Rice (Oryza sativa) is a staple food crop globally, with origins in wild progenitors within the AA genome group of Oryza species. Oryza rufipogon and Oryza meridionalis are native to tropical Asia and Northern Australia and offer unique genetic reservoirs. Here we explored the relationships of the genomes of these wild rice species with the domesticated rice genome. We utilized long read sequencing (PacBio HiFi) and chromatin mapping (Hi-C) to produce de novo chromosomal level genomes of Oryza meridionalis, the most divergent AA gnome species, and the unique Australian Oryza rufipogon like taxon that is a sister to the clade of domesticated and wild AA genome rice species of Asia and Africa. Comparative genomic analyses were conducted to identify structural variations and syntenic relationships between these wild taxa and the domesticated rice variety Nipponbare. The genome assemblies of the wild rice species achieved high completeness and contiguity, revealing the shared and unique genes in each species. Both wild species uniquely shared some genes with domesticated rice many of which were associated with disease resistance and stress tolerance. Structural differences included the large 6 Mb inversion on chromosome 6 specific to Japonica rice. Functional annotation highlighted conserved biological functions and novel genes unique to the wild taxa. These findings provide a deeper understanding of rice domestication and highlight the genetic contributions of wild species to enhancing the genetic diversity and ecological adaptability of modern rice varieties. Our study emphasizes the importance of conserving wild rice populations as genetic resources for breeding and adaptation in changing environments.

This study genetic insights of spike-related inheritance traits in wheat (Triticum aestivum L.) under water stress. Seven wheat genotypes, comprising five drought-tolerant and two drought-sensitive lines, were crossed in all possible combinations in complete diallel fashion. The F1 hybrids and parental lines were tested under both irrigated and drought conditions in a randomized complete block design. Traits such as spikes plant-1, spike length, spikelets spike-1, spike weight, grains spike-1, spike harvest index, and grain yield plant-1 were recorded and analyzed. Significant genotypic variation was observed across all traits, with additive gene and partial dominance identified as the primary genetic mechanisms. Heritability estimates were moderate to high (40%–78%), highlighting the potential for genetic improvement. Traits like spikes per plant and spike length displayed high heritability under drought conditions, making them suitable targets for early-generation selection. The findings suggest that breeding programs focusing on additive gene action can enhance drought tolerance and yield potential in wheat. This research provides a framework for developing high-yielding, resilient wheat varieties suited for water-limited environments, through Identification of drought resilient crosses on the basis of studied traits contributing to sustainable food production also.

Drought stress considerably affects the growth, yield as well as quality traits of wheat. Thus, the assessment of drought stress on the growth of wheat plants is very crucial to identify superior genotypes. This research explored how drought stress affects wheat grain yield and associated traits. Ten wheat genotypes were evaluated under both fully irrigated conditions and drought conditions, where only one irrigation was provided after rouni. Data on growth, yield, and protein content were collected for analysis. There were highly significant differences (P<0.01) observed among the genotypes for all the recorded parameters. Drought stress led to a significant decrease in the number of days to 50% heading and maturity, as well as in plant height (cm), Productive tillers/plant, Normalized difference vegetative index at anthesis (NDVI), chlorophyll index (SPAD), thousand grain weight (g), and grain yield (kg ha-1). On the other hand, protein content amplifies under drought conditions. Correlation analysis revealed a significant positive relationship between yield and several traits, including thousand grain weight, productive tillers per plant, protein content, normalized difference vegetative index at anthesis, flag leaf area, and chlorophyll SPAD. Notably, protein content exhibited a positive correlation with yield under drought stress, but a negative correlation under irrigated conditions. Bi-plot analysis indicated that genotypes HYT-70-16 and V-17086 were identified as superior performers in drought conditions for yield and related traits. These identified genotypes, i.e HYT-70-16 and V-17086 can be leveraged in future wheat breeding programs to incorporate desirable traits for developing drought-tolerant wheat varieties.

The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previ-ous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we generated two high-quality,gap-free genome assemblies for'Dangshansu'(DS;503.92 Mb)and'Lianglizaosu'(ZS;509.01 Mb),each anchored to 17 chromosomes,achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0％.Our genome-wide association studies explored the associations between genetic variations and stone cell traits,revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene,designated PbdsZF.Through genetic transformation,we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation,as it transcriptionally activates multiple genes involved in these processes.By binding to the CT-rich motifs CT1(CTTTTTTCT)and CT2(CTCTTTTT),PbdsZF significantly influences the transcription of genes essential for lignin production,underscoring its regulatory importance in plant lignin metabolism.Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation,thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.

Drought stress significantly affects the growth and yield of wheat crop. However, tremendous variability exists amongst genotypes concerning their reaction to drought stress. Therefore, figuring out the effects of drought stress on yield and growth of crop plants might assist to select the superior genotypes. In the current study, forty wheat genotypes were assessed for drought tolerance using PEG-6000 at seedling, tillering, heading and maturity stage at PMAS-Arid Agriculture University, Rawalpindi, Punjab, Pakistan during 2022-23. ANOVA revealed significant variation (P≤0.05) among genotypes for all traits in all the growth stages in both conditions (drought and normal). Mean comparison analysis showed the genotypes LLR-25 (12.73g), Lasani-08 (12.69g) and WC-26 (12.57g) were high-yielding and also performed well in terms of root-shoot-related traits under drought condition. Correlation depicted the highly significant positive association of yield per plant with 1000 grain weight (0.85**) as well as positive association with traits i.e., root length at seedling (0.08), tillering (0.27) and heading (0.14) stage, no. of crown roots at tillering (0.13), no. of seminal roots at tillering (0.04) and heading (0.17) under drought condition. Moreover, spike length showed a positive highly significant association with root length (0.48**) at seedling and no. of seminal roots (0.4**) at heading stage under drought condition. PCA bi-plot analysis emphasized genotypes related to specific traits showing their importance under drought stress condition. Moreover, PCA bi-plot revealed the distinctness and strong association with key drought-resilient traits of genotype Chakwal-50. Hence, this study identified the genotypes viz. Chakwal-50, LLR-25, Lasani-08 and WC-26 have desirable root parameters as well as found best regarding yield and related traits under water deficit condition. The selected genotypes can be sown directly under water-deficit condition and may be further utilized for drought-tolerance breeding programs for varietal improvements in the current scenario of the changing climate.

Growth in precision medicine, immunotherapy, genetics, and new therapeutic approaches is driving the rapid progression of cancer science and drug discovery. Greater tailor-made treatments attacking specific genetic abnormalities and immune systems have become an alternative to the one-size-fits-all approach, bringing renewed hope to patients for improved outcomes and fewer adverse effects. The most critical growth impacting the face of cancer research and drug discovery is summarized in this brief. Next-generation sequencing (NGS) and other methods enable complete genomic profiling, which identifies actionable mutations and guides targeted therapy. Stepping away from blanket chemotherapy, scientists can develop more effective and less toxic drugs by understanding the specific mutations that create each patient's cancer. By blocking the brakes of the immune system, these drugs allow T cells to better fight cancer cells. However, research is ongoing to maximize these treatments' efficacy and safety, particularly in the case of solid tumors. Targeting some of the TME components, such as the extracellular matrix or TME-dwelling immune cells, could provide new treatment strategies. Huge amounts of genetic information are being evaluated, potential medicine candidates are being identified, and patient outcomes are being forecast by AI algorithms. In addition, machine learning algorithms are being employed to improve patient stratification, optimize clinical trial design, and personalize treatment regimens using real-time data. Combination Treatments: Combination therapies employing multiple mechanisms of action are gaining increasing popularity as a result of the flexibility and complexity of cancer. For maximizing efficacy and overcoming resistance, researchers are incorporating immunotherapy with targeted therapy, chemotherapy, radiation therapy, and other modalities. The goal is to keep tumor cells from evading treatment by attacking cancer from a variety of angles. These combinations are currently under investigation in clinical trials, which have had promising results, particularly in cancers such as breast, lung, and melanoma.

KEY MESSAGE:This study provides novel insights into the evolution, diversification, and functions of melatonin biosynthesis genes in Prunus species, highlighting their potential role in regulating bud dormancy and abiotic stresses. The biosynthesis of melatonin (MEL) in plants is primarily governed by enzymatic reactions involving key enzymes such as serotonin N-acetyltransferase (SNAT), tryptamine 5-hydroxylase (T5H), N-acetylserotonin methyltransferase (ASMT) and tryptophan decarboxylase (TDC). In this study, we analyzed Melatonin genes in four Prunus species such as Prunus avium (Pavi), Prunus pusilliflora (Ppus), Prunus serulata (Pser), and Prunus persica (Pper) based on comparative genomics approach. Among the four Prunus species, a total of 29 TDCs, 998 T5Hs, 16 SNATs, and 115 ASMTs within the genome of four Prunus genomes. A thorough investigation of melatonin-related genes was carried out using systematic biological methods and comparative genomics. Through phylogenetic analysis, orthologous clusters, Go enrichment, syntenic relationship, and gene duplication analysis, we discovered both similarities and variations in Melatonin genes among these Prunus species. Additionally, our study revealed the existence of unique subgroup members in the Melatonin genes of these species, which were distinct from those found in Arabidopsis genes. Furthermore, the transcriptomic expression analysis revealed the potential significance of melatonin genes in bud dormancy regulation and abiotic stresses. Our extensive results offer valuable perspectives on the evolutionary patterns, intricate expansion, and functions of PavMEL genes. Given their promising attributes, PavTDCs, PavT5H, PavNAT, and three PavASMT genes warrant in-depth exploration as prime candidates for manipulating dormancy in sweet cherry. This was done to lay the foundation for future explorations into the structural and functional aspects of these factors in Prunus species. This study offers significant insights into the functions of ASMT, SNAT, T5H, and TDC genes and sheds light on their roles in Prunus avium. Moreover, it established a robust foundation for further exploration functional characterization of melatonin genes in fruit species.

Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.

The rice reference genome (Oryza sativa ssp. japonica cv. Nipponbare) has been an important resource in plant science. We now report an improved and haplotype resolved genome sequence based upon more accurate sequencing technology. This improved assembly includes regions missing in earlier genome sequences and the annotation of more than 3,000 new genes due to greater sequence accuracy. This phased genome will be a useful resource for rice research.

Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.

Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.

Background Class III peroxidase (POD) enzymes play vital roles in plant development, hormone signaling, and stress responses. Despite extensive research on POD families in various plant species, the knowledge regarding the POD family in Chinese pear (Pyrus bretschenedri) is notably limited. Results We systematically characterized 113 POD family genes, designated as PbPOD1 to PbPOD113 based on their chromosomal locations. Phylogenetic analysis categorized these genes into seven distinct subfamilies (I to VII). The segmental duplication events were identified as a prevalent mechanism driving the expansion of the POD gene family. Microsynteny analysis, involving comparisons with Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume and Prunus persica, highlighted the conservation of duplicated POD regions and their persistence through purifying selection during the evolutionary process. The expression patterns of PbPOD genes were performed across various plant organs and diverse fruit development stages using transcriptomic data. Furthermore, we identified stress-related cis-acting elements within the promoters of PbPOD genes, underscoring their involvement in hormonal and environmental stress responses. Notably, qRT-PCR analyses revealed distinctive expression patterns of PbPOD genes in response to melatonin (MEL), salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA), reflecting their responsiveness to abiotic stress and their role in fruit growth and development. Conclusions In this study, we investigated the potential functions and evolutionary dynamics of PbPOD genes in Pyrus bretschenedri, positioning them as promising candidates for further research and valuable indicators for enhancing fruit quality through molecular breeding strategies.

BACKGROUND:Cotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level. METHODS:In present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent. RESULTS:In sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum, G. arboretum, G. raimondii and A. thaliana. The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes. CONCLUSION:The positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate.

EDITORIAL article Front. Plant Sci., 02 February 2024Sec. Plant Bioinformatics Volume 15 - 2024 | https://doi.org/10.3389/fpls.2024.1368909

In the previous decades, numerous investigations have been done that the Alfin-like (AL) transcription factors (TFs) are participating in several physiological and development processes in plants including root hair elongation, development of root and meristem, etc. Although the AL-TFs had been comprehensively evaluated in several species, the little finding is reported on the AL-TFs in Chinese pear (Pyrus bretschenedri). In the current study, 15 PbAL genes were systemically characterized and nomenclature as PbAL1 to PbAL15 corresponding to their chromosomal localization. Phylogeny analysis and structural features revealed that the 15 genes could be classified into six subfamilies (S-I to S-VI).Whole-genome duplication (WGD) events are the most common mechanism and may play a crucial role in the expansion of the AL gene family. Microsynteny analysis among Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume, and Prunus persica showed that AL duplicated regions were more conserved and undergo purifying selection during the evolutionary process. Further analysis of introns-exons, physicochemical properties, and conserved motif showed their functional divergence, diversification in quantity, and structure. The expression pattern of PbAL gene family in various organs and different fruit development stages were conducted through transcriptomic data. Moreover, stress-related cis-acting elements of PbAL genes were found on the promoters regions to be associated with hormonal and environmental stress responses. Noticeably, the expression patterns evaluated by qRT-PCR demonstrated that PbAL genes were differentially expressed under indole acetic acid (IAA), Gibberellic acid (GA), Melatonin (ME) and abscisic acid (ABA) treatment, which response to abiotic stress and fruit growth development. Current work explored the potential function and evolution of PbAL genes in Pyrus bretschenedri. PbAL were investigated as candidate genes for further research and important clues for improving fruit quality through molecular breeding.

Exposure of crops to low temperature (LT) during emerging and reproductive stages influences their growth and development. In this study, we have isolated a cold induced, nucleus-localized lipid A gene from rice named OsLPXC, which encodes a protein of 321 amino acids. Knockout of OsLPXC resulted in enhance sensitivity to LT stress in rice, with increased accumulation of reactive oxygen species (ROS), malondialdehyde and electrolyte leakage, while expression and activities of antioxidant enzymes were significantly suppressed. The accumulation of chlorophyll content and net photosynthetic rate of knockout plants were also decreased compared with WT under LT stress. The functional analysis of differentially expressed genes (DEGs), showed that numerous genes associated with antioxidant defense, photosynthesis, cold signaling were solely expressed and downregulated in oslpxc plants compared with WT under LT. The accumulation of methyl jasmonate (MeJA) in leave and several DEGs related to the jasmonate biosynthesis pathway were significantly downregulated in OsLPXC knockout plants, which showed differential levels of MeJA regulation in WT and knockout plants in response to cold stress. These results indicated that OsLPXC positively regulates cold tolerance in rice via stabilizing the expression and activities of ROS scavenging enzymes, photosynthetic apparatus, cold signaling genes, and jasmonate biosynthesis.

The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.