Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean

Abstract

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.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean

“…For Al toxicity treatment, 3-day-old seedlings were transferred to 0.5 mM CaCl 2 (pH = 4.3) for one day, then to 0.5 mM CaCl 2 solution (pH = 4.3) containing 25 μM AlCl 3 (Al stress) or without Al (control). The primary root tips (0–1 cm) of ten seedlings were collected at 6, 12 and 24 h for Al stress and control, respectively [24]. For Cd and heat treatments, the soybean seedlings were transferred to containers filled with 1/2 Hoagland solution (pH = 5.8), which was replaced every three days.…”

Carbohydrate metabolism in the subtending leaf cross‐acclimates to waterlogging and elevated temperature stress and influences boll biomass in cotton (Gossypium hirsutum)

“…The qRT‐PCR was performed in a final volume of 15 µl containing 2 µl cDNA, 7.5 µl 2× SYBR Premix Ex Taq (TaKaRa), and 200 n M of forward and reverse primers. The amplification program was set as follows: initial denaturation at 95°C for 5 min; 40 cycles of denaturation at 95°C for 10 s, annealing at 58°C for 20 s and extension at 72°C for 20 s as described previously by Liu et al (). Each experiment was performed in triplicate.…”

“…The amplification program was set as follows: initial denaturation at 95 ∘ C for 5 min; 40 cycles of denaturation at 95 ∘ C for 10 s, annealing at 58 ∘ C for 20 s and extension at 72 ∘ C for 20 s as described previously by Liu et al (2016). Each experiment was performed in triplicate.…”

Breeding Maize for Tolerance to Acidic Soils: A Review

“…The MATE gene has been cloned and identified in several crops such as Arabidopsis [55], barley [133], wheat [134], sorghum [129], rice [135], bean [136], poplar [137], soybean [138], and maize [130,131] (Table 3). The Al-tolerant allele for the MATE1 locus was found to contain a tandem gene triplication and to have higher levels of gene expression compared to the sensitive allele with a single gene copy [131].…”