Plant Molecular Biology Reporter最新文献

Collecting, conserving, and using peanut germplasm depends on our ability to comprehend genetic variability in gene banks. The peanut genetic resources are not well characterized for their conservation and potential future use. Increased use of exotic and interspecific derivatives is required to reduce the yield gap, identify new alleles, and introduce them. We assessed the genetic diversity and organization of an 83-germplasm peanut population. Ninety polymorphic markers generated 326 alleles, and the similarity matrix formed three main clusters. Polymorphism information content (PIC) ranged from 0.09 to 0.85, indicating greater genetic diversity in these genotypes. Germplasm from exotic collections had the highest levels of diversity, followed by released cultivars, and interspecific derivatives had the lowest levels of diversity. The number of private alleles in interspecific derivatives, exotic collections, and cultivars was 1, 6, and 3, respectively. Overall, several SSRs showed a high probability of null alleles. In addition, gene diversity and allelic richness were 0.526 and 3.18, respectively. Analysis of molecular variance revealed variation both within and between individuals. Principal coordinate analysis and population structure analysis subdivided all germplasm lines into three populations. Bottleneck analysis revealed that all three populations experienced genetic bottlenecks, as a shifted mode was observed. This paper highlights the importance of using microsatellite markers to study the diversity of interspecific derivatives, including recently developed ones, and create effective conservation programs.

MYB transcription factors (TF) play crucial roles in regulating gene expression and orchestrating responses to abiotic and biotic stresses in plants. MYBs were demonstrated to be involved in land plant adaptation. However, little is known about these proteins in native species from heterogeneous environments. Eugenia uniflora (Myrtaceae) is widely distributed in diverse environments within the Atlantic Forest Domain (AFD). In this work, we identified 147 MYB genes in E. uniflora using an integrative approach involving the genome, transcriptome, and phylogenetics analyses. A phylogenetic approach including MYBs from E. uniflora, Eucalyptus grandis, Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa, Vitis vinifera, and Medicago truncatula allowed us to classify the EunMYB in 39 subfamilies already described. The RNA-seq data analysis unveiled the expression patterns of MYB genes under stress conditions in E. uniflora and Eucalyptus grandis. We found 50 EunMYB genes differentially expressed (DE) in E. uniflora under drought stress. In E. grandis, 11 genes were found to be DE under cold and 25 under heat stress. Integrating the expression data, phylogenetic relationships, and the available data from the literature, we highlight the potential MYBs of E. uniflora that may be acting in resistance to abiotic stress, enabling adaptation to diverse environmental conditions.

Spittlebugs cause large production losses that affect agribusiness worldwide. Understanding plant-herbivore interactions at the molecular level may be the key to developing resistant cultivars. After a nymph survival experiment, root transcriptomes were assembled from two Paspalum regnellii genotypes (BGP 248 and 344) with different first-line defense strategies, with no infestation and at two times after the initial attack of the spittlebug (Mahanarva spectabilis) nymph, thus integrating differential expression analysis and biological network modeling supplemented by root anatomical analysis. Gene Ontology terms related to different stress responses, such as salicylic acid catabolic process, were enriched in BGP 248, while some specific to spittlebugs, such as response to herbivores, were enriched in BGP 344. Enriched pathways were related to structural differences between genotypes, such as those related to cutin, suberin, and wax biosynthesis. BGP 344 also presented pathways related to induced defense, such as glutathione metabolism. Metabolic networks highlighted kinases, and coexpression networks demonstrated a complex cascade response that included lncRNAs. This study provides the first molecular insights into the defense mechanisms of P. regnellii against M. spectabilis. The genotype with the fastest response to insect attack and highest nymph mortality (BGP 344) presented kinases and an enriched glutathione pathway, in addition to constitutive barriers, such as lignin, which can make it difficult for the insect to colonize the plant.

A gap exists between the growth of active germplasm collections and their effective use because of the size of these collections and the limitations of financial resources, skilled labor, and information on the traits of each accession conserved in germplasm banks. To overcome this, the development of core collections (CCs) is of significant importance. In this study, we established the CCs of lima bean (Phaseolus lunatus) accessions from the Germplasm Bank of Phaseolus at the Universidade Federal do Piauí based on two selection strategies and performed validation based on nuclear microsatellite (ncSSR) data. Two CCs were established from 395 accessions and characterized by 11 phenotypic traits of the seed. These CCs were defined using proportional and logarithmic sampling strategies, each consisting of 79 accessions. A set of 13 ncSSRs was used to validate and estimate the genetic diversity. The estimates of parameters (means, variances, and amplitudes of variation), kurtosis, skewness, and average variability retention index indicated no differences between the two CCs when compared with the entire collection (EC). However, the comparison between the accessions that did not coincide with the two CCs through ncSSRs showed differences. The logarithmic CC showed higher expected heterozygosity, mean number of alleles, and number of private alleles (0.521, 4.308, and 30, respectively) than those of the proportional CC strategy (0.352, 2.154, and 2, respectively), indicating greater genetic diversity. Thus, the logarithmic CC proved to be more suitable for conservation purposes and should be further examined in the establishment of thematic collections of lima beans.

The plant SABATH family of methyltransferases has important biological functions by methylating hormones and signaling molecules and other metabolites. In this study, we identified 47 RcSABATH genes from the Rosa chinensis genome, the majority of which are located in the cytoplasm. Following this, a comprehensive analysis was conducted on SABATH genes of Prunus persica, Malus domestica “Golden,” Prunus avium, and Prunus dulcis, which included phylogenetic and chromosome duplication analysis, gene structure examination, and functional domain and conserved motif analysis. The results revealed that SABATH family members across these five species were divided into three categories, with Group I containing the highest number of family members and Group III the lowest. Gene clusters were observed on the chromosomes of each species, indicating the occurrence of tandem repeat events during the evolutionary process of SABATH members. Furthermore, the analysis of gene structure, conserved motif, and conserved domain highlighted the diversity and conservation among SABATH family members. The transcriptome data of R12–26 and R13–54 infected by Marssonina rosae infection was used to screen 35 RcSABATHs, which were subsequently categorized into three groups (a, b, and c) based on their expression characteristics. Notably, Group c consisted of members that were induced and up-regulated during the late stage of R12–26 infection. Among the identified genes, RcSABATH20 drew our attention due to its involvement in various hormone and abiotic stress regulation pathways. To ascertain the function of RcSABATH20, we conducted experiments by treating the leaves of the resistant line R13–54 and susceptible line R12–26 with SA and the SA synthesis inhibitor AIP. The outcomes revealed a direct correlation between the expression of RcSABATH20 and resistance to rose black spots. Furthermore, it was observed that SA could enhance the expression of RcSABATH20, thereby contributing to the resistance against rose black spots. These findings establish a theoretical foundation for exploring the molecular mechanisms underlying SABATH resistance to rose black spots.

Maize is the Philippines’ second most valuable crop based on overall value and total area planted. Still, maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogen Peronosclerospora philippinensis (Weston) Shaw, causing annual losses in maize production. The use of resistant varieties remains the most effective method of control together with integrated pest and disease management strategies. To date, there are no commercially available maize breeding lines or hybrids deployed in the country while the effectiveness of the fungicide metalaxyl versus DM has declined. Hence, it is necessary to initiate pre-breeding and breeding programs to understand the mechanism of resistance of maize against DM. To comprehend the underlying mechanisms of the presence of the disease, we performed an RNA-Seq comparative transcriptomic approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize. Among the identified differentially expressed genes (DEGs), we detected 43 DEGs shared in both genotypes which may play roles in the basal defense response of maize upon DM infection. We also identified 68 DEGs exclusive to the susceptible genotype, providing insights into the molecular responses underlying successful DM disease progression in maize. Further, we detected 651 DEGs unique to the resistant genotype. This set of genes revealed that multi-faceted defense strategies govern the molecular basis of DM resistance in maize. These include multi-process regulations such as transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Finally, transcriptome-wide variants (SNPs and indels) and their impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.

RNA silencing techniques such as RNA interference (RNAi) and artificial miRNAs (amiRNAs) are important tools for gene silencing. RNAi and amiRNA techniques allow tiny molecules of interfering RNAs to down-regulate the expression of target genes. Both techniques have been used for the functional characterization of several genes across many plant species. In this context, the current review emphasizes upon the uses of gene silencing as a potent technology for improving traits in floriculture crops such as longer vase life, flower shape, flower colour, and plant architecture, including changes in foliage colour. However, the risk assessment of RNAi and amiRNA plants should be looked at to rule out any off-target consequences. Besides, there are other limitations to the effectiveness of this technology, including the choice of target species and crops, the stability of the trigger molecules, and gene candidate selection. Over the past decade, several target genes have been discovered in a variety of flower crops for the improvement of their economic traits. The review highlights the role of gene silencing technology for flower improvement and the long-term sustainable production of floricultural crops.

Among the six oleosin genes present in the rice (Oryza sativa L.) genome, one encodes a seed-specific low molecular weight (16 kDa) protein and another one encodes a seed-specific high molecular weight (18 kDa) protein, which are known to be associated with oil bodies or lipid droplets (LDs). To understand the structure-function relationship of these two oleosins, designated as OsOle1 and OsOle2, we first carried out bioinformatic analyses of both proteins followed by transgenic expression of only OsOle1, which has potential application in lipid biotechnology. Although both oleosins have the conserved proline knot motif (PX₅SPX₃P) in the central hydrophobic domain that facilitates LD anchoring, only OsOle1 possesses the acyltransferase motif (HX₄D) within the C-terminal domain. Molecular docking of a few LD-associated molecules with the predicted structures of two oleosins revealed that OsOle1 has slightly higher binding affinities towards fatty acyl glycerol esters, suggesting its role in triacylglycerol accumulation. In fact, OsOle1 expression with the galactose-inducible promoter in Saccharomyces cerevisiae INVSc1 cells augmented lipid content and promoted early LD formation. Moreover, it successfully restored LD biogenesis in a mutant S. cerevisiae strain impaired in LD formation, producing larger LDs with fewer per cell. Ectopic expression of the OsOle1 gene in rice, under a bran-specific promoter, led to reduced seed dimensions (length, 38–39.5%; breadth, 30–32%; weight, 40%) and delayed inflorescence arrival, indicating a slower developmental pace compared to the untransformed control. However, the transgenic rice lines demonstrated a noteworthy increase in seed lipid content by an average of 57.5% in comparison to the untransformed control and accompanied by a conspicuous enlargement in LD dimensions. Thus, OsOle1 emerges as a positive regulator in the context of lipid accumulation, LD formation, and LD enlargement. These findings suggest OsOle1 as a potential target for further exploration aimed at enhancing the oil content of rice seeds.

Pear (Pyrus) is one of the most economically important fruits in temperate regions. Anhui Province is situated in the central region of China and is an area very suitable for the cultivation of pears. A variety of local pear accessions were cultivated in Anhui Province and were named “Anhui pear”, mainly contained “Dangshan pear” and “Huizhou snow pear”. However, little is known about the genetic relationships and population structure of Anhui pears. Here, we analysed the genetic diversity and population structure of 81 pear germplasm resources (48 from Anhui Province) using 242,447 genome-wide single nucleotide polymorphisms (SNPs) by genotyping-by-sequencing (GBS). In our phylogenetic tree, Anhui pears were mainly clustered together with P. pyrifolia and P. bretschneideri, indicating that Anhui pears are closely relationship-related to the sand pear (P. pyrifolia) and the white pear (P. bretschneideri). The combined result of principal component analysis and population structure analysis was sufficient to support the phylogenetic tree. In addition, Dangshan pears and P. bretschneideri were clustered together, and they had almost no genetic differentiation; however, there was rich genetic exchange between them, indicating that Dangshan pears may belong to the same evolutionary branch as white pears. However, Huizhou snow pears did not cluster together with Dangshan pears and clustered into a separate subclass, suggesting that gene flow between the southern and northern regions of Anhui Province was restricted by geographic isolation. These findings may provide important information for broadening the genetic selection of breeding sources, and further utilizing marker-assisted selection to choose new pear varieties that are suitable for Anhui Province.

Sesame (Sesamum indicum L.), an ancient oilseed crop being cultivated across geographical locations in the tropics, is known for its high-quality oil with a longer shelf life. India, being the center of diversity for this crop, understanding the genetic variability of sesame germplasm being conserved in the national Genebank (NGB) of ICAR-NBPGR, will help identify genotypes for its potential use in broadening the genetic base of the cultivars for sesame crop improvement. We report here the molecular diversity analysis performed using SSR markers on a set of 2,496 sesame germplasm. Hence, the derived data was also subjected to population structure analysis, and a molecular core was generated to assess its phenotypic variability. Parallelly, they were phenotypically characterized for important qualitative and quantitative traits as per the standard descriptor developed by IPGRI, and accessions exhibiting desirable traits were identified. The sesame germplasm used in our study represents collections from 17 countries across the globe and 26 states in India. A total of 140 alleles were obtained using seven polymorphic SSR markers selected from an initial screening comprising 43 SSR markers. The observed heterozygosity was less than the expected heterozygosity since it is a self-pollinated crop (up to 35% outcrossing is reported, categorized as often cross-pollinated). The molecular diversity analysis grouped 2496 accessions into six clusters, while the population structure analysis grouped them into three major clusters or populations. A molecular core developed using the PowerCore software identified 196 accessions, representing all the alleles from the entire 2496 accessions, that can be utilized in breeding programs after phenotypic validation. This study contributes to genetic diversity assessment for sesame germplasm, identifying genetically diverse accessions, and establishing a core set that encapsulates the genetic variability of the sesame germplasm collection. These findings hold relevance for addressing agricultural challenges and enhancing the resilience and productivity of sesame crops in various environmental conditions.