Transcriptomic analyses revealed the effect of Funneliformis mosseae on differentially expressed genes in Fusarium oxysporum

Soybean root rot is a typical soil-borne disease that severely affects the yield of soybean, and F. mosseae, the dominant strain of AMF in continuous cropping of soybean. The aim of this study was to providing an experimental basis for the study of the molecular mechanism underlying the alleviation of the obstacles associated with the continuous cropping of soybean by AMF. In this study, F. mosseae was inoculated in soil planted with soybean infected with F. oxysporum. The results showed that the incidence of soybean root rot was significantly reduced after inoculation with F. mosseae. The significantly upregulated genes encoded the ABC transporter, ATP-binding/permease protein and the ABC transporter, ATP-binding protein. The significantly downregulated genes encoded chitin-binding domain proteins; key enzymes involved in metabolic pathways such as glycolysis, including class II fructose-bisphosphate aldolase and NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, glycoside hydrolase family 61 protein, which hydrolyse cellulose and hemicellulose; actin and other major components of the cytoskeleton. The DEGs were enriched in antigen processing and presentation, carbon fixation in photosynthetic organisms, glycolysis/gluconeogenesis, the MAPK signalling pathway, protein processing in the endoplasmic reticulum and RNA degradation. Inoculation with F. mosseae could promote the growth and development of soybean and improve disease resistance. This study provides an experimental basis for further research on the molecular mechanism underlying the alleviation of challenges associated with the continuous cropping of soybean by AMF.

slowed down and eventually approached the level of the control group (CK). The highest 90 incidence in group F was almost 90%. The root rot in soybean inoculated with F. mosseae was 91 significantly reduced, indicating that F. mosseae could significantly alleviate the incidence of 92 soybean root rot.  sowing. The x-axis means different stages. The y-axis represents the soybean root rot incidence.

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Soybean growth indexes 102 After soybean ripening, soybean grains were randomly picked for determination of

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The correlation coefficients between the incidence of root rot and soybean quality 113 indicators are shown in Table 1, which shows that the incidence of soybean root rot is 114 negatively correlated with various quality indicators (P < 0.01), and the increase in disease 115 incidence has the most serious impact on the soybean fat content, which decreases upon 116 infection. In addition, the protein content and fat content of soybean were positively correlated 117 with the 100-grain weight (P < 0.01), and the fat content had a strong impact on the 100-grain 118 weight of soybean. The comparisons of gene expression levels between groups are shown in the box plot in 129 Figure 4. The y-axis represents gene expression levels, and each box represents a sample group.

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The black line in the middle of the box represents the median, and the upper and lower sides of 131 the box are quartiles. Based on the box plot, the number of genes detected in each treatment 132 group was different.

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Analysis of differentially expressed genes (DEGs) of F. oxysporum 151 The difference in gene expression among the three treatment groups was analysed by 152 edgeR software. In F-vs.-AF, the number of upregulated was 56 and downregulated genes is 35.

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Hierarchical clustering of the relationships between samples and genes was carried out based on 154 gene expression. The clustering results are presented using a heatmap, as shown in Figure 6, 155 where red indicates high expression levels, and blue indicates low expression levels.

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As shown in Figure 6, after inoculation with F. mosseae, the significantly upregulated 157 genes were ABC transporter, ATP-binding/permease protein-encoding genes and ABC 177 Figure 7A shows that the DEGs in the CK -vs.-F group were enriched in 8 GO terms 178 (Table S1). In the biological process group, most of the DEGs are involved in metabolic 179 processes(14 upregulated genes, 3 downregulated genes), cellular processes(8 upregulated genes, 180 3 downregulated genes) and the single-organism processes(8 upregulated genes, 3 181 downregulated genes). In the molecular function group, most of the DEGs are involved in 182 catalytic activity(15 upregulated genes, 4 downregulated genes) and binding (8 upregulated 183 genes). Figure 7B shows that the DEGs in the F -vs.-AF group were also enriched in 8 GO 184 terms (Table S2). In the biological process group, most of the DEGs are involved in metabolic

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Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis 194 In the CK -vs.-F group, after inoculation with F. oxysporum, the top 20 pathways were 195 enriched (Table S3). Figure 8A shows that many DEGs related to biochemical metabolism DEGs are involved in the MAPK signalling pathway, which is related to fungal virulence (Table   211 S4). There also many DEGs were enriched in other pathways, such as endoplasmic reticulum 212 and RNA degradation after inoculation with F. mosseae.    Sample treatment, root rot incidence and soybean quality determination 290 The experiment was carried out in pots, every pot is plastic bucket and mesures 50×50× 291 60 cm. Soybean seeds were wiped with alcohol, disinfected with 5% sodium hypochlorite, 292 washed with sterile water and sown in sterilized soil from continuous cropping of soybean. with F. mosseae (AF). Samples were obtained every 7 days after F. oxysporum inoculation, and 298 the incidence of root disease was counted [28]. During the period of high incidence of root rot 299 (79 d), soybean roots were taken from each treatment and subjected to transcriptomic analysis.

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After maturation, the 100-grain weight, crude fat content and protein content were measured for 301 each treated grain. Each treatment had three duplicates. The correlation analysis between the 302 incidence of root rot and soybean quality indicators were carried out using SPSS 23.0.

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Total RNA was extracted from the samples and amplified by PCR. The whole library was 305 prepared. The constructed library was subjected to Illumina HiSeqTM sequencing. The obtained 306 data were filtered as follows: 1) reads containing adapters were removed; 2) reads containing 307 more than 10% unknown nucleotides (N) were removed; and 3) low-quality reads containing 308 more than 50% low-quality (Q-value≤20) bases were removed. High-quality clean data were

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The authors declare no conflict of interest.