Two-step method for isolation of high-quality RNA from stored seeds of maize rich in starch

Combined Metabolome and Transcriptome Analyses of Maize Leaves Reveal Global Effect of Biochar on Mechanisms Involved in Anti-Herbivory to Spodoptera frugiperda

Fall armyworm (FAW, Spodoptera frugiperda) has now spread to more than 26 Chinese provinces. The government is working with farmers and researchers to find ways to prevent and control this pest. The use of biochar is one of the economic and environmentally friendly strategies to increase plant growth and improve pest resistance. We tested four v/v combinations of bamboo charcoal with coconut bran [BC1 (10:1), BC2(30:1), BC3(50:1)] against a control (CK) in maize. We found that plant height, stem thickness, fresh weight and chlorophyll content were significantly higher in BC2, in addition to the lowest FAW survival %. We then compared the metabolome and transcriptome profiles of BC2 and CK maize plants under FAW herbivory. Our results show that the levels of flavonoids, amino acids and derivatives, nucleotides and derivatives and most phenolic acids decreased, while terpenoids, organic acids, lipids and defense-related hormones increased in BC-grown maize leaves. Transcriptome sequencing revealed consistent expression profiles of genes enriched in these pathways. We also observed the increased expression of genes related to abscisic acid, jasmonic acid, auxin and MAPK signaling. Based on these observations, we discussed the possible pathways involved in maize against FAW herbivory. We conclude that bamboo charcoal induces anti-herbivory responses in maize leaves.

Exploring novel SNPs and candidate genes associated with seed allometry in Pisum sativum L

Seed size is an important agronomic trait that indicates seed quality. In legumes, pods with equal and larger seeds remain the first preference of farmers and consumers. Genetic understanding related to seed size including seed allometric traits has been limited in the case of peas. To fill this void the findings presented here used the genome-wide association studies (GWAS) to identify novel candidate gene(s) putatively linked with seed size in Pisum sativum L. The study was conducted on 240 Pea Single Plant Plus Collection (PSPPC) panels of pea germplasm. Allometric traits measured included seed_length, seed_width, seed_thickness, seed_volume, seed_biomass, and seed_biomass by volume (SB_V). GWAS was performed using the Genome Association and Prediction Integrated Tool (GAPIT) on R-studio. The Bayesian information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model provided significant single nucleotide polymorphisms (SNPs) linked with all the seed allometric traits. When analyzed the genomic regions of these SNPs provided a list of candidate genes that may be related to seed size. The present study thus provides a list of significant SNPs and relevant genes viz. Psat2g072000 for seed_length, Psat4g104320 for seed_width, Psat6g125800 and Psat6g125840 for seed_thickness, Psat6g228320 for seed_volume, Psat2g143920 for seed_biomass, and Psat2g120400 for SB_V which may prove useful in the improvement of pea seed size using breeding programs or CRISPR intervention. Understanding the genetic basis of seed size could lead to crop development with desirable seed characteristics, such as equal and larger-sized seeds with maximum yield and higher nutritional content.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01499-6.

Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number

The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.

Ectopic expression of a bacterial thiamin monophosphate kinase enhances vitamin B1 biosynthesis in plants

Plants and bacteria have distinct pathways to synthesize the bioactive vitamin B1 thiamin diphosphate (TDP). In plants, thiamin monophosphate (TMP) synthesized in the TDP biosynthetic pathway is first converted to thiamin by a phosphatase, which is then pyrophosphorylated to TDP. In contrast, bacteria use a TMP kinase encoded by ThiL to phosphorylate TMP to TDP directly. The Arabidopsis THIAMIN REQUIRING2 (TH2)-encoded phosphatase is involved in TDP biosynthesis. The chlorotic th2 mutants have high TMP and low thiamin and TDP. Ectopic expression of Escherichia coli ThiL and ThiL-GFP rescued the th2-3 mutant, suggesting that the bacterial TMP kinase could directly convert TMP into TDP in Arabidopsis. These results provide direct evidence that the chlorotic phenotype of th2-3 is caused by TDP rather than thiamin deficiency. Transgenic Arabidopsis harboring engineered ThiL-GFP targeting to the cytosol, chloroplast, mitochondrion, or nucleus accumulated higher TDP than the wild type (WT). Ectopic expression of E. coli ThiL driven by the UBIQUITIN (UBI) promoter or an endosperm-specific GLUTELIN1 (GT1) promoter also enhanced TDP biosynthesis in rice. The pUBI:ThiL transgenic rice accumulated more TDP and total vitamin B1 in the leaves, and the pGT1:ThiL transgenic lines had higher TDP and total vitamin B1 in the seeds than the WT. Total vitamin B1 only increased by approximately 25-30% in the polished and unpolished seeds of the pGT1:ThiL transgenic rice compared to the WT. Nevertheless, these results suggest that genetic engineering of a bacterial vitamin B1 biosynthetic gene downstream of TMP can enhance vitamin B1 production in rice.

Overexpression of an Inositol Phosphorylceramide Glucuronosyltransferase Gene IbIPUT1 Inhibits Na+ Uptake in Sweet Potato Roots

IPUT1 is a glycosyltransferase capable of synthesizing the glycosyl inositol phosphorylceramide (GIPC) sphingolipid. The GIPC sphingolipid is a Na⁺ receptor on cell membranes which can sense extracellular Na⁺ concentrations, promote the increase in intracellular Ca²⁺ concentrations, and plays critical roles in maintaining intracellular Na⁺ balance. Therefore, the IPUT1 gene plays an important role in the genetic improvement of crop salt tolerance. Herein, the IbIPUT1 gene, which encodes an ortholog of Arabidopsis AtIPUT1, from sweet potato was cloned. Agrobacterium rhizogenes-mediated in vivo transgenic technology, non-invasive micro-measuring technology (NMT) and Na⁺ fluorescence imaging technology were then combined to quickly study the potential function of IbIPUT1 in salt tolerance. The data showed that IbIPUT1 was involved in the regulation of root cell Na⁺ balance, and the overexpression of IbIPUT1 could not promote sweet potato root cell Na⁺ efflux under salt stress, but it could significantly inhibit the Na⁺ absorption of root cells, thereby reducing the accumulation of Na⁺ in root cells under salt stress. Additionally, Ca²⁺ efflux in transgenic root cells was slightly higher than that in control roots under salt stress. Collectively, an efficient transgenic method for gene function studies was established, and our results suggested that IbIPUT1 acts as a candidate gene for the genetic enhancement of sweet potato salt tolerance.

Expression analysis of β-carotene hydroxylase1 and opaque2 genes governing accumulation of provitamin-A, lysine and tryptophan during kernel development in biofortified sweet corn

Traditional sweet corn possesses low levels of provitamin-A (proA), lysine and tryptophan. Mutant version of β-carotene hydroxylase1 (crtRB1) gene affecting the accumulation of β-carotene (BC), β-cryptoxanthin (BCX) and proA, and opaque2 (o2) gene governing the enhancement of lysine and tryptophan were introgressed together into elite sweet corn inbreds through marker-assisted selection. Here, we analyzed the expression pattern of crtRB1 and o2 genes among introgressed and traditional sweet corn inbreds at 20-, 24- and 28-days after pollination (DAP). The introgressed inbreds possessed two- to sevenfolds higher BC, BCX, proA, lysine and tryptophan compared to their original inbreds. However, all the nutrients attained the peak at 20-DAP (BC: 9.95 µg/g, BCX: 8.21 µg/g, proA: 14.05 µg/g, lysine: 0.301%, tryptophan: 0.074%), which gradually reduced through 24-DAP (BC: 8.24 µg/g, BCX: 7.53 µg/g, proA: 12.01 µg/g, lysine: 0.273%, tryptophan: 0.057%) and 28-DAP (BC: 5.84 µg/g, BCX: 5.82 µg/g, proA: 8.75 µg/g, lysine: 0.202%, tryptophan: 0.037%). Biofortified sweet corn inbreds possessed significantly lower expression levels of crtRB1 (4.1-fold) and o2 (2.2-fold) compared to their wild type alleles in traditional sweet corn inbreds across DAPs. The expression of crtRB1 and o2 increased from 20-DAP to attain the highest peak at 24-DAP, and further decreased by 28-DAP. The transcript levels of crtRB1 were negatively correlated with BC (r = - 0.83), BCX (r = - 0.79) and proA (r = - 0.83) across dates of harvest. Lysine (r = - 0.83) and tryptophan (r = - 0.73) were also inversely associated with o2 transcript levels. This is the first report on expression of crtRB1 and o2 genes during kernel development in biofortified sweet corn. This information holds immense promise in understanding the dynamics of gene-regulation during kernel development in sweet corn.