DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Charlotte N DiBiase, Xi Cheng, Gwonjin Lee, Richard C Moore, Austin G McCoy, Martin I Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao
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Abstract

Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible), in response to P. sansomeana at two time points: 4 and 16 hours post-inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines.

DNA 甲基化分析揭示了抗性和易感性大豆品系对 Phytophthora sansomeana 的局部反应变化。
Phytophthora sansomeana 是一种新出现的卵菌病原体,会导致包括大豆在内的许多农业物种发生根腐病。然而,到目前为止,在大豆中只发现了一个潜在的抗性基因,而我们对大豆中的遗传和表观遗传调控是如何促进对这种病原体的反应的了解在很大程度上仍然是未知的。在这项研究中,我们对两个大豆品系 Colfax(抗性)和 Williams 82(易感性)在两个时间点对 P. sansomeana 的反应进行了全基因组亚硫酸氢盐测序(WGBS):接种后 4 小时和 16 小时,比较它们的甲基化变化。我们的研究结果表明,全基因组的 CG、CHG(H = A、T 或 C)和 CHH 甲基化没有显著变化。但是,我们观察到了局部甲基化的变化,特别是接种后基因和转座元件(TE)周围的 CHH 甲基化增加,这在易感品系中发生得较早,而在抗性品系中发生得较晚。接种后,我们在 Colfax 和 Williams 82 中都发现了不同的甲基化区域(DMRs),主要存在于 TEs 中。值得注意的是,我们的数据还表明,与抗性品系相比,易感品系中有更多的 TE 发生了甲基组变化。此外,我们在 Colfax 的 772 个差异表达基因 (DEG) 内或其侧翼发现了 837 个 DMRs,在 Williams 82 的 138 个差异表达基因 (DEG) 内或其侧翼发现了 166 个 DMRs。这些 DEGs 的功能各不相同,Colfax 主要参与代谢过程、防御反应、植物与病原体相互作用、阴离子和核苷酸结合以及催化活性,而 Williams 82 则与光合作用有显著关联。这些研究结果表明,抗性大豆品系和易感性大豆品系对 P. sansomeana 感染有不同的分子反应。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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