Although the genetic diversity of the cultivated tomato is limited, its wild relatives S. The genome sequence of tomato has enabled discovery of genome-wide single-nucleotide polymorphisms (SNPs) and development of advanced molecular markers. Tomato has been used in molecular genetic and genomic studies as a model for fruiting plants because of its compact genome (~950 Mb) and the simple diploid genome composition of family Solanaceae. However, tomato can also be damaged by the late blight disease, particularly in cool temperatures, high relative humidity (RH), and rainy or foggy conditions, resulting in 100% economic losses in open fields and greenhouses. The annual global productivity of tomato has increased dramatically, to 170 million tons in 2014. lycopersicum L.) is the second most agriculturally important crop in the Solanaceae family. Phytophthora infestans is well known as the causative agent of the Great Famine in Ireland between 18, which devastated potato production ( Solanum tuberosum). Late blight disease is caused by the hemibiotrophic oomycete Phytophthora infestans (Mont.) de Bary, one of the most destructive plant pathogens. Plants suffer from many biotic and abiotic stresses, which reduce quantity and quality of crop production worldwide. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: Nucleotide sequence data for the ddRAD-Seq and WGRS analyses are available in the DDBJ Sequence Read Archive under accession numbers DRA005972 and DRA005973.įunding: The study was financially supported by The Ministry of Higher Education and Scientific Research (MHESR), Egypt (Grant# 2013/2014-547), and the Kazusa DNA Research Institute Foundation, Japan. Received: SeptemAccepted: DecemPublished: December 18, 2017Ĭopyright: © 2017 Arafa et al. PLoS ONE 12(12):Įditor: Mark Gijzen, Agriculture and Agri-Food Canada, CANADA In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.Ĭitation: Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K (2017) Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Using double-digest restriction site–associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F 2 population derived from an interspecific cross. In the genome of a wild relative of tomato, Solanum habrochaites accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of P. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. Tomato late blight caused by Phytophthora infestans (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases.
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