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Inheritance of the presence/absence of seeds in Annona squamosa is mediated by a single fully recessive gene and is caused by a deletion of the INNER NO OUTER (INO) locus. For some fruits, seedless varieties are desirable for consumption and processing. In the sugar apple tree (Annona squamosa L.), the seedless trait in the Thai seedless (Ts) and Brazilian seedless (Bs) accessions was associated with defective ovules and an apparent deletion of the INNER NO OUTER (INO) ovule development gene locus. Segregation analysis of F2 and backcross descendants of crosses of Bs to fertile wild-type varieties in this species with a multi-year generation time showed that seedlessness was recessive and controlled by a single locus. Comparison of whole genome sequence of a wild-type plant and a third accession, Hawaiian seedless (Hs), identified a 16 kilobase deletion including INO in this line. Ts and Bs lines were shown to have an identical deletion, indicating a common origin from a single deletion event. Analysis of microsatellite markers could not preclude the possibility that all three seedless accessions are vegetatively propagated clones. The sequence of the deletion site enabled a codominant assay for the wild-type and mutant genes allowing observation of complete cosegregation of the seedless/defective ovule phenotype with the INO deletion, showing maximal separation of less than 3.5 cM. The observed deletion is the only significant difference between the wild-type and Hs line over 587 kilobases, likely encompassing much more than 3.5 cM, showing that the deletion is the cause of seedless trait. The codominant markers and obtained progenies will be useful for introgression of the seedless trait into elite sugar apple lines and into other Annonas through interspecific crossings.

Accurate characterization of crops or fruits leads to successful improvements in breeding programs. Mango (Mangifera indica L.) is the second most common fruit in Egypt. It is a heterozygous plant; consequently, the possibility of incorrect characterization is significant. Therefore, this study used six accessions of two M. indica cultivars, 'Keitt' and 'Ewais', to produce precise molecular characterization and prove their genetic relatedness using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers. Pollen morphology was studied for the first time for these two Egyptian cultivars to determine their correlation. Morphological traits were quantitatively and qualitatively investigated. In addition, phytochemical analyses were performed to correlate the six mango accessions. One of these accessions (accession 3) was commercially identified as 'Ewais' cv., but the obtained result revealed that it does not belong to 'Ewais' cv. This finding was proved molecularly using ISSR and SCoT markers and morphologically. Similarly, phytochemical analyses revealed a difference between accession 3 and the other accessions under investigation. Polymorphic information content (PIC) and resolving power (RP) data revealed that the SCoT technique was more informative than ISSR for studying these genotypes of mango. Accordingly, the present findings prove the necessity for molecular, morphological, palynological, and biochemical investigations for accurate characterization of mango genotypes and genetic relatedness for improving breeding programs. [ABSTRACT FROM AUTHOR]

Heavy metal and metalloid pollution caused by the industrialization became a leading stress factors for agricultural plants. The increase in the amount of nickel and boron in agricultural areas due to mining and increasing industrial activity is an important agricultural constraint. The difference between deficiency and toxicity levels of these heavy metal and metalloid is extremely critical. Nickel and boron are important micronutrients for plant growth, while they become toxic at critical densities. Plants exhibit different responses to these pollutants. It is essential to find specific biomarkers to discriminate the tolerant varieties to develop elite varieties. Transposable elements are known to have an efficient role against environmental stress factors. In this research, we evaluated the potential use of Tos17 retrotransposon movement as a molecular marker to identify the stress tolerances of two Oryza sativa L. varieties against nickel and boron pollutants. [ABSTRACT FROM AUTHOR]

Summary Southern corn rust (SCR), caused by Puccinia polysora Underw (P. polysora), is a catastrophic disease affecting maize, leading to significant global yield losses. The disease manifests primarily as pustules on the upper surface of corn leaves, obscuring our understanding of its cellular heterogeneity, the maize's response to its infection and the underlying gene expression regulatory mechanisms. In this study, we dissected the heterogeneity of maize's response to P. polysora infection using single‐cell RNA sequencing. We delineated cell‐type‐specific gene expression alterations in six leaf cell types, creating the inaugural single‐cell atlas of a maize leaf under fungal assault. Crucially, by reconstructing cellular trajectories in susceptible line N110 and resistant line R99 during infection, we identified diverse regulatory programs that fortify R99's resistance across different leaf cell types. This research uncovers an immune‐like state in R99 leaves, characterized by the expression of various fungi‐induced genes in the absence of fungal infection, particularly in guard and epidermal cells. Our findings also highlight the role of the fungi‐induced glycoside hydrolase family 18 chitinase 7 protein (ZmChit7) in conferring resistance to P. polysora. Collectively, our results shed light on the mechanisms of maize resistance to fungal pathogens through comparative single‐cell transcriptomics, offering a valuable resource for pinpointing novel genes that bolster resistance to P. polysora. [ABSTRACT FROM AUTHOR]

This study aimed to determine the morphological, pomological, biochemical contents, and molecular characterization of 11 cucumber genotypes of Egyptian origin and to reveal their molecular characterization. As a result it was determined that the highest fruit weight, the highest fruit length, and the highest fruit width were in the “Rahaf” genotype (respectively, 337.39 g, 23.25 cm, 53.97 mm). Biochemical analyses of the genotypes revealed that the highest total phenolic content was in the “Madayın” genotype (1938 mg gallic acid equivalent 100 g−1), the highest total antioxidant content was in the “C.5” genotype (59.25% inhibition), and the highest total flavonoid content was in the “Gazir” genotype (752.78 mg catechin equivalent 100 g−1). The highest Chlorophyll (a) content and Chlorophyll (a+b) was in the “Madayın” genotype (respectively, 4.33 mg g−1, 20.92 mg g−1), the highest Chlorophyll (b) content was in the “Iskay” genotype (6.59 mg g−1). It was determined that there were differences between genotypes in terms of other biochemical parameters examined. Using ten Inter Simple Sequence Repeat primers, 119 bands were obtained and the polymorphism rate was determined as 90.75%. [ABSTRACT FROM AUTHOR]

Dihydroartemisinin (or artenimol)–piperaquine is one of the six artemisinin-based combination therapies recommended in uncomplicated malaria treatment. However, artemisinin partial resistance has been reported in Cambodia, Laos, Vietnam, India, and, recently, in Africa. Polymorphisms in the Pfk13 gene have been described as molecular markers of artemisinin resistance and the amplification of the plasmepsine II/III (Pfpmp2/Pfpmp3) gene has been associated with piperaquine resistance. However, some therapeutic failures with this combination remain unexplained by strains' characterization. We provide an overview on the use of dihydroartemisinin–piperaquine in malaria treatment and discuss tools available to monitor its efficacy. [ABSTRACT FROM AUTHOR]

In recent years, artificial intelligence (AI), especially deep learning models, has increasingly been integrated into diagnosing and treating diabetic retinopathy (DR). From delving into the singular realm of ocular fundus photography to the gradual development of proteomics and other molecular approaches, from machine learning (ML) to deep learning (DL), the journey has seen a transition from a binary diagnosis of "presence or absence" to the capability of discerning the progression and severity of DR based on images from various stages of the disease course. Since the FDA approval of IDx-DR in 2018, a plethora of AI models has mushroomed, gradually gaining recognition through a myriad of clinical trials and validations. AI has greatly improved early DR detection, and we're nearing the use of AI in telemedicine to tackle medical resource shortages and health inequities in various areas. This comprehensive review meticulously analyzes the literature and clinical trials of recent years, highlighting key AI models for DR diagnosis and treatment, including their theoretical bases, features, applicability, and addressing current challenges like bias, transparency, and ethics. It also presents a prospective outlook on the future development in this domain. [ABSTRACT FROM AUTHOR]

AbstractThe molecular identification and taxonomic classification of medicinal plants are essential using various molecular markers for their accurate identification, safe utilization, and genetic conservation. The internal transcribed spacer sequence of nuclear ribosomal DNA (nrDNA-ITS) revealed the clustering of collected plant species into various clades according to their sequence similarity. The estimated total phenolic content (TPC) and total flavonoid content (TFC) in the leaves of different plant species ranged from 29.98 to 80.28 mg GAE/g DW, and 26.39 to 60.45 mg QE/g DW, respectively. Among the plant species, the content of bioactive compounds, luteolin 7-rutinoside and quercetin 3-β-D-glucoside were observed to be highest in Anagyris foetida, whereas p-coumaric acid was observed to be greatest in Astragalus spinosus. Among all plant species extracts tested, Anagyris foetida extract (AFE), Astragalus spinosus extract (ASPE), and Astragalus sieberi extract (ASIE) exhibited significant activities against the Escherichia coli (E. coli) strain, mainly AFE showed more effective activity against the E. coli pathogen (MIC-6.25 µg/mL and MBC-12.50 µg/mL). Thus, screened plant extracts of different species could be tested on other microorganisms to explore their medicinal properties to cure various diseases against pathogens as well as their application in the food industry as a food preservative. [ABSTRACT FROM AUTHOR]

Background: Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear. Results: We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259–155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections. Conclusions: The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species. [ABSTRACT FROM AUTHOR]

Gastrodia elata rhizomes have been applied as traditional medicinal materials for thousands of years. In China, G. elata f. elata (red flower and stem, Ge), G. elata f. viridis (green, Gv), and G. elata f. glauca (black, Gg) represent the primary cultivars in artificial cultivation. Although the annual output of G. elata amounts to 150,000 tons, only 20% is Gg. The long production period, low yield, and high quality of Gg led to its extremely high market prices. However, an effective method to identify this crude drug based solely on its morphological or chemical characteristics is lacking. In this study, the complete chloroplast genomes of three G. elata variants were sequenced using the Illumina HiSeq 2500 platform. Another 21 chloroplast genomes from Gastrodia species, which have published in previous reports, were combined and analyzed together. Our results showed that larger genomic sizes, fewer long tandem repeats, and more simple sequence repeats were the major features of the Gg chloroplast genomes. Phylogenetic analysis showed that the Gg samples were separately clustered in a subclade. Moreover, an accession-specific marker was successfully developed and validated for distinguishing additional rhizome samples. Our study provides investigations of the taxonomic relationships of Gastrodia species. The molecular marker will be useful for differentiating Gastrodia products on the market. [ABSTRACT FROM AUTHOR]

The genetic variability in 13 selected genotypes of Vaccinium corymbosum using re-trotransposon-based iPBS markers system was characterized in this study. The four selected iPBS primers amplified 232 fragments, average 58 fragments per primer, approximately 53.16% of which were polymorphic. The polymorphism information content of iPBS marker was 0.238. The hierarchical cluster using unweighted pair group method with arithmetic mean analysis divided selected genotypes into two main groups and several subgroups. The values of the Jaccard coefficient of genetic relatedness were between 0.036–0.243. The similarity between two sample sets was 3.6%–24.3%. This study confirmed inter-PBS amplification technique as a reproducible and trustable marker system, but has proved to be an effective DNA fingerprinting technology to generate polymorphism in Vaccinium corymbosum. [ABSTRACT FROM AUTHOR]

Foxtail millet hybrid development encounters challenges due to its self-pollinating nature, small florets, and tool availability for confirming true hybrid. Our research aimed to assess flowering phenology and explore artificial hybridization employing SiDREB2 based-SNAP marker. The research consisted of three experiments. The first experiment focused on the panicle phenology of foxtail millet, while the second experiment focused on floret phenology and reproductive organs. The artificial hybridization successfulness was validated with SNAP markers based on the SiDREB2 gene in the third experiment. Observations on two genotypes (ICERI-5 and ICERI-6) revealed panicle initiation at 49-69 days after planting (DAP), with anthesis occurring 6 days after panicle emergence (DAPE). Florets exhibited the formation of reproductive organs at 3 DAPE, delineating distinct stages of pollen development leading up to anthesis. Our findings emphasized the significance of implementing male-sterile induction treatment at 4 DAPE to regulate pollen development for successful hybridization by 6 DAPE. The hybrid evaluation revealed varied germination rates and confirmed hybrid percentages across different crossing series, validated by SiDREB2-based SNAP marker. ICERI-5xBotok-4 exhibited high germination but a low confirmed hybrid percentage, while Botok-4xICERI-5 and Botok-10xICERI-6 showed the opposite trend. Reciprocal crossings showed unilateral incompatibility in confirmed hybrid percentage. [ABSTRACT FROM AUTHOR]

Background: The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala. Results: A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker. Conclusions: The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination. [ABSTRACT FROM AUTHOR]

Background: The aim of this study was to elucidate the critical role of autophagy-related gene aggregation in gastric cancer tumor microenvironment cells and to investigate their major roles in cellular functions. In particular, the expression of these genes in tumor-associated fibroblast subtypes was scrutinized in an attempt to explain their cell-subpopulation-specific roles in cell–cell communication and regulation of cellular functions. Methods: In this study, single-cell RNA sequencing data were first analyzed in multiple steps, including data preprocessing, cell clustering, and cell classification. Cell subpopulations and gene expression patterns were identified and analyzed using unsupervised non-negative matrix factorization (NMF) techniques. The dynamic expression of autophagy-related gene aggregates in various cell types was deciphered by pseudotime trajectory analysis (PTA). Intercellular communication analysis was performed using the CellChat R software package, revealing the intricate communication patterns and exchange of key signaling molecules between cell subpopulations, and SCENIC analysis was used to identify gene regulatory networks and reveal the mechanisms behind cellular heterogeneity. Result: Cell subpopulations associated with pan-apoptosis were identified by NMF decomposition and SCENIC analysis. Cell–cell communication analysis revealed intricate communication patterns and exchange of key signaling molecules between cell subpopulations. Dynamic expression of autophagy-related genes aggregated in the pseudotemporal trajectory of STAD was observed by PTA. In the fibroblast subtype, different ligand-receptor interactions and their key roles in immunomodulation were observed. Conclusion: By deeply analyzing and comparing gene expression patterns within cellular subpopulations and intercellular communication, this study provides new insights into the role of pan-apoptosis-related genes in regulating immune responses and cellular functions in gastric cancer. These findings pave the way for further exploration of the role of these genes in tumorigenesis and immune regulation, as well as laying the foundation for potential therapeutic strategies. [ABSTRACT FROM AUTHOR]

Heterobasidion parviporum is a fungal pathogen that is drastically damaging Norway spruce (Picea abies) in Europe. The infections will result in root and stem rot, causing significant economic losses for forest owners. Previous studies have shown that the PaLAR3 gene, which encodes the leucoanthocyanidin reductase enzyme, can increase resistance to H. parviporum in Norway spruce. The presence of the B allele at the PaLAR3 locus has been associated with higher (+)‐catechin concentrations and increased enzyme production in inoculation experiments, resulting in inhibited pathogen growth. The control of H. parviporum involves a multifaceted approach, including silvicultural and sustainable forestry practices, genetic resistance and chemical/biological control. In this study, we determined the PaLAR3 genotypes in a representative sample of Norway spruce breeding materials from southern Finland and examined their effect on necrosis caused by H. parviporum in spruce stems. The results showed that the homozygous PaLAR3BB genotype was present in only 9% of the trees. However, the necrotic area interacted with homozygous PaLAR3BB under low‐water treatment. These findings support the idea that the PaLAR3 locus may be a valuable marker for identifying P. abies resistance to different strains of Heterobasidion parviporum. [ABSTRACT FROM AUTHOR]

Brachidontes variabilis (Krauss, 1848) is a common small mussel widely distributed in the intertidal zone of southern China. Firstly, we characterized four complete mitochondrial genomes of B. variabilis from four populations (Wanning, Yangjiang, Zhangzhou, and Shanwei) in Chinese waters. This study was the first to sequence and discribe the mitochondrial genome of B. variabilis, which comprised of 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 12 protein-coding genes (PCGs, lacking atp8). And then three PCGs fragments, including cytochrome oxidase subunit I (cox1, 558 bp), NADH dehydrogenase subunit 5 (nad5, 754 bp), and NADH dehydrogenase subunit 4 (nad4, 879 bp), were utilized to investigate the population genetics and demography. The cox1, nad5 and nad4 fragments revealed 55, 81, and 103 haplotypes, respectively. Results indicated high genetic diversity within populations (Hd > 0.5, Pi > 0.005) and little genetic differentiation among populations (FST<0.05), suggesting frequent gene exchanges. Further, the neutrality test and Extended Bayesian skyline plots (EBSPs) suggested that the four populations underwent population expansion at 0.9–1.1 Ma during the Pleistocene. In summary, this study on the mitochondrial genomes and population genetics of B. variabilis provides insights into the evolutionary history and demographic dynamics of this species in southern China. [ABSTRACT FROM AUTHOR]

Rind thickness (RT) is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Mansf.] and affects watermelon storability. However, genetic studies on this trait, as well as gene regulation studies, are scarce and of limited production significance. We constructed a temporary F2 generation using the highly differentiated thick-rind watermelon 'XiaoXiGua-4' and the thin-rind watermelon 'DuanMan' as parents and localized the Cla97C02G044120 gene, which controls the thickness of watermelon rind, to the intervals of chromosome 2, CL2-32303995 and CL2-32316840, through 2 years of genetic analysis. No exonic mutations were found in this gene, but two promoter mutations resulted in changes in the promoter progenitor. Fluorescence quantitative PCR analysis revealed highly significant differences in expression at 1 d and 28 d, and the expression was significantly lower in thick-skinned watermelon varieties. Marker-assisted selection (MAS) for this trait was performed using the Caps marker CL2-32303995 and the InDel marker CL2-32316840, which not only verified the stability of the localization interval but also distinguished thick rind from thin rind. These results can be used for germplasm resource screening and have strong breeding significance. [ABSTRACT FROM AUTHOR]

Poor ovarian response (POR) patients often face the risk of not having enough competent oocytes. Then, aspirating small follicles could serve as a strategy to increase their number. Many efforts have been addressed to associate follicular size with oocyte competence, but results are controversial. Therefore, our study aimed to evaluate oocyte maturation and developmental competence, along with a non-invasive oocyte-maturation-related miRNA signature in oocytes retrieved from both large and small follicles. A total of 178 follicles, from 31 POR patients, were aspirated and measured on the day of ovarian puncture. Follicular diameters, oocyte collection, oocyte maturation, fertilization, blastocysts, and good-quality blastocyst rates were recorded. Simultaneously, follicular fluids were collected to quantify their miRNA expression. The efficacy of oocyte retrieval along with oocyte maturation, fertilization, and blastulation rates tended to increase with follicular size, but few significant differences were found. Despite there being significantly more collected oocytes from follicles > 11.5 mm compared to follicles ≤ 11.5 mm (p < 0.05), oocytes from the latter were also mature, with no significant differences in the miRNA signature, but only those > 13.5 mm demonstrated developmental competence. In conclusion, 11.5 mm follicles can produce mature oocytes, but only those larger than 13.5 mm yielded transferable embryos. [ABSTRACT FROM AUTHOR]

Fresh market tomatoes are often characterized by poor flavour. Flavour is a quantitative trait difficult to assess and often neglected in breeding. Classical sensory methods are not suitable for the evaluation of early segregating generations; simple physicochemical measurements are not sufficient to predict perceived aroma. Alternative selection methods are needed, such as the recently introduced Breeders' Sensory Test or marker‐assisted selection (MAS). Two unrelated crosses were chosen to evaluate the efficiency of phenotypic selection with the Breeders' Sensory Test (breeders' sensory selection, BS) and MAS for five quantitative trait loci for sweetness, sourness and tomato aroma (mapped in 'Resi' × 'Auriga') in organic low‐input and hydroponic cultivation. Selection for sensory attributes reduced fruit weight, emphasizing the challenge of breeding flavourful, large‐fruited tomatoes. Both selection methods were more effective in 'Roterno F1'× 'Black Cherry' derived from more distant parents. A trend towards higher efficiency of MAS in early segregating generations was observed for sweetness and tomato aroma. However, a major advantage of BS is its universal applicability. To improve flavour, combining both methods is recommended. [ABSTRACT FROM AUTHOR]

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The value of red sugar beet in medical treatment, nutrition, and health care, as well as for the extraction of natural pigment, is now recognized, necessitating the selection of optimal red sugar beet varieties. However, the self-bred varieties in China are all multi-embryo varieties, with very few single embryo hybrid varieties. The use of heterosis breeding requires sterile and maintainer lines; while, the domestic red beet resources and the cytoplasmic and nuclear fertility of imported red beet varieties (lines) are unknown. In this study, we identified 50 red sugar beet varieties (lines), including both domestic and international lines, using specific TR1 primers acting on a variable number of mitochondrial tandem repeat (VNTR) loci, and s17 and o7 primers associated with the nuclear fertility Rf1 and Rf2 sites to investigate the cytoplasmic and nuclear fertility-associated genotypes of 50 red sugar beet varieties (lines). The results showed that among the 50 red sugar beet varieties tested, the proportion of fertile cytoplasm (N-type) was 54%; while, the proportion of infertile cytoplasm (S-type) was 40%. The proportion of cytoplasmic hybridization between the sterile (S-type) and fertile (N-type) types was 6%. In the genotypic identification of the Rf1 and Rf2 loci related to nuclear fertility, the highest proportion in the Rf1 locus was the homozygous 1.8 kbp genotype, accounting for 94%. Double-restriction endonuclease analysis was performed on the PCR products amplified from s17. The varieties (lines) with a homozygous 5/5 pattern after double restriction endonuclease analysis accounted for the largest proportion, namely, 88%. The band pattern with the highest proportion in the Rf2 locus was a homozygous 1.4 kbp pattern, accounting for 42%, while the homozygous 2.6 kbp type accounted for 6%. Two or more heterozygous bands accounted for a total of 52%. The results provide a preliminary understanding of the cytoplasmic and nuclear fertility-related genotypes of 50 red sugar beet varieties (lines), and combine both cytoplasmic and nuclear fertility for a comprehensive analysis of the fertility of red sugar beet varieties (lines), providing a reference for the breeding of red sugar beet heterosis varieties. [ABSTRACT FROM AUTHOR]

Abstract Background One of the wild fruit species with a natural distribution in Türkiye, and historically used for medicinal purposes due to its rich composition, is Berberis crataegina DC. Various parts of the plant, including its roots, bark, leaves, flowers, and fruits, have been utilized in traditional medicine, while its fruits are also consumed in various forms as food. This study aimed to characterize the morphological, biochemical, and molecular traits of B. crataegina genotypes naturally growing in the Kayseri region, located in central Türkiye. Results The fruit weight of the genotypes ranged from 0.047 to 0.137 g, fruit width from 3.06 to 4.64 mm, and fruit length from 5.80 to 9.05 mm. Similarly, the leaf traits of the genotypes exhibited wide variation. The total phenolic content ranged from 190.53 to 297.55 mg GAE/100 g, total flavonoid content from 82.03 to 203.89 mg QE/100 g, total anthocyanin content from 4.54 to 11.76 mg cyn-3 gluc/100 g, and total antioxidant capacity between 57.76 and 87.93%. A principal component analysis (PCA) of 11 traits identified four principal components with eigenvalues greater than 1. The first four components accounted for 71.89% of the total variation, with PCA1 explaining 23.48%, PCA2 18.68%, PCA3 16.39%, and PCA4 13.34%. ISSR molecular analysis using nine markers revealed a band count ranging from 4 to 13, polymorphic band count between 3 and 10, and polymorphism rates from 61.54 to 100%, with band lengths ranging from 200 to 1000 base pairs. According to the UPGMA dendrogram based on molecular analyses, the genetic similarity between the genotypes ranged from 0.64 to 1.00, with B2 and B13 being the most similar genotypes. Conclusions In conclusion, the Kayseri region is rich in B. crataegina genotypes with wide genetic variation. The genotypes identified in this region may serve as valuable genetic resources for future studies.

Abstract Background Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear. Results We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259–155,269 bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections. Conclusions The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.

Abstract Background The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala. Results A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker. Conclusions The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination.

Abstract Background The aim of this study was to elucidate the critical role of autophagy-related gene aggregation in gastric cancer tumor microenvironment cells and to investigate their major roles in cellular functions. In particular, the expression of these genes in tumor-associated fibroblast subtypes was scrutinized in an attempt to explain their cell-subpopulation-specific roles in cell–cell communication and regulation of cellular functions. Methods In this study, single-cell RNA sequencing data were first analyzed in multiple steps, including data preprocessing, cell clustering, and cell classification. Cell subpopulations and gene expression patterns were identified and analyzed using unsupervised non-negative matrix factorization (NMF) techniques. The dynamic expression of autophagy-related gene aggregates in various cell types was deciphered by pseudotime trajectory analysis (PTA). Intercellular communication analysis was performed using the CellChat R software package, revealing the intricate communication patterns and exchange of key signaling molecules between cell subpopulations, and SCENIC analysis was used to identify gene regulatory networks and reveal the mechanisms behind cellular heterogeneity. Result Cell subpopulations associated with pan-apoptosis were identified by NMF decomposition and SCENIC analysis. Cell–cell communication analysis revealed intricate communication patterns and exchange of key signaling molecules between cell subpopulations. Dynamic expression of autophagy-related genes aggregated in the pseudotemporal trajectory of STAD was observed by PTA. In the fibroblast subtype, different ligand-receptor interactions and their key roles in immunomodulation were observed. Conclusion By deeply analyzing and comparing gene expression patterns within cellular subpopulations and intercellular communication, this study provides new insights into the role of pan-apoptosis-related genes in regulating immune responses and cellular functions in gastric cancer. These findings pave the way for further exploration of the role of these genes in tumorigenesis and immune regulation, as well as laying the foundation for potential therapeutic strategies.

BACKGROUND: Osteosarcoma has a complex pathogenesis and a poor prognosis. While advancements in medical technology have led to some improvements in the 5-year survival rate, substantial progress in its treatment has not yet been achieved. OBJECTIVE: To screen key molecular markers in osteosarcoma, analyze their relationship with osteosarcoma treatment drugs, and explore the potential disease mechanisms of osteosarcoma at the molecular level. METHODS: GSE99671 and GSE284259 (miRNA) datasets were obtained from the Gene Expression Omnibus database. Differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) on GSE99671 were performed. Functional enrichment analysis was conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes separately for the differentially expressed genes and the module genes with the highest positive correlation to the disease. The intersection of these module genes and differentially expressed genes was taken as key genes. A Protein-Protein Interaction network was constructed, and correlation analysis on the key genes was performed using CytoScape software, and hub genes were identified. Hub genes were externally validated using the GSE28425 dataset and text validation was conducted. The drug sensitivity of hub genes was analyzed using the CellMiner database, with a threshold of absolute value of correlation coefficient |R| > 0.3 and P < 0.05. RESULTS AND CONCLUSION: (1) Differential gene expression analysis identified 529 differentially expressed genes, comprising 177 upregulated and 352 downregulated genes. WGCNA analysis yielded a total of 592 genes with the highest correlation to osteosarcoma. (2) Gene Ontology enrichment results indicated that the development of osteosarcoma may be associated with extracellular matrix, bone cell differentiation and development, human immune regulation, and collagen synthesis and degradation. Kyoto Encyclopedia of Genes and Genomes enrichment results showed the involvement of pathways such as PI3K-Akt signaling pathway, focal adhesion signaling pathway, and immune response in the onset of osteosarcoma. (3) The intersection analysis revealed a total of 59 key genes. Through Protein-Protein Interaction network analysis, 8 hub genes were selected, which were LUM, PLOD1, PLOD2, MMP14, COL11A1, THBS2, LEPRE1, and TGFB1, all of which were upregulated. (4) External validation revealed significantly downregulated miRNAs that regulate the hub genes, with hsa-miR-144-3p and hsa-miR-150-5p showing the most significant downregulation. Text validation results demonstrated that the expression of hub genes was consistent with previous research. (5) Drug sensitivity analysis indicated a negative correlation between the activity of methotrexate, 6-mercaptopurine, and pazopanib with the mRNA expression of PLOD1, PLOD2, and MMP14. Moreover, zoledronic acid and lapatinib showed a positive correlation with the mRNA expression of PLOD1, LUM, MMP14, PLOD2, and TGFB1. This suggests that zoledronic acid and lapatinib may be potential therapeutic drugs for osteosarcoma, but further validation is required through additional basic experiments and clinical studies. [ABSTRACT FROM AUTHOR]

Citrus unshiu Marc. cv. Miyagawa-wase is one of the most widely cultivated citrus varieties on Jeju Island in Republic of Korea. Mutation breeding is a useful tool for inducing genetic diversity by causing genomic mutations in a short period of time. We previously conducted mutation breeding using gamma irradiation to develop new varieties of C. unshiu. Here, we describe one of these varieties, Yein-early, which has a redder peel, greater hardness, and higher sugar content compared with the wild type (WT). Yein-early leaves also showed a unique phenotype compared with the WT, characterized by longer longitudinal length, shorter transverse length, stronger curling, and longer petiole length. Genome resequencing of Yein-early and the WT uncovered significant single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). These variations were crucial in identifying molecular markers unique to Yein-early. In addition, we developed an allele-specific PCR marker specifically targeting a homozygous SNP in Yein-early that distinguishes it from the WT and other citrus varieties. This study contributes to the understanding of pigment synthesis in fruits and provides a valuable tool for selection of the novel Yein-early variety in citrus breeding programs.

【Objective】Guizhou Province is an area for annual breeding of Spodoptera frugiperda. The use of molecular markers were used to identify the population biotypes of S. frugiperda in Guiyang, Guizhou, and its adaptability to Zea mays, Sorghum bicolor and Oryza sativa were studied, with a view to clarifying the biotype of S. frugiperda invading Guiyang and understanding the characteristics of its biotypes.【Method】A total of 32 S. frugiperda samples from three counties or cities in Guiyang, Guizhou were amplified, sequenced and analyzed for comparison by using CO Ⅰ and Tpi molecular marker methods, to determine the biotype of the population invading Guiyang, Guizhou. Additionally, the developmental duration, adult emergence rate and survival time of S. frugiperda larvae of various instars after feeding on three host plants (Zea mays, S. bicolor and O. sativa) were recorded to evaluate the adaptability of S. frugiperda to these three host plants.【Result】The results showed that among the 32 S. frugiperda samples, 93.75% belonged to the rice biotype while 6.25% belonged to the corn biotype based on the mitochondrial CO Ⅰ gene analysis. The sequence characteristics were highly consistent with the corresponding biotypes of S. frugiperda population. Meanwhile, the analysis of nuclear genome Tpi gene revealed that all samples showed the haplotype characteristics of the corn strain. The adaptability study indicated that the invasive S. frugiperda in Guiyang had the shortest larval period (13.22 d), longest adult survival time (16.42 d) and highest emergence rate (95.14 %) on Z. mays, followed by S. bicolor; while it had the longest larval period (16.59 d), shortest adult survival time (8.56 d) and lowest emergence rate (75.15 %) on O. sativa.【Conclusion】The biotypes of S. frugiperda invaded Guiyang, Guizhou Province were 93.75% rice type, 6.25% maize type using CO Ⅰ molecular marker, and 100% maize type using Tpi molecu lar marker. The life span of female S. frugiperda feeding on maize was significantly higher than those feeding on rice and S. bicolor. The results provide a basis for the prevention and control of S. frugiperda on S. bicolor.

Background: Siganidae is marine teleost family consists of a single extant genus, Siganus Forsskål, 1775, included 29 recognized species of rabbitfish. Aim: The main goal of this study was the use of mitochondrial 16S rRNA gene as a potential molecular marker in the phylogenetic relationships study of some rabbitfishes species (Siganidae: Perciformes). Methods: The samples were gathered from the Red Sea. The sequences of four rabbitfishes (Siganus argenteus, Siganus luridus, Siganus rivulatus, Siganus stellatus) were deposited into NCBI to gain the accession numbers (PP488874 - PP488877) and then analyzed with their related rabbitfishes depending on available sequence data of the mitochondrial 16S rRNA gene. Results: The results of 16S rRNA sequences illustrated that the average A+T values were greater than C+G. Conclusion: The low genetic distance between Siganus luridus and Siganus rivulatus indicated close linkage between them. [Open Vet J 2024; 14(8.000): 1936-1941]

Abstract Background Phytosulfokine (PSK) functions as a plant peptide growth factor that plays important and diverse roles in plant development and stress responses. Nevertheless, PSKs have not been systematically analyzed in wheat. Results A genome-wide comparative analysis of PSK genes in wheat was conducted and 15 TaPSKs were identified and divided into four subgroups in the wheat genome based on sequence similarity. The examination of motif compositions of TaPSK genes revealed the presence of the YIYTQ signature motif in the C-terminus of all TaPSK polypeptide precursors, with a highly conserved feature across different species. Exogenous application of TaPSK peptide promoted root growth in wheat. Quantitative RT-PCR analysis revealed that the TaPSKs exhibited preferential or tissue-specific expression patterns in wheat. In particular, three homologs of the TaPSK1 genes were specifically expressed in grains, with the strongest expression observed in the developing grains at 15 days after anthesis. Compared with wild type, transgenic rice lines overexpressing TaPSK1-A exhibited larger grain size and higher thousand-grain weight. The promoter region and genomic sequence of the wheat TaPSK1-A gene were cloned. Sequence polymorphism showed that five single-nucleotide polymorphisms (SNPs) were identified in the promoter region of TaPSK1-A. A Kompetitive Allele-Specific PCR (KASP) marker was developed for TaPSK1-A based on –806 bp SNP (C/T transition), and two haplotypes, TaPSK1-A-HapI and TaPSK1-A-HapII were detected in 260 wheat accessions collected from different regions. The expression of TaPSK1-A, promoter activity, and thousand-grain weight (TGW) in the TaPSK1-A-HapII haplotype were higher than those in the TaPSK1-A-HapI haplotype. Furthermore, yeast one-hybrid assays revealed the binding of TaNF-YB1 and TaERF39 to the promoter regions of the TaPSK1-A gene, and TaMADS29 could bind to the promoters of TaPSK1-B and TaPSK1-D genes. Conclusions Comparative genome-wide analysis of TaPSK peptide family revealed that the TaPSK1 gene is involved in wheat grain development, and the developed TaPSK1-A-KASP marker could be utilized for marker-assisted selection breeding of wheat. Graphical Abstract

Pear (Pyrus spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears. [ABSTRACT FROM AUTHOR]

This study explored the polymorphism of the leucine aminopeptidase (LAP3) gene and its relationship with milk quality characteristics in Gannan yak. A cohort of 162 Gannan yak was genotyped utilizing the Illumina Yak cGPS 7K BeadChip, and the identified single nucleotide polymorphisms (SNPs) were evaluated for their association with milk protein, casein, lactose, and fat concentrations. The results showed that four SNPs (g.4494G > A, g.5919A > G, g.8033G > C, and g.15,615A > G) in the LAP3 gene exhibited polymorphism with information content values of 0.267, 0.267, 0.293, and 0.114, respectively. All four SNPs were in Hardy–Weinberg equilibrium (p > 0.05). The g.4494G > A and g.5919A > G SNPs were significantly associated with protein content (p < 0.05), with homozygous genotypes showing significantly higher protein content than heterozygous genotypes (p < 0.05). The g.8033G > C SNP was significantly associated with casein content, protein content, non-fat solids, and acidity (p < 0.05), with the CC genotype having significantly higher casein, protein, and non-fat solids content than the GG and GC genotypes (p < 0.05). The g.15,615A > G SNP was significantly associated with average fat globule diameter (p < 0.05). In general, the mutations within the LAP3 gene demonstrated a positive impact on milk quality traits in Gannan yak, with mutated genotypes correlating with enhanced milk quality. These results indicate that the LAP3 gene could be a significant or candidate gene affecting milk quality traits in Gannan yak and offer potential genetic markers for molecular breeding programs in this species. [ABSTRACT FROM AUTHOR]

A study determining microsatellite markers was conducted to compare similarities among three different populations of Macrobrachium tenellum prawns from three different hydrological basins in Oaxaca, Mexico. In total, nine different markers in the population were used, of which six coded for the three populations and three did not. Although different, the three populations are closely genetically related, with an average allele richness from 6.845 to 16.754 and a heterozygosity of 0.166 to 0.264. However, the relationship could be much closer, particularly between them. The possible applications and scope of this knowledge are commented on and discussed. [ABSTRACT FROM AUTHOR]

Setaria italica L. or foxtail millet is known for its nutritious grains and adaptability to unfavorable environmental conditions. High productivity, early heading, medium stature, and tolerance to drought- or salinity stress are among the breeding objectives for foxtail millet. The objective of this study was to select F3 families of foxtail millet from the cross of Botok-10xICERI-6 by weighted selection index and assisted by SiDREB2-based SNAP marker. Genotyping of 178 F3 families using the SiDREB2-based SNAP marker resulted in 29 A/A genotypes, 121 A/G genotypes, and 28 G/G genotypes. Further evaluation was conducted on 48 F3 families consisting of 27 A/A genotypes and 21 A/G genotypes in an augmented randomized complete block design together with their parental genotypes (Botok-10xICERI-6) and three check genotypes (Mauliru-2, NTB-1, and Toraja). Plant height and heading time had high broad-sense heritability, whereas grain weight per plant had a moderate broad-sense heritability. Ten potential F3 families were selected based on a weighted selection index with 20% intensity, comprised of seven A/G genotypes and three A/A genotypes with a weighted selection index ranging from 0.84 to 3.76. The F3 family with pedigree numbers B10I6-15-136, B10I6-15-161, and B10I6-15-70 with A/A genotypes are considered putative transgressive segregants and could be continued to the next generation for further breeding process. [ABSTRACT FROM AUTHOR]

The inhibin alpha (INHA) serves as a marker for the number of fully developed ovarian follicles and plays a crucial role in regulating the secretion of pituitary FSH (follicle-stimulating hormone) and the frequency of ovulation. This study aims to examine the effect of INHA gene polymorphisms on the litter size of thin-tailed sheep. Detection of single nucleotide polymorphisms (SNPs) in the INHA gene was performed using PCR and DNA sequencing techniques. A total of 45 ewes were included in the study. Three SNPs were identified: g.236311141G>C, g.236311367G>A, and g.236311368G>A. Further investigation of the g.236311367G > A variant revealed that individuals with the GA genotype had a significantly higher litter size than those with the AA or GG genotype (p<0.05). SNPs at positions g.236311141G/C and g.236311368G/A were non-synonymous mutations resulting in amino acid changes p.A225P and V301I, respectively. Our results suggest that g.236311367G>A loci may serve as a potential molecular marker for improving the litter size trait in thin-tailed sheep. [ABSTRACT FROM AUTHOR]

Tumor microenvironment (TME) has been demonstrated to play a significant role in tumor initiation, progression, and metastasis. Cancer-associated fibroblasts (CAFs) are the major component of TME and exhibit heterogeneous properties in their communication with tumor cells. This heterogeneity of CAFs can be attributed to various origins, including quiescent fibroblasts, mesenchymal stem cells (MSCs), adipocytes, pericytes, endothelial cells, and mesothelial cells. Moreover, single-cell RNA sequencing has identified diverse phenotypes of CAFs, with myofibroblastic CAFs (myCAFs) and inflammatory CAFs (iCAFs) being the most acknowledged, alongside newly discovered subtypes like antigen-presenting CAFs (apCAFs). Due to these heterogeneities, CAFs exert multiple functions in tumorigenesis, cancer stemness, angiogenesis, immunosuppression, metabolism, and metastasis. As a result, targeted therapies aimed at the TME, particularly focusing on CAFs, are rapidly developing, fueling the promising future of advanced tumor-targeted therapy. [ABSTRACT FROM AUTHOR]

Lineage plasticity in small cell lung carcinoma (SCLC) causes therapeutic difficulties. This study aimed to investigate the pathological findings of plasticity in SCLC, focusing on combined SCLC, and elucidate the involvement of YAP1 and other transcription factors. We analysed 100 surgically resected SCLCs through detailed morphological observations and immunohistochemistry for YAP1 and other transcription factors. Component‐by‐component next‐generation sequencing (n = 15 pairs) and immunohistochemistry (n = 35 pairs) were performed on the combined SCLCs. Compared with pure SCLCs (n = 65), combined SCLCs (n = 35) showed a significantly larger size, higher expression of NEUROD1, and higher frequency of double‐positive transcription factors (p = 0.0009, 0.04, and 0.019, respectively). Notably, 34% of the combined SCLCs showed morphological mosaic patterns with unclear boundaries between the SCLC and its partner. Combined SCLCs not only had unique histotypes as partners but also represented different lineage plasticity within the partner. NEUROD1‐dominant combined SCLCs had a significantly higher proportion of adenocarcinomas as partners, whereas POU2F3‐dominant combined SCLCs had a significantly higher proportion of squamous cell carcinomas as partners (p = 0.006 and p = 0.0006, respectively). YAP1 expression in SCLC components was found in 80% of combined SCLCs and 62% of pure SCLCs, often showing mosaic‐like expression. Among the combined SCLCs with component‐specific analysis, the identical TP53 mutation was found in 10 pairs, and the identical Rb1 abnormality was found in 2 pairs. On immunohistochemistry, the same abnormal p53 pattern was found in 34 pairs, and Rb1 loss was found in 24 pairs. In conclusion, combined SCLC shows a variety of pathological plasticity. Although combined SCLC is more plastic than pure SCLC, pure SCLC is also a phenotypically plastic tumour. The morphological mosaic pattern and YAP1 mosaic‐like expression may represent ongoing lineage plasticity. This study also identified the relationship between transcription factors and partners in combined SCLC. Transcription factors may be involved in differentiating specific cell lineages beyond just 'neuroendocrine'. [ABSTRACT FROM AUTHOR]

In order to give wide-ranging and long-lasting disease resistance that reduces rice output, breeding techniques are used such as the importance of selection assisted by markers and gene pyramiding. Bacterial leaf blight (BLB), which is carried on by the pathogen Xanthomonas oryzae pv. oryzae, is one such disease that significantly reduces rice yield. Numerous molecular marker techniques have already been developed because molecular markers are crucial for both marker-assisted selection and gene pyramiding. Currently, DNA-based markers, sometimes referred to as molecular markers, are the most frequently employed ones. Based on the methods used to find them, the molecular markers are divided into two main types. These markers are based on hybridization and polymerase chain reaction. The morphological (traditionally based) and biochemical (enzyme-based) markers are two more types of markers that are available. The best method for preventing rice BLB disease is host plant/varietal resistance. Gene pyramiding with the help of markers offers the potential to speed up breeding operations and ensure that the host plant's acquired resistance will last. This research explores the use, economic significance, constraints, and potential of marker-assisted selection and gene pyramiding for rice BLB disease resistance. [ABSTRACT FROM AUTHOR]

Background: Phytosulfokine (PSK) functions as a plant peptide growth factor that plays important and diverse roles in plant development and stress responses. Nevertheless, PSKs have not been systematically analyzed in wheat. Results: A genome-wide comparative analysis of PSK genes in wheat was conducted and 15 TaPSKs were identified and divided into four subgroups in the wheat genome based on sequence similarity. The examination of motif compositions of TaPSK genes revealed the presence of the YIYTQ signature motif in the C-terminus of all TaPSK polypeptide precursors, with a highly conserved feature across different species. Exogenous application of TaPSK peptide promoted root growth in wheat. Quantitative RT-PCR analysis revealed that the TaPSKs exhibited preferential or tissue-specific expression patterns in wheat. In particular, three homologs of the TaPSK1 genes were specifically expressed in grains, with the strongest expression observed in the developing grains at 15 days after anthesis. Compared with wild type, transgenic rice lines overexpressing TaPSK1-A exhibited larger grain size and higher thousand-grain weight. The promoter region and genomic sequence of the wheat TaPSK1-A gene were cloned. Sequence polymorphism showed that five single-nucleotide polymorphisms (SNPs) were identified in the promoter region of TaPSK1-A. A Kompetitive Allele-Specific PCR (KASP) marker was developed for TaPSK1-A based on –806 bp SNP (C/T transition), and two haplotypes, TaPSK1-A-HapI and TaPSK1-A-HapII were detected in 260 wheat accessions collected from different regions. The expression of TaPSK1-A, promoter activity, and thousand-grain weight (TGW) in the TaPSK1-A-HapII haplotype were higher than those in the TaPSK1-A-HapI haplotype. Furthermore, yeast one-hybrid assays revealed the binding of TaNF-YB1 and TaERF39 to the promoter regions of the TaPSK1-A gene, and TaMADS29 could bind to the promoters of TaPSK1-B and TaPSK1-D genes. Conclusions: Comparative genome-wide analysis of TaPSK peptide family revealed that the TaPSK1 gene is involved in wheat grain development, and the developed TaPSK1-A-KASP marker could be utilized for marker-assisted selection breeding of wheat. [ABSTRACT FROM AUTHOR]

The utilization of saline land is a global challenge, and cultivating salt-tolerant soybean varieties is beneficial for improving the efficiency of saline land utilization. Exploring the genetic basis of salt-tolerant soybean varieties and developing salt-tolerant molecular markers can effectively promote the process of soybean salt-tolerant breeding. In the study, the membership function method was used to evaluate seven traits related to salt tolerance and comprehensive salt tolerance at the soybean seedling stage; genome-wide association analysis (GWAS) was performed in a natural population containing 200 soybean materials; and linkage analysis was performed in 112 recombinant inbred lines (RIL) population to detect quantitative trait loci (QTLs) of salt tolerance. In the GWAS, 147 SNPs were mapped, explaining 5.28–17.16% of phenotypic variation. In the linkage analysis, 10 QTLs were identified, which could explain 6.9–16.16% of phenotypic variation. And it was found that there were two co-located regions between the natural population and the RIL population, containing seven candidate genes of salt tolerance in soybean. In addition, one colocalization interval was found to contain qZJS-15-1, rs47665107, and rs4793412, all of which could explain more than 10% of phenotypic variation rates, making it suitable for molecular marker development. The physical positions of rs47665107 and rs47934112 were included in qZJS-15-1. Therefore, a KASP marker was designed and developed using Chr. 15:47907445, which was closely linked to the qZJS-15-1. This marker could accurately and clearly cluster the materials of salt-tolerant genotypes in the heterozygous population tested. The QTLs and KASP markers found in the study provide a theoretical and technical basis for accelerating the salt-tolerant breeding of soybean. [ABSTRACT FROM AUTHOR]

【Objective】Guizhou Province is an area for annual breeding of Spodoptera frugiperda. The use of molecular markers were used to identify the population biotypes of S. frugiperda in Guiyang, Guizhou, and its adaptability to Zea mays, Sorghum bicolor and Oryza sativa were studied, with a view to clarifying the biotype of S. frugiperda invading Guiyang and understanding the characteristics of its biotypes.【Method】A total of 32 S. frugiperda samples from three counties or cities in Guiyang, Guizhou were amplified, sequenced and analyzed for comparison by using CO I and Tpi molecular marker methods, to determine the biotype of the population invading Guiyang, Guizhou. Additionally, the developmental duration, adult emergence rate and survival time of S. frugiperda larvae of various instars after feeding on three host plants (Zea mays, S. bicolor and O. sativa) were recorded to evaluate the adaptability of S. frugiperda to these three host plants.【Result】The results showed that among the 32 S. frugiperda samples, 93.75% belonged to the rice biotype while 6.25% belonged to the corn biotype based on the mitochondrial CO I gene analysis. The sequence characteristics were highly consistent with the corresponding biotypes of S. frugiperda population. Meanwhile, the analysis of nuclear genome Tpi gene revealed that all samples showed the haplotype characteristics of the corn strain. The adaptability study indicated that the invasive S. frugiperda in Guiyang had the shortest larval period (13.22 d), longest adult survival time (16.42 d) and highest emergence rate (95.14 %) on Z. mays, followed by S. bicolor; while it had the longest larval period (16.59 d), shortest adult survival time (8.56 d) and lowest emergence rate (75.15 %) on O. sativa.【Conclusion】The biotypes of S. frugiperda invaded Guiyang, Guizhou Province were 93.75% rice type, 6.25% maize type using CO I molecular marker, and 100% maize type using Tpi molecu lar marker. The life span of female S. frugiperda feeding on maize was significantly higher than those feeding on rice and S. bicolor. The results provide a basis for the prevention and control of S. frugiperda on S. bicolor. [ABSTRACT FROM AUTHOR]

Traumatic brain injury (TBI) is a major cause of injury-related death and disability, and its treatment and prognosis evaluation present challenges. The heterogeneity of TBI complicates diagnostic and therapeutic strategies, considering factors such as injury nature, timing, and severity. Several comprehensive guidelines currently guide the entire process of TBI management. However, there are still controversies regarding surgical timing and intervention methods, prognosis accuracy, and imaging checkpoints. Both overly conservative and overly aggressive decisions can impact patients and their families. With the rapid development of biological technologies in recent years, an increasing number of biomolecular markers have proven to be significant in TBI assessment. Current TBI prognosis models provide clinical references, and further integration with biomarkers and other clinical characteristics may enhance predictive accuracy. Future advancements in single-cell genomics, metabolomics, and the establishment of large-scale clinical databases are expected to drive precision medicine in TBI, improving personalized treatment strategies and outcomes. [ABSTRACT FROM AUTHOR]

Background: Siganidae is a marine teleost family consisting of a single extant genus, Siganus Forsskål, 1775, which included 29 recognized species of rabbitfish. Aim: The main goal of this study was the use of the mitochondrial 16S rRNA gene as a potential molecular marker in the phylogenetic relationships study of some rabbitfishes species (Siganidae: Perciformes). Methods: The samples were gathered from the Red Sea. The sequences of four rabbitfishes (Siganus argenteus, Siganus luridus, Siganus rivulatus, and Siganus stellatus) were deposited into NCBI to gain the accession numbers (PP488874–PP488877) and then analyzed with their related rabbitfishes depending on available sequence data of the mitochondrial 16S rRNA gene. Results: The results of 16S rRNA sequences illustrated that the average A+T values were greater than C+G. Conclusion: The low genetic distance between S. luridus and Siganus rivulatus indicated a close linkage between them. [ABSTRACT FROM AUTHOR]

• This is the first report on morphological, phytochemical, and genetic diversity assessment along with ENM for Allium stracheyi Baker in Uttarakhand, western Himalaya. • The species have important ethnomedical value such as being used as an appetizer, cardioactive, carminative, expectorant, cordial, and stomach troubles. • Correlation studies revealed a strong positive relationship among studied parameters. • Population structure and UPGMA analysis separated the 103 accessions into two sub-populations (ΔK=2). • Population attributes and ecological niche modeling (ENM) displayed suitable habitats for conservation strategies. Allium stracheyi Baker (Himalayan Allium spice) is an economically important herbaceous plant commonly known for its unique flavor and therapeutic potential. The species is distributed from 2000 to 4000 m above sea level in the western Himalayan region. A. stracheyi is used as an appetizer, cardioactive, carminative, expectorant, cordial, in curing stomach troubles, and in treating constipation. However, systematic information on the diversity and distribution of A. stracheyi species is not available to date. In this study, 14 populations of A. stracheyi gathered from Uttarakhand were subjected to morphological, phytochemical, genetic diversity assessment and mapping potential habitat areas through ecological niche modelling tools. Considerable differences (p < 0.05) were recorded in plant height, fresh weight, dry weight, leaf diameter, and stem diameter of species. Maximum total phenols (3.93 mg GAE/g) and flavonoids (6.17 mg QE/g) content were observed in the Kailashpur population, while total tannin content (1.84 mg TAE/g) was higher in the Malari population. The HPLC analysis enabled the identification of five phenolic constituents, namely, gallic acid, catechin, naringin, salicylic acid, and p-coumaric acid, and recorded high variations among the populations. A total of 53 clear and reproducible fragments were recorded using 15 inter-simple sequence repeats (ISSRs) markers. The highest (He = 0.338; Pp = 90.57 %) genetic diversity was recorded in the Kailashpur population, and the lowest (He = 0.185; Pp = 47.17 %) in the Niti population. UPGMA and a Bayesian-based population structure analysis unanimously grouped A. stracheyi populations into two sub-populations (ΔK = 2). It is observed that A. stracheyi possesses high antioxidant activity and genetic diversity. The study also identified and predicted Niti, Mana, and Jawar valley of Uttarakhand as highest suitability areas under the current climate scenario. These findings can be helpful in planning effective conservation strategies and breeding programs for A. stracheyi. [Display omitted] [ABSTRACT FROM AUTHOR]

Tripos is one of the largest dinoflagellate genera with ~800 reported taxa widely distributed in global marine ecosystems. These diverse Tripos species are ecologically important as critical primary producers and some Tripos species are also harmful algal bloom (HAB) species that may pose significant negative impact on marine ecosystems. However, due to the high morphological intraspecific variability and plasticity of numerous Tripos species, morphology-based identification and tracking of their dynamic changes have been both technically challenging and inconclusive. In this project, we carried out metabarcoding analysis of Tripos species in Jiaozhou Bay (JZB) through amplifying and sequencing of the common molecular marker 18S rDNA V4. The analysis identified five Tripos species (T. furca, T. fusus, T. eugrammus, T. falcatus and T. massiliensis), including two (T. eugrammus and T. falcatus) identified for the first time in JZB, demonstrating the competitive strength of metabarcoding analysis. This analysis of time-series samples collected in JZB revealed interesting seasonal dynamic changes of Tripos species, with different species demonstrating differential seasonal preferences. This analysis also suggested the possible existence of 11 additional Tripos species in JZB. The inconclusive identification of these 11 potential Tripos species indicated that the resolution of the common molecular marker 18S rDNA V4 applied in this study is inadequate and that the molecular reference data for Tripos is still limited. Selection of molecular markers with higher resolution (such as 28S rDNA D1-6) and the completion of reference sequences of Tripos species may facilitate more accurate identification of and tracking of their dynamic changes. [ABSTRACT FROM AUTHOR]

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations. [ABSTRACT FROM AUTHOR]

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize. [ABSTRACT FROM AUTHOR]

This article explores the applications of fast breeding technologies in crop improvement and functional genomics studies. These technologies, including molecular selection, gene mapping, haploid induction, and genome editing, have greatly expedited the process of modifying crop traits and mapping genes. Examples of these technologies being used include the use of CRISPR/Cas9 to modify crop traits and the development of new haploid inducer lines in various plants. The article also highlights specific research papers on genetic improvement in melon, potato, wheat, rice, and tomato crops using these technologies. Additionally, the document discusses various research papers in the field of plant science, covering topics such as stress tolerance in tomatoes, doubled haploid plants in maize and wheat, and gene exploration in different crops. These papers provide valuable insights into breeding materials, marker development, and the cloning of new genes, contributing to the development of new germplasms and varieties in crops. [Extracted from the article]

In the world's flower trade, gladiolus (Gladiolus spp.) is ranked first among bulbous flowers and eighth among cut flowers, with more than 30,000 different cultivars being grown. Mass multiplication and commercialization are restricted by the traditional propagation methods. However, the large-scale proliferation and improvement of the gladiolus have been accomplished with the aid of plant tissue culture and other biotechnological techniques. The current review includes a thorough examination of the growth and development parameters required for successful in vitro gladiolus development as well as cormel formation. Moreover, focus is being given to various techniques and methods such as in vitro cytogenetic stability and modification of chromosome number, in vitro mutagenesis and selection of pest resistance, in vitro identification and selection to develop virus-free germplasm, cryopreservation, synthetic seed technology, identifying virus diseases by RT-PCR, somaclonal variation, and protoplast and somatic hybridization. Molecular markers and their applications for genetic diversity analysis, relationships between different genotypes, and clonal stability analysis in Gladiolus species have been conducted by several research groups worldwide and are also being discussed. The article also covers efforts to enhance the functionality of plant phenotypes through genetic transformation. Future prospects for further improvement of ornamental gladiolus are also explored. Overall, the current review provides insight into the applications of basic and advanced biotechnological tools for gladiolus improvement. [ABSTRACT FROM AUTHOR]

Functional genomics through transgenesis has provided faster and more reliable methods for identifying, characterizing, and utilizing genes or quantitative trait loci linked to agronomic traits to target yield. The present study explored the role of Big Grain1 (BG1) gene of rice (Oryza sativa L.) in yield improvement of crop plants. We aimed to identify the genetic variation of OsBG1 in various indica rice cultivars by studying the allelic polymorphism of the gene, while also investigating the gene's potential to increase crop yield through the transgenic approach. Our study reports the presence of an extra 393 bp sequence having two 6 bp enhancer elements in the 3′ regulatory sequence of OsBG1 in the large-grain cultivar IR64 but not in the small-grain cultivar Badshahbhog. A single copy of the OsBG1 gene in both the cultivars and a 4.1-fold higher expression of OsBG1 in IR64 than in Badshahbhog imply that the grain size is positively correlated with the level of OsBG1 expression in rice. The ectopic expression of OsBG1 under the endosperm-specific glutelin C promoter in Badshahbhog enhanced the flag leaf length, panicle weight, and panicle length by an average of 33.2%, 33.7%, and 30.5%, respectively. The length of anthers, spikelet fertility, and grain yield per plant increased in transgenic rice lines by an average of 27.5%, 8.3%, and 54.4%, respectively. Heterologous expression of OsBG1 under the constitutive 2xCaMV35S promoter improved the number of seed pods per plant and seed yield per plant in transgenic tobacco lines by an average of 2.2-fold and 2.6-fold, respectively. Improving crop yield is crucial to ensure food security and socio-economic stability, and identifying suitable genetic factor is the essential step towards this endeavor. Our findings suggest that the OsBG1 gene is a promising candidate for improving the grain yield of monocot and dicot plant systems by molecular breeding and genetic engineering. Key message: Rice Big Grain1 increases grain yield in rice by improving panicle architecture and spikelet fertility rate. [ABSTRACT FROM AUTHOR]