Dataset Information

Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.

ABSTRACT: Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.

SUBMITTER: Chu S

PROVIDER: S-EPMC7555642 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.

Chu Shanshan S Zhang Xiangqian X Yu Kaiye K Lv Lingling L Sun Chongyuan C Liu Xiaoqian X Zhang Jinyu J Jiao Yongqing Y Zhang Dan D

International journal of molecular sciences 20200917 18

Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean gen ...[more]

PMID: 32957498

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Project description:Southwest of China is one of the major soybean (Glycine max L.) production regions in China with low availability of soil phosphorus (P). Whereas little information is available on P-efficient soybean genotypes in this region, even though using P-efficient soybean genotypes is a sustainable P management strategy for enhancing yield and P use efficiency. To assess the genetic variation on P use efficiency, 274 soybean genotypes were employed to compare the yields and P acquisition potentials in the field. Additionally, 10 representational genotypes (5 P-efficient genotypes and 5 P-inefficient genotypes) were grown in hydroponic media containing low P treatment (0.05 mM L-1) and high P treatment (0.25 mM L-1) to further investigate P assimilation characteristics and the related mechanisms of P-efficient soybean genotypes. In the field trial, the models described the relationships between yield and seed P concentration (R2 = 0.85), shoot P accumulation (R2 = 0.84), HI (R2 = 0.82) well. The yield, seed P concentration and shoot P accumulation ranged from 5.5 to 36.0 g plant-1, from 0.045 to 0.93% and from 0.065 to 0.278 mg plant-1, respectively. In the hydroponic trial, P-efficient genotypes under low P treatment showed significantly better plant growth, P accumulation and root: shoot ratio than P-inefficient genotypes. Simultaneously, total root length, specific root length, root surface area and root volume of P-efficient were significantly greater than P-inefficient under low P treatment. Higher rate of organic acid exudation and acid phosphatase activities was observed in the P-efficient soybean genotypes under low P condition when compared to the P-inefficient soybean genotypes. It indicated that significant genetic variation for P use efficiency existed in this region, and the P-efficient soybean genotypes, especially E311 and E141, demonstrated great tolerance to P deficiency, which could be potential materials using in improving production and P use efficiency in low availability of soil P region.

Project description:IntroductionPlants undergo divergent adaptations to form different ecotypes when exposed to different habitats. Ecotypes with ecological adaptation advantages are excellent germplasm resources for crop improvement.Methodshis study comprehensively compared the differences in morphology and physiological mechanisms in the roots of two different ecotypes of wild soybean (Glycine soja) seedlings under artificially simulated low-phosphorus (LP) stress.ResultThe seedlings of barren-tolerant wild soybean (GS2) suffered less damage than common wild soybean (GS1). GS2 absorbed more phosphorus (P) by increasing root length. In-depth integrated analyses of transcriptomics and metabolomics revealed the formation process of the ecological adaptability of the two different ecotypes wild soybean from the perspective of gene expression and metabolic changes. This study revealed the adaptation process of GS2 from the perspective of the adaptation of structural and molecular metabolism, mainly including: (1) Enhancing the metabolism of phenolic compounds, lignin, and organic acid metabolism could activate unavailable soil P; (2) Up-regulating genes encoding pectinesterase and phospholipase C (PLC) specifically could promote the reuse of structural P; (3) Some factors could reduce the oxidative damage to the membranes caused by LP stress, such as accumulating the metabolites putrescine and ascorbate significantly, up-regulating the genes encoding SQD2 (the key enzyme of sulfolipid substitution of phospholipids) substantially and enhancing the synthesis of secondary antioxidant metabolite anthocyanins and the AsA-GSH cycle; (4) enhancing the uptake of soil P by upregulating inorganic phosphate transporter, acid phosphatase ACP1, and purple acid phosphatase genes; (5) HSFA6b and MYB61 are the key TFs to resist LP stress.DiscussionIn general, GS2 could resist LP stress by activating unavailable soil P, reusing plant structural P, rebuilding membrane lipids, and enhancing the antioxidant membrane protection system. Our study provides a new perspective for the study of divergent adaptation of plants.

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Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.

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Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.

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