Abstract
BackgroundBean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far.ResultsUsing whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82–178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing.ConclusionsGenome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.
Highlights
Bean pyralid is one of the major leaf-feeding insects that affect soybean crops
There were 89.57, 89.92, 92.09 and 90.50% clean reads were mapped to the reference soybean genome of Glycine_max_v2.0 (Table 1)
Identification of the differentially methylated genes To study the differential methylation among different resistant soybean varieties, we successfully identified the differentially methylated regions (DMRs)
Summary
Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. Trypsin inhibitor A-like; chalcone isomerase 4-like; lipoxygenase-9; alpha-dioxygenase 1-like; lectin precursor; peroxidase 12-like; stress-induced protein SAM22; and so on, may be the potential target proteins (genes) for soybean to resist bean pyralid larvae [8,9,10]. Such miRNAs as gma-miR156q; gmamiR166u; gma-miR166b; gma-miR319d; gma-miR394a3p; and gma-miR396e, may participate in the regulation of soybean resistance to bean pyralid larvae [11]. Very little is known regarding the mechanism of epigenetic regulation related to soybean resistance to bean pyralid
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