BackgroundMultidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean.ResultsA total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes.ConclusionsA total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2559-8) contains supplementary material, which is available to authorized users.

BackgroundAldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited.ResultsIn present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis. These groupings were supported by their gene structures and conserved motifs. Soybean ALDH superfamily expanded mainly by whole genome duplication/segmental duplications. Gene network analysis identified 1146 putative co-functional genes of 51 GmALDHs. Gene Ontology (GO) enrichment analysis suggested the co-functional genes of these 51 GmALDHs were enriched (FDR < 1e-3) in the process of lipid metabolism, photosynthesis, proline catabolism, and small molecule catabolism. In addition, 22 co-functional genes of GmALDHs are related to plant response to water deprivation/water transport. GmALDHs exhibited various expression patterns in different soybean tissues. The expression levels of 13 GmALDHs were significantly up-regulated and 14 down-regulated in response to water deficit. The occurrence frequencies of three drought-responsive cis-elements (ABRE, CRT/DRE, and GTGCnTGC/G) were compared in GmALDH genes that were up-, down-, or non-regulated by water deficit. Higher frequency of these three cis-elements was observed for the group of up-regulated GmALDH genes as compared to the group of down- or non- regulated GmALDHs by drought stress, implying their potential roles in the regulation of soybean response to drought stress.ConclusionsA total of 53 ALDH genes were identified in soybean genome and their phylogenetic relationships and duplication patterns were analyzed. The potential functions of GmALDHs were predicted by analyses of their co-functional gene networks, gene expression profiles, and cis-regulatory elements. Three GmALDH genes, including GmALDH3H2, GmALDH12A2 and GmALDH18B3, were highly induced by drought stress in soybean leaves. Our study provides a foundation for future investigations of GmALDH gene function in soybean.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3908-y) contains supplementary material, which is available to authorized users.

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Ariadne (ARI) subfamily of RBR (Ring Between Ring fingers) proteins have been found as a group of putative E3 ubiquitin ligases containing RING (Really Interesting New Gene) finger domains in fruitfly, mouse, human and Arabidopsis. Recent studies showed several RING-type E3 ubiquitin ligases play important roles in plant response to abiotic stresses, but the function of ARI in plants is largely unknown. In this study, an ariadne-like E3 ubiquitin ligase gene was isolated from soybean, Glycine max (L.) Merr., and designated as GmARI1. It encodes a predicted protein of 586 amino acids with a RBR supra-domain. Subcellular localization studies using Arabidopsis protoplast cells indicated GmARI protein was located in nucleus. The expression of GmARI1 in soybean roots was induced as early as 2–4 h after simulated stress treatments such as aluminum, which coincided with the fact of aluminum toxicity firstly and mainly acting on plant roots. In vitro ubiquitination assay showed GmARI1 protein has E3 ligase activity. Overexpression of GmARI1 significantly enhanced the aluminum tolerance of transgenic Arabidopsis. These findings suggest that GmARI1 encodes a RBR type E3 ligase, which may play important roles in plant tolerance to aluminum stress.

Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed “phenylpropanoid biosynthesis” and “phenylalanine metabolism” pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity.

Aluminum (Al) toxicity is a major factor limiting crop productivity on acid soils. Soybean (Glycine max) is an important oil crop and there is great variation in Al tolerance in soybean germplasms. However, only a few Al-tolerance genes have been reported in soybean. Therefore, the purpose of this study was to identify candidate Al tolerance genes by comparative transcriptome analysis of two contrasting soybean varieties in response to Al stress. Two soybean varieties, M90-24 (M) and Pella (P), which showed significant difference in Al tolerance, were used for RNA-seq analysis. We identified a total of 354 Al-tolerance related genes, which showed up-regulated expression by Al in the Al-tolerant soybean variety M and higher transcript levels in M than P under Al stress. These genes were enriched in the Gene Ontology (GO) terms of cellular glucan metabolic process and regulation of transcription. Five out of 11 genes in the enriched GO term of cellular glucan metabolic process encode cellulose synthases, and one cellulose synthase gene (Glyma.02G205800) was identified as the key hub gene by co-expression network analysis. Furthermore, treatment of soybean roots with a cellulose biosynthesis inhibitor decreased the Al tolerance, indicating an important role of cellulose production in soybean tolerance to Al toxicity. This study provides a list of candidate genes for further investigation on Al tolerance mechanisms in soybean.

Litchi (Litchi chinensis Sonn.) pericarp contains abundant polyphenols that are suitable materials for developing active packaging films. In this study, 1 wt%, 3 wt% and 5 wt% of litchi pericarp extract (LPE) was added into qua-ternary ammonium chitosan (QAC) and polyvinyl alcohol (PVA) matrix to develop active packaging films. The structural, physical and functional properties of QAC-PVA (QP) films were compared with LPE (QP-LPE films) and without LPE (QP films). Results showed QP film had a heterogenous cross-section whereas QP-LPE films displayed rough and uneven cross-sections. After adding LPE, the N–H, O–H, C–H and C=O stretching bands of QP films shifted due to the formation of intermolecular interactions between LPE and film matrix. LPE made the colorless QP film turned brown. QP-LPE films presented lower ultraviolet–visible light transmittance than QP film. After adding LPE, film thickness increased from 0.091 to 0.103 mm, film water vapor permeability increased from 14.98 × 10−11 to 17.21 × 10−11 g m−1 s−1 Pa−1, film oxygen permeability increased from 0.16 to 0.22 cm3 mm m−2 day−1 atm−1, film tensile strength increased from 14.10 to 17.41 MPa, and film elongation at break decreased from 36.94% to 25.13%. QP-LPE films quickly released polyphenols in distilled water within 4 h and displayed potent antioxidant activity. The antimicrobial ratio of the film against Escherichia coli, Salmonella typhimurium, Staphylococcus aureus and Listeria monocytogenes was elevated from 50.40−68.04% to 58.93−91.38% after adding LPE. Results suggested QP-LPE films could be utilized as antioxidant and antimicrobial packaging materials in food industry.

To determine the combining effects of nitrogen application rate and planting density on rice yield and grain quality formation under salinity conditions, a field experiment was conducted in the coastal saline area using Oryza sativa L. cv. Nangeng 9108 from 2019 to 2020. The experiment was designed with six nitrogen rates (0, 210, 255, 300, 345, and 390 kg ha−1; denoted as N0-N390, respectively) and two transplanting densities (334,000 and 278,000 hills ha−1; denoted as D1 and D2, respectively). The results indicated that, with the increase of nitrogen input rate, the panicles number and spikelets per panicle increased first, subsequently decreased, and peaked under 300 kg ha−1 N, whereas the filled-kernel rate and grain weight displayed a decreasing trend. The panicle number and grain weight were higher under D1 treatment compared to those under D2 treatment, while the spikelet number per panicle and the filled-kernel rate displayed an opposite trend. The grain yield displayed highest under N300D1 treatment among all treatments, accompanied by the highest agronomic N use efficiency, and the actual yield reached 8060.4 kg ha−1 and 7869.8 kg ha−1 in 2019 and 2020, respectively. Increased nitrogen application rate significantly improved the grain processing quality and nutritional quality, while reducing the appearance quality and cooking/eating quality. Higher transplant density was conductive to grain nutritional quality, but notably reduced the processing quality, appearance quality and cooking/eating quality. Overall, a combination of 300 kg ha−1 nitrogen rate and 334,000 hills ha−1 planting density was recommended for relatively higher rice yield and better grain quality in the saline area.