Plant Gene最新文献

In Japan, Lithospermum erythrorhizon grows in the wild, and its roots are traditionally used for dyeing and medicinal purposes. However, due to excessive harvesting and changes in the natural environment, the population of this species has significantly declined over the past decades. To conserve the domestic varieties, it is important to obtain genomic information that accurately represents their pure lineage. The objective of this study was to characterize the chloroplast genome, which serves as a valuable phylogenetic marker, using next-generation sequencing. The results revealed that the DNA has a typical quadripartite structure, spanning 150,478 bp with a GC content of 35.5%. A total of 113 unique genes are encoded, including 80 protein-coding genes, 4 ribosomal RNA genes, and 29 transfer RNA genes. Comparative plastome analyses involving 13 Boraginaceae species, including L. erythrorhizon, showed high similarities in the gene order and codon usage, while an accelerated substitution rate was observed in matK. Phylogenetic analyses using this gene and 71 common protein-coding genes indicated a close evolutional relationship between L. erythrorhizon and Glandora prostrata. Furthermore, when comparing the chloroplast genome assembly data of a Chinese variety, a total of 44 structural variants were identified. Most of these variants were mononucleotide or dinucleotide in size, but a 70 bp insertion/deletion was identified in the intergenic region flanked by the accD and psaI genes. The presence of this relatively substantial structural variant indicates that the maternal lineages of the Japanese and Chinese varieties examined in this study are distinctly different.

Anthocyanin biosynthesis, a process regulated by distinct MYB and MYC transcription factors, plays a crucial role in determining pigmentation in various tissue of plants. This study aimed to investigate the impact of overexpressing the OsC1 gene from black rice, encoding a MYB transcription factor, on anthocyanin pigmentation in red indica rice cv. Kasalath. Anthocyanin pigmentation was readily observed as purple spots in calli and as purple shoot tips and purple leaf sheath in transgenic seedlings. We confirmed the presence of the transgene using GUS assay and PCR analysis, and the pigmentation segregated following a 3:1 Mendelian ratio. T₀ and T₁ transgenic plants exhibits anthocyanin accumulation in various tissues including leaf sheaths, auricles, nodes, stigma, apiculus and awns, excluding the pericarp. Notably, the pigmentation in node tissues has not been previously reported for the OsC1 gene, and this gene does not involve in pericarp pigmentation. RT-PCR analysis of transgenic seedlings demonstrated that the overexpression of the OsC1 gene upregulated anthocyanin structural genes, particularly OsDFR, leading to anthocyanin accumulation. Intriguingly, the absence of OsB2 expression, encoding a MYC transcription factor, in transgenic seedlings suggests the involvement of alternative MYC factors in purple leaf sheaths. This study not only expands our understanding of OsC1's role in tissue specific anthocyanin pigmentation but also proposes OsC1 as a potential visible marker in rice transformation. Utilizing OsC1 as a marker provides an alternative approach to address concerns related to antibiotic-resistant genes while providing visually striking pigmentation.

Nitrogen (N) is an indispensable macronutrient for crop growth and yield. The N can be acquired and assimilated from a variety of sources such as nitrate (NO₃⁻), ammonium (NH₄⁺), and urea [CO(NH₂)₂]. Due to its low cost, urea is a popular N source in pastures. The urea transporter DUR3 gene, which can mediate direct urea uptake by roots, has received little attention in grasses. The purpose of the current study was to identify and characterize in silico the DUR3 gene in 29 grass species in comparison to Arabidopsis thaliana. Physicochemical properties, gene structure, motifs, and phylogenetic tree relationships were predicted. Furthermore, the relative expression patterns of the DUR3 gene were evaluated in two commercial cultivars (Mombaça and Aruana) of Megathyrsus maximus. Plants were grown in a nutritive solution containing 2 mM of N supplied as NO₃⁻, NH₄⁺, or [CO(NH₂)₂]. To investigate the relative expression of the DUR3 gene in leaves and roots we used the 2^-ΔΔCt method. The in silico characterization revealed that the DUR3 gene is highly conserved among grasses. Plants were submitted to 3 days of N starvation and the tissue was harvested 3 h after transfer to ammonium or urea solution. In general, the DUR3 gene was down-regulated in leaves and up-regulated in roots for both cultivars. Twenty-four hours after transfer, only the Mombaça cultivar showed a significant decrease of DUR3 mRNA levels in leaves and an increase in roots under urea, demonstrating that the DUR3 gene expression pattern is variable between cultivars of M. maximus. Characterizing of the DUR3 gene in grasses is the first step toward biotechnological approaches aiming to improve urea uptake in pastures.

Sugarcane smut, caused by Sporisorium scitamineum, is a major disease worldwide. Breeding resistant cultivars is the main management strategy. However, occasional failure to detect susceptible clones due to unfavorable environmental conditions, inconsistency in disease ratings between experiments, and continued clone losses due to pathogen adaptability are some of the challenges for this strategy. The development and use of molecular markers associated with smut resistance may overcome these limitations allowing more accurate identification of resistant parents and progeny. A genetic analysis was conducted using an inoculated population of 162 F₁ progeny from a biparental cross between susceptible/female and resistant/male parents to identify quantitative trait loci (QTLs) associated with resistance. A total of 1574 single dose (SD) single-nucleotide polymorphisms (SNP) markers used to construct a genetic map resulted in 253 linkage groups (LGs) of which 150 LGs were assigned to the female parent and 204 LG to the male parent with a genome coverage of 24,580 cM. (Composite) interval mapping with selective sub-populations identified six consistent QTLs that cumulatively explained 25.74% of the phenotypic variance with LOD scores ranging from 3.17 to 23.7. Four out of 12 SNP markers closest to the QTL peaks had effect >10 for resistance in the heterozygous condition. Genes known to be involved in disease resistance, such as cellulose synthase, expansin, protein degradation, and receptor-kinase were linked to the genomic regions associated with smut resistance. The markers upon validation in different populations can be utilized for marker-assisted selection.

Pigeonpea production is limited in Benin due to the undesirable agronomic and organoleptic characteristics of cultivated landraces. For a breeding program, some exotic cultivars were introduced for improving the available genepool in the country. The present study aims to assess the genetic diversity within a collection comprising of 32 local and 28 exotic cultivars, with the objective of selecting suitable parental lines for pigeonpea genetic improvement. All of the 60 accessions were genotyped with 14 SSR makers and a total of 38 alleles were detected with an average of 2.71 alleles per locus. The mean value of PIC (Polymorphism Information Content) and overall gene diversity were 0.37 and 0.43, respectively, while the mean value of heterozygosity was 0.11, indicating moderate genetic diversity within the 60 accessions with a deficit of heterozygous genotypes. As expected, the diversity was higher in exotic cultivars than in local landraces. Based on the genetic relationship among accessions, the entire collection formed 3 clusters, one of which comprised four specific exotic accessions. Population structure analysis using model-based and DAPC (Discriminant Analysis for Principal Components) methods subdivided the 60 accessions into two major groups reflecting their geographic origins with a minimal number (02) of admixtures. This indicates significant genetic divergence between local and exotic cultivars. Analysis of Molecular Variance (AMOVA) results with an overall Fst value of 0.13 confirmed the significant genetic divergence between the two collections. The findings of this study will significantly benefit for pigeonpea breeding programs in Benin. For practical applications, selected exotic cultivars, particularly those within the specific cluster can immediately serve as donor parents in crossbreeding schemes with the local landraces, for developing new varieties.

Diseases and insect pests greatly impact sustainable production in maize. Maize inbred lines have varying levels of resistance to these pathogens and insects, but little is known about the diversity of their resistance proteins. In this study, genes encoding seven proteins that are involved in resistance to insects and pathogens in maize were analyzed in 46 maize inbred lines to elucidate the differences in amino acid sequences. The proteins of interest are superlectin, maizewin, hydrolase, geranyl geranyl transferase, quinone oxidoreductase, AIL1, and defensin. The protein sequences encoded by genes for superlectin, AIL1, and defensin were found to be disrupted in some maize inbreds but were conserved in others. The characterized disruptions resulted from single amino acid changes, insertions, or deletions. While the effect of single amino acid changes is hard to predict, insertions and deletions likely disrupt protein function, increasing the susceptibility of maize plants to insects and/or diseases. Functional resistance genes can be incorporated from the identified maize inbreds into commercial hybrids to promote enhanced insect and pathogen resistance.

Temperature stress is a factor limiting agricultural production in many regions. High and low temperatures can cause irreversible damage to plants, affecting the development and profitability of crops, and are a threat to national and global food security. Raising agricultural outputs by developing elite crop cultivars capable of coping with damaging environmental temperatures is a primary objective of plant breeders. Gene editing systems offer opportunities to rapidly develop improved cultivars. Gene editing has already been applied to several species to improve valuable traits, including yield, quality, nutritional values and tolerance to abiotic and biotic stresses. This review focuses on the recent progress and future potential of gene editing in developing new cultivars with greater heat and cold stress tolerance.

We evaluated the selected populations of eighteen open-pollinated short-day onion genotypes for FBR-Fusarium basal rot (Fusarium oxysporum f. sp. cepae-FOC) susceptibility; population genetic variation via ISSR marker; and transcriptome analysis using qRT-PCR with six novel selected marker genes: R1, R5, RGA29, lectin, LOX, and Osmotin, at tree time post inoculation (wpi). Screening for resistance showed the average severity between 4.7 and 88.9%; of which, the lowest one was in ‘Saba’ and ‘Saba – HS (6.7 and 4.7%, respectively). ISSR analysis recorded 226 amplified bands, of which 160 bands showed polymorphism, of which ISSR1 and ISSR10 primers showed the best performance. We also found that following inoculation with FOC could regulate defense-related marker genes; R1, PR5, Lectin, LOX, Osmotin, and RGA29 in resistant onion “Saba” and ‘Saba’-HS in comparison to susceptible and controls, non-inoculated ones ranging from 1.23 to 6.99 -fold significantly. Surprisingly, marker genes; Lectin, LOX, and Osmotin were also expressed to FOC simultaneous, though basically are resistance to other biotic and abiotic stress: Lectin to Rhizoctonia solani, Aphid, and major sap-sucking pests; LOX to root-knot and cyst nematode, Heterodera glycines; Osmotin to drought stredd, and oxidative burst in plants. This indicates the double, and or multiple roles of our selected marker genes covering two or more functions at a time. The findings introduce newly resistant onion genotypes, and also can be used in management programs to reduce damages caused by FOC disease. Cumulatively, the transcriptome-data provide novel-insights into the response of onions for improving onion-breeding to FOC.

Measurement of chlorophyll fluorescence is one of the methods to detect a disorder in the photosynthetic system, which reflects the photochemical state of the plant. Identification of the genetic structure of chlorophyll fluorescence parameters can provide useful solutions for breeding varieties with higher potential. The present study was conducted with the aim of identifying quantitative loci (QTL) related to chlorophyll fluorescence parameters in an Iranian RILs wheat population. One hundred and twenty F8 RILs of wheat derived from crossing Kohdasht (KHD) and Gonbad (GND) cultivars in the form of an alpha lattice design were studied in 2019 and 2020. The analysis of QTLs was performed in the software R using the package QTL.gCIMapping.GUI v2.0. The genetic map was constructed with 423 SSR markers, 21 CBDP markers, 58 ISJ markers, and 19 SCoT markers (521 polymorphic alleles) distributed on 21 wheat chromosomes. This map covered 3167.9 cM of the wheat genome and had an average marker spacing of 6.1, 6, and 6.2 cM for the A, B, and D genomes, respectively. Thirteen of the fourteen QTLs discovered in 2019 and four of the nine QTLs discovered in 2020 had an explanatory coefficient greater than 15% and were considered major QTLs. In 2019, pleiotropic QTLs were found at position 1.79 cM on chromosome 3A and between two markers Xwmc11-3A and BARC1177. In 2020, two QTLs, qABS/ RC 1B and qTRo/ RC 1B were located at position 36.80 cM 1B and between two markers Xgpw4331-1B and Xgpw5162-1B, and two QTLs, qETo/ RC-5D and qREo / RC-5D were located at position 63.25 cM chromosome 5D and correspond to the position of marker cfd266. Pleiotropic QTLs as well as major QTLs can be used in marker-assisted selection for chlorophyll fluorescence traits in wheat breeding projects.