Genetic Distance Research Articles

Cryopreservation of Fegra Fig (Ficus palmata Forssk.) and Genetic Fidelity of the Recovered Micropropagated Plants

Cryopreservation allows for the long-term storage of biological materials, ensuring their viability for future use and preserving biodiversity. This study aimed to develop an efficient protocol for the long-term in vitro conservation of fegra fig. In vitro precultured shoot tips of fegra fig with 0.3 M sucrose showed the highest regrowth percentage (100%) before plunging into liquid nitrogen. After plunging into liquid nitrogen, the regrowth percentage was 43.33%. Following cryopreservation, the recovered shoots were rooted and acclimatized to ex vitro conditions. The genetic fidelity of the acclimatized 8-week-old fegra fig plantlets after cryopreservation with their mother plant was tested using randomly amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR), and start codon targeted (SCoT) molecular markers. Genetic similarity between the stored plantlets with their mother plant was 100% ensuring uniformity and true-to-type regenerated plants following cryopreservation. This study presents, for the first time, an efficient protocol for the genetic conservation of fegra fig.

Elucidating genetic variability between randomly bred domestic cats and Persian domestic cats from different geographical locations using microsatellite markers.

The domestic cat (Felis catus) is a newly evolved species in the family Felidae that has developed some great features among mammals. It is critical to conserve these species and prevent inbreeding from reducing their genetic diversity by understanding their genetic relationships and applying the information to breeding management. The diverse population was an excellent choice for studying genetic diversity and inbreeding phenomena. To conduct this research, 128 individuals from 8 populations, including Azerbaijan, Persian, Ahar, Uermia, Tehran, Karaj, Turkish and Shop cat (both genders), were randomly selected from different geographical regions. We selected eight STR markers with different chromosomal locations based on polymorphism and observed allele numbers in the next step. DNA extraction was performed using tail hair root, PCR and electrophoresis, and gel staining was performed according to routine laboratory protocol. For statistical analysis, CONVERT versions POPGENE, ARLEQUIN GenAlEx and R script analysis. Remarkably, our results showed that 23 alleles were identified in 128 samples. The highest number of alleles belonged to the FCa096 locus (eight alleles) in the Persian population, followed by FCa045 (seven alleles) in the Persian and Ahar populations. Another new finding is that the lowest number of alleles belonged to the 35 and FCa77 locus (two alleles). In addition, pairwise differentiation between and within populations was examined using the genetic distance index. Overall, the results showed that the degree of differentiation within the population is high in the Turkish population compared to other population groups and lower in the Azerbaijan population. In addition, principal component discriminant analysis-based analysis based on the ADAGENET package shows the distribution of samples by geographical location. The results show that genetic mixing between populations is high. On this basis, we conclude that randomly bred domestic cats have a higher level of diversity than Persian domestic cats. This is an interesting topic for future work.

Caenorhabditis elegans as an Outstanding Model to Explore Flavonoids Under Stress Conditions

Abstract: Plants produce promising chemicals called secondary metabolites in response to stress, which protect against oxidative damage in both plants and humans. Reactive oxygen species (ROS) levels combined with an imbalance in the antioxidant responses can trigger oxidative stress that is related to many conditions such as Alzheimer's disease, diabetes, and cancer. One way to counteract or avoid the stress excess is by flavonoid administration, a class of plant metabolites with a consistent antioxidant action and the ability to inactivate the free radical excess. The mechanisms, as well as the benefits and toxicity of antioxidant products, can be tested in alternative animal models. The mechanisms, as well as the benefits and toxicity of antioxidant products, can be tested in alternative animal models. In this review, we explored how Caenorhabditis elegans, a nematode with high genetic similarity to human genes and the antioxidant response pathway conserved, can be considered an attractive model organism for testing flavonoid compounds. Here, we emphasize the crucial results regarding C. elegans and the flavonoid quercetin, focusing on oxidative stress and aging investigations. Also, this review highlights the quercetin benefits in C. elegans lifespan, healthspan, neurodegeneration, and impacts on insulin/IGF-1 signaling (IIS).

Zebrafish Experimental Animal Models for AD: A Comprehensive Review.

AD disease (AD) is a multifaceted and intricate neurodegenerative disorder characterized by intracellular neurofibrillary tangle (NFT) formation and the excessive production and deposition of Aβ senile plaques. While transgenic AD models have been found instrumental in unravelling AD pathogenesis, they involve cost and time constraints during the preclinical phase. Zebrafish, owing to their simplicity, well-defined behavioural patterns, and relevance to neurodegenerative research, have emerged as a promising complementary model. Zebrafish possess glutaminergic and cholinergic pathways implicated in learning and memory, actively contributing to our understanding of neural transmission processes. This review sheds light on the molecular mechanisms by which various neurotoxic agents, including okadaic acid (OKA), cigarette smoke extract, metals, and transgenic zebrafish models with genetic similarities to AD patients, induce cognitive impairments and neuronal degeneration in mammalian systems. These insights may facilitate the identification of effective neurotoxic agents for replicating AD pathogenesis in the zebrafish brain. In this comprehensive review, the pivotal role of zebrafish models in advancing our comprehension of AD is emphasized. These models hold immense potential for shaping future research directions and clinical interventions, ultimately contributing to the development of novel AD therapies.

Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing.

Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination ofenvironment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.

HIV-1 transmission clusters and drug resistance in men who have sex with men in Portugal

Abstract Introduction In 2022, 45.8% of diagnoses in the EU/EEA with known route of transmission were in Men who have Sex with Men (MSM). We aim to characterise HIV transmission clusters and transmission of drug resistance (TDR), as well as its determinants, using integrated sociodemographic, behavioural, clinical, and viral genomic data of MSMs newly diagnosed in Portugal between 2014 and 2019. Methods This study included data from 340 MSM who were diagnosed with HIV-1 infection. These individuals were newly diagnosed at 17 hospitals in Portugal between September 2014 and December 2019. Phylogenies were constructed and transmission clusters were identified with branch support ≥ 90% and 1.5% genetic distance. Logistic regression models were computed to examine the factors associated with clusters of transmission and with the presence of TDR. Results We identified 38 transmission clusters with 104 MSM, which included 26.6% of the total 305 MSM from our database used for cluster analysis. The overall prevalence of TDR was 8.2%. Only subtype C was significantly associated with TDR. 10.5% of the clusters had at least 1 drug resistance mutation (K103N, L90M or N88S). There was no significant difference in the prevalence of TDR between MSM inside and outside clusters. 50% of the clusters were composed of portuguese native MSM only, whereas 16% had exclusively migrant MSMs. No significant difference was found in the proportion of portuguese and migrant MSM inside and outside clusters. Factors associated with HIV-1 transmission clusters were age at diagnosis, district of residence, unprotected anal or vaginal sex with a woman, HIV testing frequency, presenter status and subtype. 87% of men engaged in sexual activity only with other men, while 13% with both men and women. Conclusions Specific subgroups of MSM are contributing to HIV dissemination in Portugal. Direct and precise prevention measures based on molecular epidemiology should be developed. Key messages • Specific subgroups of MSM are contributing to HIV dissemination in Portugal. • Direct and precise prevention measures based on molecular epidemiology should be developed.

DNA barcode identification of a tropical liver fluke (Fasciola gigantica) in cattle from Oyo, southwestern Nigeria

BackgroundFascioliasis is a major parasite illness that affects ruminants, both domesticated and free, and has an impact on public health and animals’ productivity. The genetic diversity of Fasciola species in cattle from Oyo, Oyo State, Nigeria is yet not well understood. In this study, the genetic diversity of Fasciola gigantica in slaughtered cattle in Oyo was examined using a molecular-based approach targeting the mitochondrial cytochrome C oxidase subunit I (COI) gene region.ResultsOne hundred flukes were gathered from slaughtered cattle, and their COI gene sequences were analyzed using maximum likelihood methods. The results of phylogenetic analysis showed genetic similarities between Nigerian F. gigantica and isolates from Algeria, Egypt, Iran, Sudan, China, Japan and Nigeria. The predominant DNA substitution was the A to T transversion, while the least common substitution was the G to A transition.ConclusionOur results show how useful the COI gene region is for examining intraspecific differences between F. gigantica isolates. The genetic similarity observed among the sampled F. gigantica populations suggests the value of mitochondrial DNA sequences as a marker for the accurate identification and characterization of Fasciola species across different ruminants.

Genetic spatialization in Montana cattle breed.

Brazil is among the world's top beef producers and exporters, and the Montana breed of livestock has gained popularity due to its exceptional meat quality and ability to adapt to the tropical climate. This differentiates it from other breeds, such as the Zebu and Taurine. A methodology that mapped sixteen farms across five Brazilian states was adopted to investigate the link between SNP genetic data and animal collection location. The data was georeferenced using the Geographic Information System and the ArcGIS 10.3 software, considering a geographic coordinate system and the WGS 84 datum. The Alleles in Space (AIS) software was used to study the relationship between the SNP genetic data and the animal collection location. Various analyses were conducted, including the Mantel correlation, genetic barrier identification, and spatial autocorrelation. The results suggest that there is a correlation between genetic and geographical distances, supporting the idea that geographical distance can affect genetic diversity. This information is vital to understand the genetic structure of populations concerning geographical space and is crucial for optimizing Brazilian agricultural production.

Artificial Intelligence in Medical Diagnostics

Artificial intelligence (AI) is an essential tool in the medical sector that contributes significantly to medical imaging, medical pathology, histology, genomic study, predictive analysis, etc. It is being increasingly used not only in breast and lung cancer diagnosis and screening, and genetic disease identification but also in personalized decision-making during the treatment of these diseases. The quality and availability of unbiased data is a key challenge. Algorithmic bias and interpretability are significant concerns as well. Improving the use of AI in medical diagnostics could be achieved through continuous monitoring, access to highly accurate datasets, and timely intervention by healthcare professionals. J Bangladesh Coll Phys Surg 2024; 42: 379-382

Molecular transmission clusters in newly HIV-1 diagnosed migrants in Portugal from 2014 to 2019

Abstract Background Portugal has an important HIV burden with a total of 804 diagnosed cases in 2022. Migrants remain a significant source of HIV infections, with 45% of newly reported cases. We aimed to evaluate the characteristics of HIV-1 molecular transmission clusters (MTCs) among migrants followed in Portugal, diagnosed between 2014 and 2019. Methods 265 migrants, newly HIV-1 diagnosed were included in the BESTHOPE project with clinical, socio-behavioral and genomic data. Pol nucleotide-based phylogenetic analyses were used to infer HIV-1 MTC. Those were constructed using ClusterPickerGUI_1.2.3 considering SH-aLRT higher than 90 of branch support and a pairwise genetic distance of ≤ 4.5. Logistic regression analyses were used to examine the relationship between the sociodemographic and clinical data associated with HIV-1 clustering. Results 66.8% of the migrants included in the study were males with a median age at diagnosis of 36.0 years old (IQR:29-45). Most migrants were from African countries (50.6%) followed by Brazil (39.6%). Sixty-eight (33%) of the migrants were included in clusters. Being in cluster was significantly associated with region of origin, with individuals from South America more likely to be in cluster (OR = 14.85, 95%CI:1.52-144.79), compared to individuals from Africa; with transmission route, with men who have sex with men (MSM) more likely to be in cluster (OR = 23.52, 95%CI:2.35-235.10), compared to the heterosexuals and with subtype, with subtypes B less likely to be in cluster (OR = 0,017, 95%CI:0,001-0,254) compared with subtype non-B. Conclusions Migrants HIV transmission clusters in Portugal are associated with specific health determinants, such as region of origin, transmission route and subtype. Targeted prevention health strategies are needed to mitigate transmission of HIV within this population. Funded by FCT to GHTM - UID/04413/2020 and LA-REAL - LA/P/0117/2020; BESTHOPE (HIVERA:249697); and MARVEL (PTDC/SAU-PUB/4018/2021). Key messages • HIV transmission clusters in migrant are associated with their region of origin, transmission route and subtype. • Targeted prevention health strategies are needed for the migrant population.

Virulence perspective genomic research unlocks the secrets of Rhizoctonia solani associated with banded sheath blight in Barnyard Millet (Echinochloa frumentacea)

IntroductionBanded sheath blight (Bsb) disease, caused by Rhizoctonia solani, is an emerging problem in barnyard millet cultivation. One of the significant goals of pathogenomic research is to identify genes responsible for pathogenicity in the fungus.MethodsA virulence profiling-based approach was employed and six R. solani isolates were collected from various ecological zones of India. The morphological parameters and virulence of all of the six R. solani isolates were investigated. The most virulent strain was designated as RAP2 and its genome has been sequenced, assembled, and annotated.ResultsThe RAP2 genome is 43.63 megabases in size and comprises 10.95% repetitive DNA, within which 46% are retroelements, 8% are DNA transposons, and 46% are unidentified DNA. The Gene Ontology (GO) annotation of RAP2 proteins revealed that “phosphorylation”, “membrane”, and “ATP binding” have the highest gene enrichment in the “biological process”, “cellular component” and “molecular function” domains, respectively. The genome comprises a majority of secretory proteins in the pectin lyase fold/virulence factor superfamily, which break down plant cell wall polymers to extract saccharides. The RAP2 genome is comparable to R. solani, which infects maize and rice, but it diverges further from soybean in terms of nucleotide-level genetic similarity. Orthologous clustering of RAP2 protein sequences with R. solani infecting maize, rice, and soybean yields 5606 proteins shared across all genomes. GO analysis of 25 proteins specific to the RAP2 genome found enrichment in the ethylene response, which can cause spore germination and infection in host plants.DiscussionInterestingly, a 28-bp deletion in the RAP2 strain’s cutinase domain was discovered in the cutinase protein, which might be important in the infection process, perhaps rendering the enzyme inactive or allowing the pathogen to infect barnyard millet while avoiding host defense. This study sheds light on the genetic makeup of R. solani, allowing researchers to discover critical genes related with pathogenicity as well as potential targets for fungicide development.

Exome sequencing identifies a novel FBN1 variant in a Chinese family with Marfan syndrome that includes aberrant right subclavian artery

Abstract Background Marfan syndrome (MFS) is an inherited autosomal dominant disorder that affects connective tissue with an incidence of about 1 in 5,000 to 10,000 people. Ninety percent of MFS is caused by mutations in the fibrillin-1 (fbn1) gene. We recruited a family with MFS phenotype in South China and identified a novel variant in fbn1 by whole exome sequencing (WES). The zebrafish share high genetic similarity to humans. This study aimed to generate this novel mutation in the fbn1 gene of zebrafish using the CRISPR/Cas9 technology and researched whether this variant is pathogenic. Methods A three-generation consanguineous family was recruited in this study, which was visited and interviewed for the clinical data and family history. Peripheral blood samples were collected from family members for DNA isolation and WES. The 3D structure of the protein was predicted by Alphafold. CRISPR/Cas9 was applied to generate an fbn1 nonsense mutation (fbn1+/−) in zebrafish. Morphological abnormalities were assessed in F2 fbn1+/− zebrafish by comparing with the wild-type (WT) controls at different development stages. Results Our study recruited a family with MFS phenotype in South China and identified a novel variant [NM_000138.5; c.7764C&amp;gt;G: p.(Y2588*)] in fbn1. Through Sanger sequencing, we found that family members Ⅲ-1 (son) and Ⅲ-2 (daughter) had the fbn1 variant segregated with MFS in the family. The p.Y2588* mutation resulted in the absence of 283 amino acids, thereby leading to the deficiency of 17 β-folded structures, 4 α-helix structures, and various loop structures. Compared with WT zebrafish, F2 fbn1+/− zebrafish exhibited aortic arches bleeding, abnormal angiogenesis, decreased cardiac volume, cardiac function defects, curly tail, and cartilage malformations. Conclusion A novel variant [NM_000138.5; c.7764C&amp;gt;G: p.(Y2588*)] was identified in fbn1 gene, which has not been reported in previous literature. The variant caused loss of function through premature protein truncation or nonsense-mediated mRNA decay. In zebrafish, we identified functional evidence of the detected nonsense mutation, which aligns with the clinical significance, suggesting a pathogenic variant of fbn1. Zebrafish as a novel, efficient tool to allow for the quick classification of unknown variants in fbn1 and improve the clinical diagnosis and treatment of MFS. It has brought the implementation of personal and precision medicine in the clinic within reach and made it possible to find patient-specific treatments.Marfanoid symptoms of the patient.Phenotypic Spectrum of fbn1+/− Zebrafish

NEW RECORD SPECIES OF GIANT FRESH WATER SHRIMP FROM THE DOWNSTREAM OF SERAYU RIVER

Indonesia is characterized by great diversity of freshwater shrimp, consisting of several islands due to the geographical location on the equator. A recent investigation conducted in Central Java has identified Serayu River as the major habitat of freshwater shrimp genus Macrobrachium. Therefore, this research aimed to determine the type of giant freshwater shrimp found downstream of Serayu River using explanatory method. The experiment was conducted for one year (January - December 2023) and the results found two freshwater giant prawn species, namely Macrobrachium rosenbergii and Macrobrachium spinipes. Moreover, this research is the first record of M. spinipes based on the Cytochrome C oxidase Subunit I (CO1) gene. The mtDNA segment of M. rosenbergii was 631 bp (base pairs) (GenBank accession: LC813231.1), while M. spinipes was 616 bp (GenBank accession: PP735157.1). M. spinipes and M. rosenbergii downstream of Serayu River showed similar locations and characteristics. Genetic distance conducted on 15 species of the genus Macrobrachium showed that giant freshwater prawn serayu had a matrix value of 0.09 - 0.18. Genetic analysis conducted with GenBank indicated that M. spinipes showed significant differences from other species, suggesting the natural dispersal of juvenile through currents across Wallace Line. This research also found that M. rosenbergii was similar to M. dacqueti and related to M. malcolmsonii, while M. spinipes was close to M. suphanense. To support these results, recommendation was made to explore further the rivers in the western part of Java, Indonesia.

First support for phylogenetically segregated ecotypes and delineating thresholds for inter‐ and intraspecific ranks in phytophagous Central Asian beetles (Coleoptera)

AbstractAs defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detailed morphology (using SEM) of taxa assigned to the rank of species, subspecies and ecotype were used to verify their taxonomic status and attempt to more precisely establish the boundaries between these concepts. The minimum threshold for the COI genetic distance between species was found to be approximately 3%, while at the threshold of 4%–5% the morphology left no doubt as to the species distinctiveness. The threshold of approximately 2% was accepted as adequate for a subspecies rank, whereas intraspecific variability among individuals of the same subspecies (including its ecotypes) ranged from 0% to 2%. A newly presented colour/elytral pattern form, possibly another ecotype of A. halodendri distributed in western Mongolia, exemplifies adaptation to different environmental conditions via ecological speciation. Our results provide support that ecotypes can form phylogenetically distinct clades. Based on the results of the haplotype network, it can be tentatively concluded that the sand ecotype was the incipient form from which further ecotypes and subspecies developed.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Characterisation of Tomato (Solanum lycopersicon Mill.) Genotypes for Morphological and Disease Resistance Traits through Cluster Analysis

The characterization of germplasm is crucial for breeding and developing improved seed varieties. In this study, seed material was collected from M/s. Noble Seeds Pvt. Ltd., Yelhanka, focusing on genotypes with varying resistance to Tomato Leaf Curl Virus (ToLCV). The research was conducted during the Kharif seasons of 2021 and 2022 in Kestur Village, Doddballapura. Morphological characterization was performed according to DUS guidelines set by PPV&amp;FRA, assessing 20 qualitative and 22 quantitative traits. The genotypes were grown in a randomized complete block design for reliability. Multivariate cluster analysis was employed to group the genotypes based on the morphological traits assessed, enabling the identification of patterns and relationships among them. This analysis facilitated the formation of distinct clusters, highlighting the genetic diversity and similarities among the genotypes, which are crucial for targeted breeding strategies. Through multivariate cluster analysis, two main clusters (A and B) were identified, each further divided into two sub-clusters (C and D). Overall, 66.67% of the 30 genotypes (20 in total) were grouped in Cluster E, while 5 genotypes were placed in Cluster C, 3 in Cluster D, and only 2 in Cluster F. The analysis revealed that NBLTM-22 and NBLTM-11 exhibited the highest variation between them, while genotypes within clusters demonstrated greater similarity. These findings underscore the importance of genetic diversity in breeding programs, highlighting that closer proximity in clustering correlates with trait similarity among genotypes. This information can guide further breeding efforts aimed at developing ToLCV-resistant varieties.

Genetic Diversity of Maize (Zea mays L.) Genotypes under Low Level of Nitrogen

Maize (Zea mays L.) is India's second most significant crop, behind rice. As a cross-pollinated crop, hybrid vigour is commonly used to achieve the best production potential. The selection of various genotypes is a primary goal in the maize hybrid breeding programme. Maize is a voracious feeder and requires a lot of fertiliser. The biggest limits on maize production in India are low soil nitrogen and high fertiliser costs. Jharkhand consumes only 82.5 kg of total fertiliser nutrients per acre. In order to discover genetically varied maize genotypes for nitrogen usage efficiency, the current study evaluated 121 maize genotypes in a randomised block design with two replications at low nitrogen levels. Plant height, days to 50% pollen shed, days to 50% silk, anthesis-silking interval (ASI), days to75% maturity, number of leaves per plant, root length, stover yield per plant, grain yield per plant, and harvest index were all recorded. Statistical analysis was performed using the morphological trait data. Analysis of variance revealed substantial (p≤0.05) variations in morphological features between maize genotypes. For statistical analysis, a clustering method was used to locate various genotypes with greater genetic distance in order to develop good heterotic combinations. One hundred twenty one genotypes were divided into six clusters using the dendogram-by-ward minimum variance approach. Cluster III and V had the greatest inter-cluster distance (79.26), followed by cluster III and VI (74.77) and cluster II and III (73.80). The many heterotic combinations developed from these clusters can be employed in subsequent breeding programmes to produce low nitrogen-requiring hybrids with a low yield penalty.

Multiple Maternal Lineages of &lt;i&gt;Strauchbufo raddei&lt;/i&gt; (Strauch, 1876) in Mongolia Revealed by Mitochondrial DNA

The Mongolian toad Strauchbufo raddei (Strauch, 1876) is one of widely distributed and dominated amphibian species in eastern Asian, including Mongolia. In this study, we amplified and sequenced a total of 50 samples of S. raddei, from three main regions in its Mongolian distribution range namely, Northern, Eastern, and Gobi regions. Our phylogenetic trees (Bayesian inference; BI and time-calibrated) and network analysis clearly support presence of multiple maternal mitochondrial DNA lineages for S. raddei in Mongolia. As expected, samples from these three regions were clustered separately in BI tree (Bayesian posterior probability (BPP 0.52). In addition, the population specific haplotypes, estimated genetic distances (e.g. uncorrelated p distance; ranged from 1% to 25%) and hierarchical AMOVA suggested relatively strong population genetic structure of S. raddei across Mongolia. Time-calibrated tree and ancestral range analysis showed that the first colonization of S. raddei may have occurred in Northern part of Mongolia approximately 9.63 mya, then dispersed over other parts of the country. Estimated approximate time for crossing event of S. raddei over dry steppe and semi-desert regions in Mongolia was 5.02 – 2.50 mya. Finally, high level of genetic diversity (overall; haplotype diversity, Hd = 0.93; nucleotide diversity, π = 0.011) of S. raddei were observed in Mongolia. Importantly, through this study, we contributed to closing sampling gaps in distribution range of S. raddei in Eastern Asia, which is key to better understanding species history, as well as describing cryptic lineages.

Comparative targeted genome profiling between solid and liquid biopsies in gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs): a proof-of-concept pilot study.

Clinical presentation and genetic profile of gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) are highly variable, hampering their management. Sequencing of circulating tumor DNA (ctDNA) from liquid biopsy (LB) has been proposed as a less invasive alternative to solid biopsy (SB). Our aim is to compare the mutational profile (MP) provided by LB with that deriving from SB in GEP-NETs. SB and LB derived simultaneously from 6 GEP-NETs patients. A comparative targeted Next Generation Sequencing (NGS) analysis was performed on DNA from SB and LB to evaluate the mutational status of 11 genes (MEN1, DAXX, ATRX, MUTYH, SETD2, DEPDC5, TSC2, ARID1A, CHECK2, MTOR, PTEN). Patients (M:F =2:1; median age 64 yrs) included 3 with pancreatic and 3 with ileal NETs. NGS detected a median number of 55 variants/sample in SB and 66.5 variants/sample in LB specimens (mutational burden: 0.2-1.9 and 0.3-1.8 mut/Mb, respectively). Missense and nonsense mutations were prevalent in both, mainly represented by C&gt;T transitions. ARID1A, MTOR, and ATRX were consistently mutated in SB and ARID1A, TSC2, MEN1, PTEN, SETD2, and MUTYH were consistently mutated in LB. DAXX mutations were absent in LB. 17 recurrent mutations were shared between SB and LB; in particular, MTOR single nucleotide variants (SNVs) c.G4731A and c.C2997T were shared by 5 out of 6 patients. Hierarchical clustering supported genetic similarity between SB and LB. This pilot study explores the applicability of LB in GEP-NETs MP evaluation. Further studies with larger cohorts are needed to validate LB and to define the clinical impact.

Studies on Genetic Divergence in Faba Bean (Vicia faba L.)

Background: The genetic divergence in faba bean genotypes is critical for breeding programs aiming to improve yield and other agronomic traits. Understanding the extent of genetic variability among different genotypes can guide the selection of superior varieties and enhance crop improvement efforts. This study was conducted to evaluate the genetic diversity among 47 faba bean genotypes grown under the specific agro-climatic conditions of Chhattisgarh. Methods: The experiment was conducted during the Rabi season of 2022-23 at the Hi-Tech-Nursery, Dau Kalyan Singh College of Agriculture and Research Station, Bhatapara, under Indira Gandhi Krishi Vishwavidyalaya, Chhattisgarh. A total of 47 faba bean genotypes were evaluated for genetic divergence using Mahalanobis D2 statistics and Tocher’s method. Ten quantitative characters, including marketable pod yield per plant and marketable pod weight appearance, were measured and analyzed. The genotypes were grouped into clusters based on their genetic distances. Result: The clustering pattern indicated that genetic diversity was independent of geographical diversity. Cluster II contained the highest number of genotypes (19), followed by Cluster I (13), while Cluster IV had the least (1). Among the ten quantitative characters studied, marketable pod yield per plant contributed most to genetic divergence, followed by marketable pod weight appearance. The maximum intra-cluster D2 value was observed in Cluster IV (477.35), followed by Cluster III (250.07). The highest inter-cluster D2 value was between Cluster I and Cluster IV (7917.34), followed by Cluster IV and Cluster V (6156.43).