similar insertion of retrotransposon was detected in the second exon of the MS-10 gene in the ms-36 mutant. Based on these retrotransposon sequences, codominant insertion–deletion (InDel) markers, MS-24I and MS-35I, were developed for the precise identification of the ms-24, ms-10, ms-35, and ms-36 alleles. These findings establish a foundational basis for subsequent investigations into the molecular mechanisms underlying male sterility and enhance the selection process of male sterile lines in tomato hybrid breeding programs.

Microsatellite markers development and molecular fingerprinting of cashew cultivars.

Cashew (Anacardium occidentale L.) is a widely cultivated tree with great economic significance. In cashew, several elite cultivars have been developed for commercial cultivation, which form the underpinning for the cashew-based industries and the several billion-dollar world trade. However, frequently the genetic purity of the planting material is not maintained, resulting in great economic losses. Therefore, there is a need to develop a reliable method for the identification of cultivars to avoid economic losses to the cultivators and the protection of cultivars by the breeders. In this study, 35 new microsatellite/simple sequence repeat (SSR) markers were developed, and a set of 20 highly polymorphic and reproducible markers were used for DNA fingerprinting and genetic diversity analysis in 32 cashew cultivars. The polymorphic information content (PIC) of newly developed markers varied from 0.19 to 0.67, with an average of 0.44. The probability of identifying any two genotypes with identical fingerprints using the 20 SSR markers used for fingerprinting here in cashew cultivars was less than 2.8 × 10-11. Of the set of 20 markers, eight were sufficient for uniquely fingerprinting all the cultivars. Genetic diversity analysis by the neighbor-joining (NJ) method grouped 32 cultivars into three main clusters, and the grouping had no relationship to the geographic regions or the pedigree. The findings of this study are useful for the conservation and protection of cultivars under the PVP Act for ensuring the trading of quality planting material and are also useful for cashew breeding programs.

Development of Functional Molecular Markers for Viviparous Germination Resistance in Rice

Rice (Oryza sativa) plays a pivotal role in global food security. Understanding the genetics of rice cultivation is crucial, particularly for traits such as viviparous germination, which significantly influences germination and yield. Our research aimed to elucidate the genetic and molecular mechanisms by which the Sdr4 gene influences viviparous germination and to develop novel molecular markers for this gene to enhance breeding strategies against viviparous germination. In all, 683 rice cultivars and 100 F2 plants were used for viviparous germination and genetic analysis using KASP (Kompetitive Allele-Specific PCR) and agarose gel-based markers related to viviparous germination tolerance. We developed and used a polymorphic agarose gel-based marker and a KASP marker targeting the Sdr4 gene. A genetic analysis of field-grown rice cultivars and the F2 population revealed that the two markers on Sdr4 were functional for the genomic selection of SNPs and InDels related to dormancy. The Pearson correlation coefficient (r = 0.74, p-value = 3.31 × 10−8) between the Sdr4-IND KASP marker genotype and viviparous germination rate demonstrated a significant positive correlation, supporting the marker’s utility for selecting rice varieties with diminished viviparous germination. This insight serves as a critical theoretical foundation for breeding strategies for developing early-maturing rice varieties with enhanced resistance to viviparous germination, addressing pivotal challenges in rice cultivation, and ensuring food security.