Mining candidate genes associated with resistance to TYLCV in tomato based on BSA-seq and RNA-seq analysis

摘要

Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomato in tropical and subtropical regions. In recent years, research into TYLCV-resistant varieties has sought resistant genes by molecular marker techniques. In this study, a high-throughput sequencing method was used for the localization and selection of disease-resistant genes. Mutation detection, note, and correlation analysis of SNP and In Del were used to obtain seven hot regions associated with traits on chromosomes 1, 9, and 11; the total length of those hot regions was 21.68 Mb, and they contained 1,864 annotated genes, including 266 non-synonymous mutational genes of SNP loci and 52 frame-shift mutational genes, some of which were directly related to candidate genes. By using Gene Ontology (GO) analysis and SNP detection, we gained nine non-synonymous mutational candidate genes (So1yc09g011540.2.1, So1yc09g014720.1.1, Solyc09g011550.2.1, Solyc090011590.2.1, Solyc09g 014910.2.1, Solyc09g0113902.1, So1yc09g014990.2.1, Solyc019111250.2.1, and Solyc09g011350.1.1) in seven hot regions. These were involved in defense response, response to biotic stimulus, the auxin-activated signaling pathway, transferase activity, glutathione transferase activity, sequence-specific DNA binding, and in signal transduction mechanisms. RAN-seq had four treatments: R, RT, S, and ST. R-VS-RT yielded 4,171 up-regulated genes and 4,568 down-regulated genes, S-VS-ST yielded 4,055 up-regulated genes and 4,844 down-regulated genes, RT-VS-ST yielded 1,212 up-regulated genes and 1,608 down-regulated genes. These nine candidate genes were also analyzed by gene expression up- and down-regulation; all nine genes were up-regulated in R-VS-RT and down-regulated in RT-VS-ST. The further indicated that these nine candidate genes are related to anti-TYLCV. In addition, we randomly selected 12 differentially expressed genes and confirmed their expression with RNA-Seq by qRT-PCR. Our study provides a basis for further gene functional verification and cloning, In addition, the associated SNPs will be used for marker-assisted breeding of Ty-5 resistance tomato.