Junbo Du

Dormancy and germination: How does the crop seed decide?

Whether seeds germinate or maintain dormancy is decided upon through very intricate physiological processes. Correct timing of these processes is most important for the plants life cycle. If moist conditions are encountered, a low dormancy level causes pre-harvest sprouting in various crop species, such as wheat, corn and rice, this decreases crop yield and negatively impacts downstream industrial processing. In contrast, a deep level of seed dormancy prevents normal germination even under favourable conditions, resulting in a low emergence rate during agricultural production. Therefore, an optimal seed dormancy level is valuable for modern mechanised agricultural systems. Over the past several years, numerous studies have demonstrated that diverse endogenous and environmental factors regulate the balance between dormancy and germination, such as light, temperature, water status and bacteria in soil, and phytohormones such as ABA (abscisic acid) and GA (gibberellic acid). In this updated review, we highlight recent advances regarding the molecular mechanisms underlying regulation of seed dormancy and germination processes, including the external environmental and internal hormonal cues, and primarily focusing on the staple crop species. Furthermore, future challenges and research directions for developing a full understanding of crop seed dormancy and germination are also discussed.

Transcriptome Analysis of Shade-Induced Inhibition on Leaf Size in Relay Intercropped Soybean

Multi-species intercropping is a sustainable agricultural practice worldwide used to utilize resources more efficiently. In intercropping systems, short crops often grow under vegetative shade of tall crops. Soybean, one important legume, is often planted in intercropping. However, little is known about the mechanisms of shade inhibition effect on leaf size in soybean leaves at the transcriptome level. We analyzed the transcriptome of shaded soybean leaves via RNA-Seq technology. We found that transcription 1085 genes in mature leaves and 1847 genes in young leaves were significantly affected by shade. Gene ontology analyses showed that expression of genes enriched in polysaccharide metabolism was down-regulated, but genes enriched in auxin stimulus were up-regulated in mature leaves; and genes enriched in cell cycling, DNA-replication were down-regulated in young leaves. These results suggest that the inhibition of higher auxin content and shortage of sugar supply on cell division and cell expansion contribute to smaller and thinner leaf morphology, which highlights potential research targets such as auxin and sugar regulation on leaves for crop adaptation to shade in intercropping.

Karrikins delay soybean seed germination by mediating abscisic acid and gibberellin biogenesis under shaded conditions

Karrikins (KAR) are a class of signal compounds, discovered in wildfire smoke, which affect seed germination. Currently, numerous studies have focused on the model plant Arabidopsis in the KAR research field, rather than on crops. Thus the regulatory mechanisms underlying KAR regulation of crop seed germination are largely unknown. Here, we report that KAR delayed soybean seed germination through enhancing abscisic acid (ABA) biosynthesis, while impairing gibberellin (GA) biogenesis. Interestingly, KAR only retarded soybean seed germination under shaded conditions, rather than under dark and white light conditions, which differs from in Arabidopsis. Phytohormone quantification showed that KAR enhanced ABA biogenesis while impairing GA biosynthesis during the seed imbibition process, and subsequently, the ratio of active GA4 to ABA was significantly reduced. Further qRT-PCR analysis showed that the transcription pattern of genes involved in ABA and GA metabolic pathways are consistent with the hormonal measurements. Finally, fluridone, an ABA biogenesis inhibitor, remarkably rescued the delayed-germination phenotype of KAR-treatment; and paclobutrazol, a GA biosynthesis inhibitor, inhibited soybean seed germination. Taken together, these evidences suggest that KAR inhibit soybean seed germination by mediating the ratio between GA and ABA biogenesis.

Fungal Diversity in Field Mold-Damaged Soybean Fruits and Pathogenicity Identification Based on High-Throughput rDNA Sequencing

Continuous rain and an abnormally wet climate during harvest can easily lead to soybean plants being damaged by field mold (FM), which can reduce seed yield and quality. However, to date, the underlying pathogen and its resistance mechanism have remained unclear. The objective of the present study was to investigate the fungal diversity of various soybean varieties and to identify and confirm the FM pathogenic fungi. A total of 62,382 fungal ITS1 sequences clustered into 164 operational taxonomic units (OTUs) with 97% sequence similarity; 69 taxa were recovered from the samples by internal transcribed spacer (ITS) region sequencing. The fungal community compositions differed among the tested soybeans, with 42 OTUs being amplified from all varieties. The quadratic relationships between fungal diversity and organ-specific mildew indexes were analyzed, confirming that mildew on soybean pods can mitigate FM damage to the seeds. In addition, four potentially pathogenic fungi were isolated from FM-damaged soybean fruits; morphological and molecular identification confirmed these fungi as Aspergillus flavus, A. niger, Fusarium moniliforme, and Penicillium chrysogenum. Further re-inoculation experiments demonstrated that F. moniliforme is dominant among these FM pathogenic fungi. These results lay the foundation for future studies on mitigating or preventing FM damage to soybean.

Salt Stress Represses Soybean Seed Germination by Negatively Regulating GA Biosynthesis While Positively Mediating ABA Biosynthesis

Soybean is an important and staple oilseed crop worldwide. Salinity stress has adverse effects on soybean development periods, especially on seed germination and post-germinative growth. Improving seed germination and emergence will have positive effects under salt stress conditions on agricultural production. Here we report that NaCl delays soybean seed germination by negatively regulating gibberellin (GA) while positively mediating abscisic acid (ABA) biogenesis, which leads to a decrease in the GA/ABA ratio. This study suggests that fluridone (FLUN), an ABA biogenesis inhibitor, might be a potential plant growth regulator that can promote soybean seed germination under saline stress. Different soybean cultivars, which possessed distinct genetic backgrounds, showed a similar repressed phenotype during seed germination under exogenous NaCl application. Biochemical analysis revealed that NaCl treatment led to high MDA (malondialdehyde) level during germination and the post-germinative growth stages. Furthermore, catalase, superoxide dismutase, and peroxidase activities also changed after NaCl treatment. Subsequent quantitative Real-Time Polymerase Chain Reaction analysis showed that the transcription levels of ABA and GA biogenesis and signaling genes were altered after NaCl treatment. In line with this, phytohormone measurement also revealed that NaCl considerably down-regulated active GA1, GA3, and GA4 levels, whereas the ABA content was up-regulated; and therefore ratios, such as GA1/ABA, GA3/ABA, and GA4/ABA, are decreased. Consistent with the hormonal quantification, FLUN partially rescued the delayed-germination phenotype caused by NaCl-treatment. Altogether, these results demonstrate that NaCl stress inhibits soybean seed germination by decreasing the GA/ABA ratio, and that FLUN might be a potential plant growth regulator that could promote soybean seed germination under salinity stress.

WATER USE EFFICIENCY AND WATER DISTRIBUTION RESPONSE TO DIFFERENT PLANTING PATTERNS IN MAIZE–SOYBEAN RELAY STRIP INTERCROPPING SYSTEMS

Understanding crop water use in mixed crops over sole cropping is vital for developing optimum water management systems for crop production. In this study, a two-year field experiment with typical maize (Zea mays L.) and soybean [Glycine max (L.) Merr.] relay strip intercropping (2:2 maize-to-soybean rows; 200 cm bandwidth) was carried out in the 2013 and 2014 growing seasons. The quantitative effects of various planting patterns on the water-use efficiency (WUE) and water distribution were investigated. Our results indicated that soil volumetric water content and soil evaporation in the intercropping systems showed decreasing trends in the order: maize row (MM) < maize-to-soybean row (MS) < soybean row (SS). The highest leaf transpiration (1.91 and 2.07 mmol m⁻² s⁻¹) for the intercropped maize was measured in each of the two years in the 20 cm maize narrow-row planting pattern and decreased thereafter. Opposite trend was observed for the intercropped soybean; the highest soybean leaf transpiration (7.01 and 6.80 mmol m⁻² s⁻¹ for 2013 and 2014, respectively) was recorded in the 70 cm. The WUE of maize and soybean intercrops was lower than that of sole crop counterparts. However, the maximum group water use efficiency (GWUE) of 26.08 and 26.20 kg ha⁻¹ mm⁻¹ in the 40–50 cm maize narrow-row planting pattern was, respectively, 39.6% and 23% higher compared with that of sole crops. The water equivalent ratio (WER) values ranged from 1.60–1.79, suggesting better crop water use in the intercrops over sole cropping. Planting patterns provided by 40–50 cm maize narrow-row spacing were considered the most efficient in terms of maximum total yields, GWUE and WER. These results suggest that an appropriate reduction in the spacing of narrow maize row with wide soybean row could be an efficient crop management method to achieve optimal WUE and homogeneous water distribution in maize–soybean intercropping systems.

Metabolomic tool to identify soybean [ Glycine max (L.) Merrill] germplasms with a high level of shade tolerance at the seedling stage

The isoflavone profiles of seeds of various soybean genotypes with different levels of shade tolerance at the seedling stage were investigated. High-performance liquid chromatography (HPLC) was used to quantify 12 isoflavones, and the data were analyzed using a multivariate statistical analysis. Combined with field experimental data and an orthogonal partial least-squares discriminant analysis (OPLS-DA), several aglycones (genistein (GE), daidzein (DE), and glycitein (GLE)) were selected and identified as key compounds involved in the shade tolerance of soybean seedlings. Additional correlation analysis and laboratory shading stress experiments with soybean seedlings also confirmed the function of these selected isoflavones, especially GE, in the discrimination of soybean seedlings with different levels of shade tolerance. Furthermore, the structure–antioxidant activity relationships between a range of isoflavones and the plant shade-tolerance mechanism are discussed. Targeted metabolomic analyses of isoflavones could reveal the diversity of shade tolerance in soybean seedlings, thus contributing to the breeding of excellent soybean varieties.

Exogenous auxin represses soybean seed germination through decreasing the gibberellin/abscisic acid (GA/ABA) ratio

Auxin is an important phytohormone which mediates diverse development processes in plants. Published research has demonstrated that auxin induces seed dormancy. However, the precise mechanisms underlying the effect of auxin on seed germination need further investigation, especially the relationship between auxins and both abscisic acid (ABA) and gibberellins (GAs), the latter two phytohormones being the key regulators of seed germination. Here we report that exogenous auxin treatment represses soybean seed germination by enhancing ABA biosynthesis, while impairing GA biogenesis, and finally decreasing GA1/ABA and GA4/ABA ratios. Microscope observation showed that auxin treatment delayed rupture of the soybean seed coat and radicle protrusion. qPCR assay revealed that transcription of the genes involved in ABA biosynthetic pathway was up-regulated by application of auxin, while expression of genes involved in GA biosynthetic pathway was down-regulated. Accordingly, further phytohormone quantification shows that auxin significantly increased ABA content, whereas the active GA1 and GA4 levels were decreased, resulting insignificant decreases in the ratiosGA1/ABA and GA4/ABA.Consistent with this, ABA biosynthesis inhibitor fluridone reversed the delayed-germination phenotype associated with auxin treatment, while paclobutrazol, a GA biosynthesis inhibitor, inhibited soybean seed germination. Altogether, exogenous auxin represses soybean seed germination by mediating ABA and GA biosynthesis.

Effect of narrow-row planting patterns on crop competitive and economic advantage in maize-soybean relay strip intercropping system

Abstract Narrow-row planting patterns directly affect crop yield and competition in intercropping systems. A two-year (2012 and 2013) field experiment was conducted to determine the interactive behavior between intercrops in a maize–soybean relay strip intercropping system. Maize plants were planted in different narrow-wide row planting patterns, whereas soybean was planted in wide rows. The total biomass and grain yield of maize increased with increasing maize narrow-row spacing, but the opposite trend was observed for soybean. The aggressivity, competitive ratio, and partial relative crowding advantage values for maize were greater than those for soybean. Moreover, the competitive interaction of the intercrops was affected by the distance between maize and soybean rows. The highest intercrop land equivalent ratio (LER) 1.61 and 1.59 was found in the 40:160 planting pattern (i.e. 40 cm narrow-row spacing and 160 cm wide-row spacing of maize) during 2012 and 2013, respectively. Combined with actual yield loss and LER, the intense intra-specific competition of maize plants reduced the depression for the associated soybeans when the maize narrow-row spacing was less than 30 cm. When the narrow-row spacing was wider than 50 cm, soybean growth was seriously depressed by maize because of the stronger inter-specific competition between maize and soybean. The maximum yield and economic advantage appeared in the 40:160 narrow-wide row planting pattern. Therefore, intercropping advantage may be achieved by changing the row spacing and distance between intercrop rows to coordinate the inter-specific competition between maize and soybean.

Metabolism variation and better storability of dark- versus light-coloured soybean (Glycine max L. Merr.) seeds

The effects of storage duration on the seed germination and metabolite profiling of soybean seeds with five different coloured coats were studied. Their germination, constituents and transcript expressions of isoflavones and free fatty acids (FFAs) were compared using chromatographic metabolomic profiling and transcriptome sequencing. The seed water content was characterized using nuclear magnetic resonance (NMR) relaxometry. Results showed that dark-coloured seeds were less inactivated than light-coloured seeds. The aglycone and β-glucoside concentrations of upstream constituents increased significantly, whereas the acetylglucosides and malonylglucosides of downstream constituents decreased with an increase in the storage period. FFAs increased considerably in the soybean seeds as a result of storage. These results indicate that dark-coloured soybean seeds have better storability than light-coloured seeds, and seed water content plays a role in seed inactivation. It was concluded that there are certain metabolic regularities that are associated with different coloured seed coats of soybeans under storage conditions.