Identification of an ATP-Binding Cassette Transporter Implicated in Aluminum Tolerance in Wild Soybean (Glycine soja).
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ABSTRACT:
SUBMITTER: Wen K
PROVIDER: S-EPMC8706246 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We obtained a new hybrid soybean (Hybrid) by hybridizing β-carotene-enhanced soybean (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild-type soybean (Wild; Glycine soja). To investigate metabolic changes between variants, we performed metabolic profiling of leaves (three growth stages) and seeds. Multivariate analyses revealed significant metabolic differences between genotypes in seeds and leaves, with seeds showing accumulation of phytosterols, tocopherols, and carotenoids (BCE only), indicating co-induction of the methylerythritol 4-phosphate and mevalonic acid pathways. Additionally, Hybrid produced intermediate levels of carotenoids and high levels of amino acids. Principal component analysis revealed metabolic discrimination between growth stages of soybean leaves and identified differences in leaf groups according to different genotypes at 8, 12, and 16 weeks, with Wild showing higher levels of environmental stress-related compounds relative to BCE and Hybrid leaves. The metabolic profiling approach could be a useful tool to identify metabolic links in various soybean cultivars.
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Project description:Salinity is an important abiotic stress factor that affects growth and yield of soybean. NY36-87 is a wild soybean germplasm with high salt tolerance. In this study, two F2:3 mapping populations derived from NY36-87 and two salt-sensitive soybean cultivars, Zhonghuang39 and Peking, were used to map salt tolerance-related genes. The two populations segregated as 1 (tolerant):2 (heterozygous):1 (sensitive), indicating a Mendelian segregation model. Using simple sequence repeat (SSR) markers together with the bulked segregant analysis (BSA) mapping strategy, we mapped a salt tolerance locus on chromosome 03 in F2:3 population Zhonghuang39×NY36-87 to a 98-kb interval, in which the known gene GmSALT3 co-segregated with the salt tolerance locus. In the F2:3 population of Peking×NY36-87, the dominant salt tolerance-associated gene was detected and mapped on chromosome 18. We named this gene GmSALT18 and fine mapped it to a 241-kb region. Time course analysis and a grafting experiment confirmed that Peking accumulated more Na+ in the shoot via a root-based mechanism. These findings reveal that the tolerant wild soybean line NY36-87 contains salt tolerance-related genes GmSALT3 and GmSALT18, providing genetic material and a novel locus for breeding salt-tolerant soybean.
| S-EPMC8637416 | biostudies-literature
Project description:The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G. soja resistance to SCN race 1. Ten SNPs were significantly associated with the response to race 1. Three SNPs on chromosome 18 were localized within the previously identified quantitative trait loci (QTLs), and two of which were localized within a strong linkage disequilibrium block encompassing a nucleotide-binding (NB)-ARC disease resistance gene (Glyma.18G102600). Genes encoding methyltransferases, the calcium-dependent signaling protein, the leucine-rich repeat kinase family protein, and the NB-ARC disease resistance protein, were identified as promising candidate genes. The identified SNPs and candidate genes can not only shed light on the molecular mechanisms underlying SCN resistance, but also can facilitate soybean improvement employing wild genetic resources.
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Project description:Glycine soja (wild soybean) is known as the wild progenitor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmers. In this study, we determined the complete mitochondrial genome of G. soja. The results revealed that G. soja mt genome is 402,545?bp with 45% GC contents. Furthermore, based on entire mitochondrial genome the evolutionary relationship and phylogenetic analysis revealed that G. soja closely related to G. max.
| S-EPMC7800914 | biostudies-literature
Project description:BackgroundPlant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of saline-alkaline stress transcriptome is mostly focused on saline (NaCl) stress and only limited information on alkaline (NaHCO3) stress is available.ResultsUsing Affymetrix Soybean GeneChip, we conducted transcriptional profiling on Glycine soja roots subjected to 50 mmol/L NaHCO3 treatment. In a total of 7088 probe sets, 3307 were up-regulated and 5720 were down-regulated at various time points. The number of significantly stress regulated genes increased dramatically after 3 h stress treatment and peaked at 6 h. GO enrichment test revealed that most of the differentially expressed genes were involved in signal transduction, energy, transcription, secondary metabolism, transporter, disease and defence response. We also detected 11 microRNAs regulated by NaHCO3 stress.ConclusionsThis is the first comprehensive wild soybean root transcriptome analysis under alkaline stress. These analyses have identified an inventory of genes with altered expression regulated by alkaline stress. The data extend the current understanding of wild soybean alkali stress response by providing a set of robustly selected, differentially expressed genes for further investigation.
| S-EPMC3017823 | biostudies-literature
Project description:The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The G. soja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between G. max and G. gracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with G. cyrtoloba. The sequence of the accD gene from G. soja was highly divergent from those of the other species except for G. max and G. gracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that G. soja is closely related to G. max and G. gracilis. The complete G. soja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.
| S-EPMC5538705 | biostudies-literature
Project description:Aluminum (Al) toxicity limits plant growth and has a major impact on the agricultural productivity in acidic soils. The zinc-finger protein (ZFP) family plays multiple roles in plant development and abiotic stresses. Although previous reports have confirmed the function of these genes, their transcriptional mechanisms in wild soybean (Glycine soja) are unclear. In this study, GsGIS3 was isolated from Al-tolerant wild soybean gene expression profiles to be functionally characterized in Arabidopsis. Laser confocal microscopic observations demonstrated that GsGIS3 is a nuclear protein, containing one C2H2 zinc-finger structure. Our results show that the expression of GsGIS3 was of a much higher level in the stem than in the leaf and root and was upregulated under AlCl3, NaCl or GA3 treatment. Compared to the control, overexpression of GsGIS3 in Arabidopsis improved Al tolerance in transgenic lines with more root growth, higher proline and lower Malondialdehyde (MDA) accumulation under concentrations of AlCl3. Analysis of hematoxylin staining indicated that GsGIS3 enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. Moreover, GsGIS3 expression in Arabidopsis enhanced the expression of Al-tolerance-related genes. Taken together, our findings indicate that GsGIS3, as a C2H2 ZFP, may enhance tolerance to Al toxicity through positive regulation of Al-tolerance-related genes.
| S-EPMC7215988 | biostudies-literature
Project description:Background and aimsWild soybean (Glycine soja), a native species of East Asia, is the closest wild relative of the cultivated soybean (G. max) and supplies valuable genetic resources for cultivar breeding. Analyses of the genetic variation and population structure of wild soybean are fundamental for effective conservation studies and utilization of this valuable genetic resource.MethodsIn this study, 40 wild soybean populations from China were genotyped with 20 microsatellites to investigate the natural population structure and genetic diversity. These results were integrated with previous microsatellite analyses for 231 representative individuals from East Asia to investigate the genetic relationships of wild soybeans from China.Key resultsAnalysis of molecular variance (AMOVA) revealed that 43·92 % of the molecular variance occurred within populations, although relatively low genetic diversity was detected for natural wild soybean populations. Most of the populations exhibited significant effects of a genetic bottleneck. Principal co-ordinate analysis, construction of a Neighbor-Joining tree and Bayesian clustering indicated two main genotypic clusters of wild soybean from China. The wild soybean populations, which are distributed in north-east and south China, separated by the Huang-Huai Valley, displayed similar genotypes, whereas those populations from the Huang-Huai Valley were different.ConclusionsThe previously unknown population structure of the natural populations of wild soybean distributed throughout China was determined. Two evolutionarily significant units were defined and further analysed by combining genetic diversity and structure analyses from Chinese populations with representative samples from Eastern Asia. The study suggests that during the glacial period there may have been an expansion route between south-east and north-east China, via the temperate forests in the East China Sea Land Bridge, which resulted in similar genotypes of wild soybean populations from these regions. Genetic diversity and bottleneck analysis supports that both extensive collection of germplasm resources and habitat management strategies should be undertaken for effective conservation studies of these important wild soybean resources.
| S-EPMC3423801 | biostudies-literature
Project description:Salt stress is a major factor limiting the growth and yield of soybean (Glycine max). Wild soybeans (Glycine soja) contain high allelic diversity and beneficial alleles that can be re-introduced into domesticated soybeans to improve adaption to the environment. However, very few beneficial alleles have been identified from wild soybean. Here, we demonstrate that wild soybean is more salt tolerant than cultivated soybean and examine dehydration responsive element-binding (DREB) family transcription factor genes to look for advantageous alleles that might improve drought tolerance in cultivated soybean. Our genome-wide analysis identified 103 DREB genes from the Glycine max genome. By combined RNA-sequencing and population genetics of wild, landrace, and cultivated soybean accessions, we show that the natural variation in DREB3a and DREB3b is related to differences in salt tolerance in soybean accessions. Interestingly, DREB3b, but not DREB3a, appears to have undergone artificial selection. Soybean plants carrying the wild soybean DREB3b allele (DREB3b39Del ) are more salt tolerant than those containing the reference genome allele (DREB3bRef ). Together, our results suggest that the loss of the DREB3b39Del allele through domestication of cultivated soybean may be associated with a reduction in salt tolerance. Our findings provide crucial information for improving salt tolerance in soybean through molecular breeding.
| S-EPMC8931524 | biostudies-literature
Project description:Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of the saline-alkaline stress transcriptome is most focused on salt (NaCl) stress. Only a little alkaline (NaHCO3) stress transcriptome is limited to one time point after stress. Time-course analysis and comparative investigation on roots in the alkaline stress condition are needed to understand the gene response networks that are subject to alkaline tolerance. We used microarrays to detail the global programme of gene expression underlying NaHCO3 treatment and identified distinct classes of regulated genes during this process.
2010-08-14 | GSE17883 | GEO