Effects of Biological Nitrogen Metabolism on Glufosinate-Susceptible and -Resistant Goosegrass (Eleusine indica L.).

Glufosinate is a broad-spectrum herbicide used to control most weeds in agriculture worldwide. Goosegrass (Eleusine indica L.) is one of the top ten malignant weeds across the world, showing high tolerance to glufosinate via different mechanisms that are not yet fully understood. This study revealed that nitrogen metabolism could be a target-resistant site, providing clues to finally clarify the mechanism of glufosinate resistance in resistant goosegrass populations. Compared to susceptible goosegrass (NX), the resistant goosegrass (AUS and CS) regarding the stress of glufosinate showed stronger resistance with lower ammonia contents, higher target enzyme GS (glutamine synthetase) activity, and lower GOGAT (glutamine 2-oxoglutarate aminotransferase) activity. The GDH (glutamate dehydrogenase) activity of another pathway increased, but its gene expression was downregulated in resistant goosegrass (AUS). Analyzing the transcriptome and proteome data of goosegrass under glufosinate stress at 36 h showed that the KEGG pathway of the nitrogen metabolism was enriched in glufosinate-susceptible goosegrass (NX), but not in glufosinate-resistant goosegrass (CS and AUS). Several putative target genes involved in glufosinate stress countermeasures were identified. This study provides specific insights into the nitrogen metabolism of resistant goosegrass, and gives a basis for future functional verification of glufosinate-tolerance genes in plants.

QTL mapping for aluminum tolerance in RIL population of soybean (Glycine max L.) by RAD sequencing.

Aluminum (Al3+) toxicity is a typical abiotic stress that severely limits crop production in acidic soils. In this study, an RIL (recombinant inbred line, F12) population derived from the cross of Zhonghuang 24 (ZH 24) and Huaxia 3 (HX 3) (160 lines) was tested using hydroponic cultivation. Relative root elongation (RRE) and apical Al3+ content (AAC) were evaluated for each line, and a significant negative correlation was detected between the two indicators. Based on a high-density genetic linkage map, the phenotypic data were used to identify quantitative trait loci (QTLs) associated with these traits. With composite interval mapping (CIM) of the linkage map, five QTLs that explained 39.65% of RRE and AAC variation were detected on chromosomes (Chrs) Gm04, Gm16, Gm17 and Gm19. Two new QTLs, qRRE_04 and qAAC_04, were located on the same region of bin93-bin94 on Chr Gm04, which explained 7.09% and 8.98% phenotypic variation, respectively. Furthermore, the results of the expression analysis of candidate genes in the five genetic regions of the QTLs showed that six genes (Glyma.04g218700, Glyma.04g212800, Glyma.04g213300, Glyma.04g217400, Glyma.04g216100 and Glyma.04g220600) exhibited significant differential expression between the Al3+ treatment and the control of two parents. The results of qRT-PCR analysis indicated that Glyma.04g218700 was upregulated by Al3+ treatment with the hundreds-fold increased expression level and may be a candidate gene with potential roles in the response to aluminum stress. Therefore, our efforts will enable future functional analysis of candidate genes and will contribute to the strategies for improvement of aluminum tolerance in soybean.

The differences of cell wall in roots between two contrasting soybean cultivars exposed to cadmium at young seedlings.

The plant root cell wall (CW) is the first structure that comes into contact with extracellular cadmium (Cd), and it plays an important role in the absorption, immobilization, and translocation of Cd in the roots. However, the differences in the cell wall components between Cd-tolerant and Cd-sensitive cultivars are unclear. A hydroponic experiment was carried out to investigate the differences in the concentrations of Cd, total sugars, and uronic acid in pectin, hemicellulose 1, hemicellulose 2, cellulose, and lignin, as well as pectin methylesterase enzyme activity (PME) in the roots of two soybean cultivars that differ with respect to Cd tolerance exposed to 0 and 23 µM Cd treatments. The bound forms of Cd in the roots were found to differ between the two soybean genotypes; 50.2% of the Cd in the root cell wall accumulates in the pectin in the highly Cd-tolerant and low Cd-accumulating cultivar HX3, while 50.6% of the root cell wall Cd accumulates in cellulose in the Cd-sensitive and high Cd-accumulating cultivar BX10. The total sugar and uronic acid concentrations of the cell wall components increased in response to Cd stress, while the concentrations of total sugars and uronic acid in BX10 were higher than in HX3 (except for hemicellulose 1). Increased demethylation of pectin may be the main reason that Cd is mainly concentrated in the primary wall in HX3, because the PME activity was higher in HX3 than it was in BX10 under Cd treatment. Furthermore, BX10 had a higher lignin concentration after Cd treatment, and showed the same change in cellulose. Cd in the root cell wall of BX10 was fixed in the secondary cell wall, which may be a result of the coupling to cellulose and lignin. In conclusion, root cell walls in soybean cultivars that differ in Cd tolerance may possess different mechanisms to prevent Cd from entering cells, and the sequestration of Cd in different cell wall components may determine the differences in Cd tolerance between the two genotypes.

Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses.

BACKGROUND: The P1B-ATPase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as Arabidopsis thaliana and Oryza sativa. Emerging evidence indicates that one homolog in Glycine max is also involved in cadmium (Cd) stress, but the gene family has not been fully investigated in soybean. RESULTS: Here, we identified 20 heavy metal ATPase (HMA) family members in the soybean genome, presented as 10 paralogous pairs, which is significantly greater than the number in Arabidopsis or rice, and was likely caused by the latest whole genome duplication event in soybean. A phylogenetic analysis divided the 20 members into six groups, each having conserved or divergent gene structures and protein motif patterns. The integration of RNA-sequencing and qRT-PCR data from multiple tissues provided an overall expression pattern for the HMA family in soybean. Further comparisons of expression patterns and the single nucleotide polymorphism distribution between paralogous pairs suggested functional conservation and the divergence of HMA genes during soybean evolution. Finally, analyses of the HMAs expressed in response to Cd stress provided evidence on how plants manage Cd tolerance, at least in the two contrasting soybean genotypes examined. CONCLUSIONS: The genome-wide identification, chromosomal distribution, gene structures, and evolutionary and expression analyses of the 20 HMA genes in soybean provide an overall insight into their potential involvement in Cd responses. These results will facilitate further research on the HMA gene family, and their conserved and divergent biological functions in soybean.

Root morphological responses of five soybean [Glycine max (L.) Merr] cultivars to cadmium stress at young seedlings.

To examine the differences in root morphological responses of soybean cultivars with different cadmium (Cd) tolerance and accumulation to Cd stress, the biomass, Cd concentration, and root morphological features of five soybean cultivars were determined under 0, 9, 23, 45, and 90 µM Cd stress via hydroponic experiments. Significantly genotypic differences in Cd tolerance and Cd concentration were observed between five soybean cultivars at four Cd levels. For Cd tolerance, HX3 showed a strong Cd tolerance with tolerance indexes of shoot biomass at 92.49, 76.44, 60.21, and 46.45% after 18 days at four Cd levels, and others had similar weak tolerance at young seedling. For Cd accumulation, Cd concentration in roots showed far higher than that in shoots. The different accumulation features in roots and shoots among five cultivars were found at four Cd levels. Comparing with the control, the total root length (RL), root surface area (SA), and root volume (RV) of all cultivars were decreased significantly at four Cd levels. Tolerant cultivar HX3 had the largest root system and sensitive cultivar BX10 had the smallest root system at young seedling stage. Correlation analysis indicated that RL, SA, and RV were positively correlated with root biomass and shoot biomass under 9 and 23 µM Cd treatments, but root average diameter (RD) was negatively correlated with shoot biomass and root biomass only under 9 µM Cd treatments, while RL and SA were negatively correlated with root Cd concentration under 23 and 45 µM Cd treatments. The results suggested that root morphological traits were closely related to Cd tolerance at young seedlings under Cd treatments.

Comparison of subcellular distribution and chemical forms of cadmium among four soybean cultivars at young seedlings.

The hydroponic experiment was carried out to investigate the Cd subcellular distribution and chemical forms in roots and shoots among four soybean seedling cultivars with two Cd treatments. HX3 and GC8, two tolerant and low-grain-Cd-accumulating cultivars, had the lowest Cd concentration in roots and high Cd concentration in shoots, while BX10 and ZH24, two sensitive and high-grain-Cd-accumulating cultivars, had the highest Cd concentration in roots and the lowest Cd concentration in shoots at young seedling stage. Furthermore, the sequence of Cd subcellular distribution in roots at two Cd levels was cell wall (53.4-75.5 %) > soluble fraction (15.8-40.4 %) > organelle fraction (2.0-14.7 %), but in shoots, was soluble fraction (39.3-74.8 %) > cell wall (16.0-52.0 %) > organelle (4.8-19.5 %). BX10 and ZH24 had higher Cd concentration in all subcellular fractions in roots, but HX3 and GC8 had higher Cd concentration of soluble fraction in shoots. The sequence of Cd chemical forms in roots was FNacl (64.1-79.5 %) > FHAC (3.4-21.5 %) > Fd-H2O (3.6-13.0 %) > Fethanol (1.4-21.8) > FHCl (0.3-1.6 %) > Fother (0.2-1.4 %) at two Cd levels but, in shoots, was FNacl (19.7-51.4 %) ≥ FHAC (10.2-31.4 %) ≥ Fd-H2O (8.8-28.2 %) ≥ Fethanol (8.9-38.6 %) > FHCl (0.2-9.6 %) > Fother (2.5-11.2 %). BX10 and ZH24 had higher Cd concentrations in each extracted solutions from roots, but from shoots for GC8 and HX3. Taken together, the results uncover that root cell walls and leaf vacuoles might play important roles in Cd detoxification and limiting the symplastic movement of Cd.

Identification and comparative analysis of cadmium tolerance-associated miRNAs and their targets in two soybean genotypes.

MicroRNAs (miRNAs) play crucial roles in regulating the expression of various stress responses genes in plants. To investigate soybean (Glycine max) miRNAs involved in the response to cadmium (Cd), microarrays containing 953 unique miRNA probes were employed to identify differences in the expression patterns of the miRNAs between different genotypes, Huaxia3 (HX3, Cd-tolerant) and Zhonghuang24 (ZH24, Cd-sensitive). Twenty six Cd-responsive miRNAs were identified in total. Among them, nine were detected in both cultivars, while five were expressed only in HX3 and 12 were only in ZH24. The expression of 16 miRNAs was tested by qRT-PCR and most of the identified miRNAs were found to have similar expression patterns with microarray. Three hundred and seventy six target genes were identified for 204 miRNAs from a mixture degradome library, which was constructed from the root of HX3 and ZH24 with or without Cd treatment. Fifty five genes were identified to be cleaved by 14 Cd-responsive miRNAs. Gene ontology (GO) annotations showed that these target transcripts are implicated in a broad range of biological processes. In addition, the expression patterns of ten target genes were validated by qRT-PCR. The characterization of the miRNAs and the associated target genes in response to Cd exposure provides a framework for understanding the molecular mechanism of heavy metal tolerance in plants.

Identification of wild soybean miRNAs and their target genes responsive to aluminum stress.

BACKGROUND: MicroRNAs (miRNAs) play important regulatory roles in development and stress response in plants. Wild soybean (Glycine soja) has undergone long-term natural selection and may have evolved special mechanisms to survive stress conditions as a result. However, little information about miRNAs especially miRNAs responsive to aluminum (Al) stress is available in wild soybean. RESULTS: Two small RNA libraries and two degradome libraries were constructed from the roots of Al-treated and Al-free G. soja seedlings. For miRNA identification, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries, respectively, were generated, and 97 known miRNAs and 31 novel miRNAs were identified. In addition, 49 p3 or p5 strands of known miRNAs were found. Among all the identified miRNAs, the expressions of 30 miRNAs were responsive to Al stress. Through degradome sequencing, 86 genes were identified as targets of the known miRNAs and five genes were found to be the targets of the novel miRNAs obtained in this study. Gene ontology (GO) annotations of target transcripts indicated that 52 target genes cleaved by conserved miRNA families might play roles in the regulation of transcription. Additionally, some genes, such as those for the auxin response factor (ARF), domain-containing disease resistance protein (NB-ARC), leucine-rich repeat and toll/interleukin-1 receptor-like protein (LRR-TIR) domain protein, cation transporting ATPase, Myb transcription factors, and the no apical meristem (NAM) protein, that are known to be responsive to stress, were found to be cleaved under Al stress conditions. CONCLUSIONS: A number of miRNAs and their targets were detected in wild soybean. Some of them that were responsive to biotic and abiotic stresses were regulated by Al stress. These findings provide valuable information to understand the function of miRNAs in Al tolerance.

Root plasma membrane H+-ATPase is involved in the adaptation of soybean to phosphorus starvation.

The plasma membrane H+-ATPase plays an important role in the plant response to nutrient and environmental stresses. However, the involvement of plant root plasma membrane H+-ATPase in adaptation to phosphate (P) starvation is not yet fully elucidated. In this study, experiments were performed with soybean roots in low-P nutrient solution (10 microM). Treatment with fusicoccin, an activator of the plasma membrane H+-ATPase, increased P uptake by 35%, while vanadate, an inhibitor of plasma membrane H+-ATPase, severely suppressed it. These results suggested that P uptake might be regulated via the modulation of the activity of plasma membrane H+-ATPase under P starvation. The relationship between P uptake and the activity of plasma membrane H+-ATPase was examined further by using plasma membrane H+-ATPase transgenic Arabidopsis thaliana under low-P conditions. Transgenic plants absorbed more P compared with wild-type Arabidopsis. Results from real-time RT-PCR, western-blotting and immunolocalization analysis indicated that the increase in activity of the plasma membrane H+-ATPase by P starvation was caused by its transcriptional and translational regulation. A higher expression was observed at the translational level than at the transcriptional level. P starvation could induce a transient increase of endogenous indole-3-acetic acid (IAA) in soybean roots. The exogenous application of IAA stimulated the activity of plasma membrane H+-ATPase and P uptake, while naphthylphthalamic acid (NPA), an IAA transport inhibitor, blocked IAA effects. Taken together, these results suggested an involvement of root plasma membrane H+-ATPase in the adaptation of soybean to P starvation. IAA might be involved in signal transduction of P starvation by activating the plasma membrane H+-ATPase in soybean roots.