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   Eur.J.Hortic.Sci. 85 (3) 145-159 | DOI: 10.17660/eJHS.2020/85.3.2
ISSN 1611-4426 print and 1611-4434 online | © ISHS 2020 | European Journal of Horticultural Science | Original article
Mining candidate genes associated with resistance to TYLCV in tomato based on BSA-seq and RNA-seq analysis

Qingqi Chen1, Jingbin Jiang1, Haixia Zhang2, Na Lei3, Tingting Zhao1 and Jingfu Li1
1 College of Horticulture, Northeast Agricultural University, Harbin, China
2 Harbin Examining and Inspection Center for Agricultural Products Safety and Quality, Harbin, China
3 Harbin Academy of Agriculture Science, Harbin, China

SUMMARY
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 InDel 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 (Solyc09g011540.2.1, Solyc09g014720.1.1, Solyc09g011550.2.1, Solyc09g011590.2.1, Solyc09g014910.2.1, Solyc09g011390.2.1, Solyc09g014990.2.1, Solyc01g111250.2.1, 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.

Keywords SNPs, small InDels, DEGs, candidate genes, up-regulated genes, down-regulated genes, qRT-PCR

Significance of this study

What is already known on this subject?

  • Ty-5 gene was located by molecular markers and certain results were obtained. However, more advanced next generation high-throughput sequencing technology has not been used to study this aspect.
What are the new findings?
  • We employed the recently developed BSA-seq and RNA-seq approach to achieve candidate regions on chromosomes 1, 9, and 11, and nine candidate genes.
What is the expected impact on horticulture?
  • This study was a good basis for further research on these candidate genes so as to improve the resistance of cultivated tomato to TYLCV.

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E-mail: lijf_2005@126.com  

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Received: 10 May 2018 | Accepted: 10 December 2019 | Published: 22 June 2020 | Available online: 22 June 2020

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