Physiological and molecular aspects of aspartate-derived amino acid metabolism during germination and post-germination growth in two maize genotypes differing in germination efficiency

Assessing sequence variation, haplotype analysis and molecular characterisation of aspartate kinase2 (ask2) gene regulating methionine biosynthesis in diverse maize inbreds

Traditional maize grain is deficient in methionine, an essential amino acid required for proper growth and development in humans and poultry birds. Thus, development of high methionine maize (HMM) assumes great significance in alleviating malnutrition through sustainable and cost-effective approach. Of various genetic loci, aspartate kinase2 (ask2) gene plays a pivotal role in regulating methionine accumulation in maize. Here, we sequenced the entire ask2 gene of 5394 bp with 13 exons in five wild and five mutant maize inbreds to understand variation at nucleotide level. Sequence analysis revealed that an SNP in exon-13 caused thymine to adenine transversion giving rise to a favourable mutant allele associated with leucine to glutamine substitution in mutant ASK2 protein. Gene-based diversity analysis with 11 InDel markers grouped 48 diverse inbreds into three major clusters with an average genetic dissimilarity of 0.570 (range, 0.0-0.9). The average major allele frequency, gene diversity and PIC are 0.693, 0.408 and 0.341, respectively. A total of 45 haplotypes of the ask2 gene were identified among the maize inbreds. Evolutionary relationship analysis performed among 22 orthologues grouped them into five major clusters. The number of exons varied from 7 to 17, with length varying from 12 to 495 bp among orthologues. ASK2 protein with 565 amino acids was predicted to be in homo-dimeric state with lysine and tartaric acid as binding ligands. Amino acid kinase and ACT domains were found to be conserved in maize and orthologues. The study depicted the presence of enough genetic diversity in ask2 gene in maize, and development of HMM can be accelerated through introgression of favourable allele of ask2 into the parental lines of elite hybrids using molecular breeding.

Genome-wide association study reveals that the cupin domain protein OsCDP3.10 regulates seed vigour in rice

Seed vigour is an imperative trait for the direct seeding of rice. In this study, we examined the genetic regulation of seedling percentage at the early germination using a genome-wide association study in rice. One major quantitative trait loci qSP3 for seedling percentage was identified, and the candidate gene was validated as qSP3, encoding a cupin domain protein OsCDP3.10 for the synthesis of 52 kDa globulin. Disruption of this gene in Oscdp3.10 mutants reduced the seed vigour, including the germination potential and seedling percentage, at the early germination in rice. The lacking accumulation of 52 kDa globulin was observed in the mature grains of the Oscdp3.10 mutants. The significantly lower amino acid contents were observed in the mature grains and the early germinating seeds of the Oscdp3.10 mutants compared with those of wild-type. Rice OsCDP3.10 regulated seed vigour mainly via modulating the amino acids e.g. Met, Glu, His, and Tyr that contribute to hydrogen peroxide (H₂ O₂ ) accumulation in the germinating seeds. These results provide important insights into the application of seed priming with the amino acids and the selection of OsCDP3.10 to improve seed vigour in rice.

Time-Course Comparative Metabolome Analysis of Different Barley Varieties during Malting

Malt production is one of the important uses of barley, and its quality differs greatly depending on the barley varieties used. In this study, ultraperformance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry technology was used to investigate the temporal changes of metabolites during malting in two barley varieties: Franklin (malt barley) and Yerong (non-malt barley). Also, differences in metabolite profiles were compared in the kilned malt between two other malt barley varieties (Copeland and Planet) and two non-malt varieties (ZD10 and Hua30). Results showed that degradation of trisaccharide and accumulation of UDP-glucose and mannose-1-phosphate are the key metabolic events during steeping, with Franklin showing earlier and greater changes. Earlier increase of sugars and amino acids in Franklin is associated with its faster germination rate. Comparative metabolome analysis of kilned malt from the different barley varieties indicated that malt barley accumulated more sugars, hordatine-glucoside, and oxoproline, and non-malt barley accumulated more polyphenols and monogalactosylmonoacylglycerol. These results improved the understanding of the genotypic difference in the formation of malt quality at the metabolomic level.

A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice

Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.

Dynamic Transcriptomic and Metabolomic Analyses of Madhuca pasquieri (Dubard) H. J. Lam During the Post-germination Stages

The wild population of Madhuca pasquieri (Dubard) H. J. Lam is currently dwindling; its understory seedlings are rare, and there is a lack of molecular studies, which impedes the conservation of this species. This study exploited second-generation sequencing and widely targeted metabolomics analysis to uncover the dynamic changes in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in five post-germination stages of M. pasquieri whole organism. Notably, the weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analyses all indicated significant enrichment of the flavonoid biosynthesis pathway in stage 4 (two-leaf), and an upregulation of the genes encoding flavonol biosynthesis in this stage. In stage 5 (nine-leaf), the flavonols were significantly accumulated, indicating that the changes in metabolites were driven at the transcript level. According to the significant changes in gene expression encoding auxin transport carriers and their correlation with flavonols during stage 5, the flavonols were speculated to have a direct inhibitory effect on the expression of PIN4 encoding gene, which may inhibit the process of polar auxin transport. The results provided important insights into the molecular network relationships between the transcription and metabolism of this rare and endangered species during the post-germination stages and explained the reasons for the slow growth of its seedlings at the molecular level.

Gibberellin Increases the Bud Yield and Theanine Accumulation in Camellia sinensis (L.) Kuntze

Tea (Camellia sinensis) is one of the most important cash crops in the world. Theanine, as an important amino acid component in tea, is a key quality index for excellent tea quality and high economic value. People increase theanine accumulation in tea mainly through the application of nitrogen fertilizer, shading and pruning. However, these methods are not effective. In this study, we treated tea buds with a 100 μM solution of GA₃ containing 1‰ tween-20, investigated the effects of GA₃ on theanine accumulation, bud yield, chlorophyll fluorescence parameters and expression level of theanine biosynthesis pathway genes in tea plant by qPCR, LC-MS/MS etc. Results showed that change trends of theanine and GA₃ was extremely positively correlated with each other. Exogenous GA₃ upregulated the expression level of theanine biosynthesis pathway genes, caused an increase of theanine content (mg·g^-1) by 27% in tea leaves compared with Mock, and accelerated the germination of buds and elongation of shoots, which lead to a significant increase of tea yield by 56% (w/w). Moreover, the decrease of chlorophyll contents, photochemical quenching coefficient (qP) and relative electron transport rate (rETR) under GA₃ treatment suggested that GA₃ reduced photosynthesis in the tender tea leaves, indicating that the decline of carbon assimilation in tea plants was conducive to the nitrogen metabolism, and it was beneficial to the accumulation of theanine. This study provided a new technical and theoretical support for the precise control of tea quality components and phenophase.

Field-based assessment of the mechanism of maize yield enhancement by Azospirillum lipoferum CRT1

Plant Growth-Promoting Bacteria (PGPB) of the genus Azospirillum are known to enhance root growth and yield in many plant species including cereals. To probe the underlying mechanisms, correlations between modifications of yield and 6-leaf plantlet characteristics were estimated on maize in four fields with contrasting soil properties over two consecutive years using the commercial isolate A. lipoferum CRT1. In both years, plantlet metabolome, photosynthetic potential and organ morphology were found to display field- and inoculation-specific signatures. Metabolomic analyses revealed that A. lipoferum CRT1 mostly affected sugar metabolism with no suggested impact on N and P assimilation. Mineral nitrogen feeding increased yield but did not affect yield enhancement by the bacterial partner. However, greater improvements of leaf photosynthetic potential correlated with yield diminutions and larger plantlets in all of their proportions correlated with yield enhancements. Bacterial inoculation restored proper seed-to-adult plant ratio when it accidentally dropped below 80%. Only in these cases did it raise yield. All in all, securing mature plant density is hypothesized as being the primary driver of A. lipoferum CRT1-mediated yield enhancement in maize fields.

Nitrogen metabolism in the developing ear of maize (Zea mays): analysis of two lines contrasting in their mode of nitrogen management

*The main steps of nitrogen (N) metabolism were characterized in the developing ear of the two maize (Zea mays) lines F2 and Io, which were previously used to investigate the genetic basis of nitrogen use efficiency (NUE) in relation to yield. *During the grain-filling period, we monitored changes in metabolite content, enzyme activities and steady-state levels of transcripts for marker genes of amino acid synthesis and interconversion in the cob and the kernels. *Under low N fertilization conditions, line Io accumulated glutamine, asparagine and alanine preferentially in the developing kernels, whereas in line F2, glutamine and proline were the predominant amino acids. Quantification of the mRNA-encoding enzymes involved in asparagine, alanine and proline biosynthesis confirmed that the differences observed between the two lines at the physiological level are likely to be attributable to enhanced expression of the cognate genes. *Integrative analysis of physiological and gene expression data indicated that the developing ear of line Io had higher N use and transport capacities than line F2. Thus, in maize there is genetic and environmental control of N metabolism not only in vegetative source organs but also in reproductive sink organs.

Ureide metabolism during seedling development in French bean (Phaseolus vulgaris)

French bean (Phaseolus vulgaris) is a legume that transports most of the atmospheric nitrogen fixed in its nodules to the aerial parts of the plant as ureides. Changes in ureide content and in enzymatic activities involved in their metabolism were identified in the cotyledons and embryonic axes during germination and early seedling development. Accumulation of ureides (ca. 1300 nmol per pair of cotyledons) was observed in the cotyledons of dry seeds. Throughout germination, the total amount of ureides slightly decreased to about 1200 nmol, but increased both in cotyledons and in embryonic axes after radicle emergence. In the axes, the ureides were almost equally distributed in roots, hypocotyls and epicotyls. The pattern of ureide distribution was not affected by the presence of nitrate or sucrose in the media up to 6 days after imbibition. Ureides are synthesized from purines because allopurinol (a xanthine dehydrogenase inhibitor) blocks the increase of ureides. Allantoin and allantoate-degrading activities were detected in French bean dried seeds, whereas no ureidoglycolate-degrading activity was detected. During germination, the levels of the three activities remain unchanged in cotyledons. After radicle emergence, the levels of activities in cotyledons changed. Allantoin-degrading activity increased, allantoate-degrading activity decreased and ureidoglycolate-degrading activity remained undetectable in cotyledons. In developing embryonic axes, the three activities were detected throughout germination and early seedling development. The embryonic axes are able to synthesize ureides, because those compounds accumulated in axes without cotyledons.

Genetic variability of nitrogen accumulation during vegetative development and remobilization during the forcing process in witloof chicory tuberized root (Cichorium intybus L.)

A better knowledge of genetic variability of traits related to nitrogen use efficiency (NUE) is a potential strategy to optimize N fertilization and to reduce environmental pollution without decreasing marketable yield and quality. To this aim, in this study, 13 cultivars of witloof chicory were compared with three reference cultivars known for their adaptation to low, intermediate and high N availability in the field during the vegetative phase of development. Pertinent criteria used for this study were determined by a thorough comparison of nitrogen reserve accumulation in tuberized roots during vegetative development and mobilization during the forcing process in the three reference cultivars. Cluster analysis allowed us to sort the cultivars into four main groups we named G1, G2, G3 and G4. Cultivars of group G4, better adapted to soils with high nitrogen contents (N-demanding cultivars), showed higher total N, nitrate, total amino acids (AA), glutamine contents and lower total N and AA mobilization for chicon growth than did cultivars of group G1, adapted to soils with low nitrogen content (N-sensitive cultivars). An intermediate behavior was exhibited by cultivars of groups G2 and G3, characterized as N tolerant. It is proposed that either chicory growers or breeders may take advantage of the genetic variability revealed in the present study to gain flexibility in choosing the right cultivar for the type of soil available (N-rich soil vs N-poor soil) or to adapt the level of N fertilization to the type of cultivar (N-demanding vs N-sensitive) in order to target the highest NUE for the best chicon yield and trade quality.

Differential transcription initiation and alternative RNA splicing of Knox7, a class 2 homeobox gene of maize

Knox7, a class 2 homeobox gene has been characterized in maize. A combination of experimental (3'- and 5'-RACE) and bioinformatics approaches supported the idea that Knox7 would be transcribed into two alternative transcripts by differential initiation of transcription. Sequence differences between alternative transcripts, Knox7L the larger and Knox7S the smaller, were confined to their 5' end regions and exon 1 was only found in Knox7L transcripts. Deduced proteins shared the same homeodomain, while an Ala and Ala/Gly rich domain was found only in KNOX7L protein. We hypothesize that KNOX7L and KNOX7S might regulate (differentially) the expression of the same gene(s) by binding competitively to the same cis-acting element(s). Further expression analysis using RT-PCR to amplify cDNA portions corresponding to ORFs of both Knox7 alternative transcripts showed that seven cDNA clones were probably generated by alternative splicing of Knox7L. Alignment of these sequences showed that they are in frame suggesting the existence of the corresponding proteins. Quantitative RT-PCR experiments indicated that Knox7S and Knox7L were expressed in maize embryos during germination. In the same tissue, expression of Knox7S was stimulated by light and ABA and inhibited by GA, two hormones that control germination process.