Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245

Abstract

Core Ideas Genetic characterization of a new source of late blight resistance in tomato Identification of new SNP markers using GBS approach Development of a new genetic map of tomato Late blight (LB), caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most devastating diseases of tomato (Solanum lycopersicum L.) and potato (S. tuberosum L.) worldwide. The importance of LB on tomato has increased due to the occurrence of aggressive and fungicide‐resistant clonal lineages of P. infestans. Consequently, identification and characterization of new sources of genetic resistance to LB has become a priority in tomato breeding. Previously, we reported accession PI 163245 as a promising source of highly heritable LB resistance for tomato breeding. The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this accession using a trait‐based marker analysis (a.k.a. selective genotyping). An F2 mapping population (n = 560) derived from a cross between a LB‐susceptible tomato breeding line (Fla. 8059) and PI 163245 was screened for LB resistance, and the most resistant (n = 39) and susceptible (n = 35) individuals were selected for genotyping. Sequencing and comparison of the reduced representation libraries (RRLs) derived from genomic DNA of the two parents resulted in the identification of 33,541 putative single nucleotide polymorphism (SNP) markers, of which, 233 genome‐wide markers were used to genotype the 74 selected F2 individuals. The marker analysis resulted in the identification of four LB resistance QTLs conferred by PI 163245, located on chromosomes 2, 3, 10, and 11. Research is underway to develop near‐isogenic lines (NILs) for fine mapping the QTLs and develop tomato breeding lines with LB resistance introduced from PI 163245.

The Genetic Basis of Tomato Aroma

“…A further progress in the application of NGS is represented by the genotyping-by-sequencing (GBS) approaches, based on the use of restriction enzymes to decrease genome complexity before sequencing. These techniques include over a dozen of reduced-representation sequencing (RRS) approaches [39] and have been recently applied for high-resolution QTL mapping in tomato, especially in interspecific crosses [40][41][42][43]. These protocols have been applied in the development of high-density genetic maps in many different species [44][45][46][47][48][49][50][51][52][53][54][55], making it possible to perform comparative and quantitative genetics in virtually any genomic background.…”

QTL mapping in salad tomatoes

“…The allele detected on chromosome 11 giving resistance to isolate 8_A1 originated from Koralik. To our knowledge, only one other Ph locus has been mapped on chromosome 11 (Ohlson et al 2018) but it is not in the same region, so our QTL may thus represent a novel resistance locus.…”

“…Ph-3, Ph-2 and the newly identified QTL on chromosome 11). In addition, breeders could combine them all with other recently mapped loci (Merk et al2012;Ohlson et al 2018;Arafa et al 2017). Stacking a diverse range of resistance genes is especially appropriate when developing new cultivars for amateur gardeners given the high genetic variation harboured within the P. infestans population in gardens (Stroud et al 2016).…”

Genomics and Marker-Assisted Improvement of Vegetable Crops

“…The updated annotation of tomato genome ITAG4.0 reported a total of 34,075 protein-coding genes using RNA-seq, resistance gene enrichment sequencing (RenSeq), and other forms of expression data (Hosmani et al, 2019). The concurrent release of the tomato reference genome (The Tomato Genome Consortium, 2012) and the development of GBS method (Elshire et al, 2011;Poland et al, 2012) further revolutionized genetic mapping in tomato for traits, such as fruit, leaf, and root characteristics as well as disease resistance (Fulop et al, 2016;Celik et al, 2017;Ohlson et al, 2018;Xie et al, 2019).…”