Dataset Information

Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.).

ABSTRACT: Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. In the present study, systematic identification and functional analysis of miRNAs under chilling stress were carried out to clarify the molecular mechanism of chilling resistance. Two independent small RNA libraries from leaves of soybean were constructed and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and 3 novel miRNAs were identified. Thirty-five miRNAs were verified by qRT-PCR analysis. Furthermore, their gene targets were identified via high-throughput degradome sequencing. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 51 miRNAs differentially expressed between chilling stress and control conditions. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. Our qRT-PCR analysis confirmed a negative relationship among the miRNAs and their targets under chilling stress. Our work thus provides comprehensive molecular evidence supporting the involvement of miRNAs in chilling-stress responses in vegetable soybean.

SUBMITTER: Xu S

PROVIDER: S-EPMC4877674 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.).

Xu Shengchun S Liu Na N Mao Weihua W Hu Qizan Q Wang Guofu G Gong Yaming Y

Scientific reports 20160524

Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. In the present study, systematic identification and functional analysis of miRNAs under chilling stress were carried out to clarify the molecular mechanism of chilling resistance. Two independent small RNA libraries from leaves of soybean were constructed and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and 3 novel miRNAs were identif ...[more]

PMID: 27216963

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Project description:BackgroundMicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this context, miRNAs and siRNAs are coming to the forefront as molecular mediators of gene regulation in plant responses to annual temperature cycling and cold stress. For this reason, we chose to identify and characterize the conserved and non-conserved miRNA component of peach (Prunus persica (L.) Batsch) focusing our efforts on both the recently released whole genome sequence of peach and sRNA transcriptome sequences from two tissues representing non-dormant leaves and dormant leaf buds. Conserved and non-conserved miRNAs, and their targets were identified. These sRNA resources were used to identify cold-responsive miRNAs whose gene targets co-localize with previously described QTLs for chilling requirement (CR).ResultsAnalysis of 21 million peach sRNA reads allowed us to identify 157 and 230 conserved and non-conserved miRNA sequences. Among the non-conserved miRNAs, we identified 205 that seem to be specific to peach. Comparative genome analysis between peach and Arabidopsis showed that conserved miRNA families, with the exception of miR5021, are similar in size. Sixteen of these conserved miRNA families are deeply rooted in land plant phylogeny as they are present in mosses and/or lycophytes. Within the other conserved miRNA families, five families (miR1446, miR473, miR479, miR3629, and miR3627) were reported only in tree species (Populustrichocarpa, Citrus trifolia, and Prunus persica). Expression analysis identified several up-regulated or down-regulated miRNAs in winter buds versus young leaves. A search of the peach proteome allowed the prediction of target genes for most of the conserved miRNAs and a large fraction of non-conserved miRNAs. A fraction of predicted targets in peach have not been previously reported in other species. Several conserved and non-conserved miRNAs and miRNA-regulated genes co-localize with Quantitative Trait Loci (QTLs) for chilling requirement (CR-QTL) and bloom date (BD-QTL).ConclusionsIn this work, we identified a large set of conserved and non-conserved miRNAs and describe their evolutionary footprint in angiosperm lineages. Several of these miRNAs were induced in winter buds and co-localized with QTLs for chilling requirement and bloom date thus making their gene targets potential candidates for mediating plant responses to cold stress. Several peach homologs of genes participating in the regulation of vernalization in Arabidopsis were identified as differentially expressed miRNAs targets, potentially linking these gene activities to cold responses in peach dormant buds. The non-conserved miRNAs may regulate cellular, physiological or developmental processes specific to peach and/or other tree species.

Project description:Soluble sugar is a major indicator of the intrinsic quality of vegetable soybean [Glycine max (L.) Merr. ]. The improvement of soluble sugar content in soybean is very important due to its healthcare functions for humans. The genetic mechanism of soluble sugar in soybean is unclear. In this study, 278 diverse soybean accessions were utilized to identify the quantitative trait nucleotides (QTNs) for total soluble sugar content in soybean seeds based on a genome-wide association study (GWAS). A total of 25,921 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected for GWAS. Totally, thirteen QTNs associated with total soluble sugar content were identified, which were distributed on ten chromosomes. One hundred and fifteen genes near the 200-kb flanking region of these identified QTNs were considered candidate genes associated with total soluble sugar content in soybean seed. Gene-based association analysis and haplotype analysis were utilized to further identify the effect of candidate genes on total soluble sugar content. Totally, 84 SNPs from seventeen genes across four chromosomes were significantly associated with the total soluble sugar content. Among them, three SNPs from Glyma.02G292900 were identified at two locations, and other eighty-one SNPs from sixteen genes were detected at three locations. Furthermore, expression level analysis of candidate genes revealed that Glyma.02G293200 and Glyma.02G294900 were significantly positively associated with soluble sugar content and Glyma.02G294000 was significantly negatively associated with soluble sugar content. Six genes (i.e., Glyma.02G292600, Glyma.02G292700, Glyma.02G294000, Glyma.02G294300, Glyma.02G294400, and Glyma.15G264200) identified by GWAS were also detected by the analysis of differential expression genes based on soybean germplasms with higher and lower soluble sugar content. Among them, Glyma.02G294000 is the only gene that was identified by gene-based association analysis with total soluble sugar content and was considered an important candidate gene for soluble sugar content. These candidate genes and beneficial alleles would be useful for improving the soluble sugar content of soybean.

Dataset Information

Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.).

Publications

Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.).

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