Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum)

Abstract

BackgroundLeaf mold, one of the major diseases of tomato caused by Cladosporium fulvum (C. fulvum), can dramatically reduce the yield and cause multimillion dollar losses annually worldwide. Mapping the resistance genes (R genes) of C. fulvum and devising MAS based strategies for breeding new cultivars is an effective approach to improve the resistance in tomato. Up to now, many C. fulvum genes or QTLs have been mapped using different genetic materials, but few studies focused on Cf-10 gene positioning.ResultsIn this study, we investigated the genetic rules for Cf-10 and used a novel combinatorial strategy to rapidly map the Cf-10 gene. Initially, the performance of F1, F2 and BC1F1 individuals after infection, demonstrated that the resistance against C. fulvum was controlled by a single dominant gene. Two pools of resistant and susceptible individuals from F2 population were investigated, using mapping by sequencing approach and Cf-10 was found to be localized to 3.35 Mb and 3.74 Mb on chromosome 1, employing SNP/InDel index methods, respectively. After accounting for overlapping regions, these two algorithms yielded a total length of 3.29 Mb, narrowing down the target region. We further developed five serviceable KASP markers for this region based on sequencing data and conducted local QTL mapping using individuals from the F2 population, except for mapping by sequencing as mentioned above. Finally Cf-10 gene was mapped spanning a region of 790 kb, where only one gene (Solyc01g007130.3) was annotated as probable receptor protein kinase TMK1 with a LRR motif, a common R gene characteristic. The RT-qPCR analysis further confirmed the localization and the relative expression of Solyc01g007130.3 in Ontario 792 and was found to be significantly higher than that in Moneymaker at 9 dpi and 12 dpi, respectively.ConclusionThis study proposed a novel combinatorial strategy by combining SNP-index, InDel-index analyses and local QTL mapping using KASP genotyping approach to rapidly map genes responsible for specific traits and provided a robust base for cloning the Cf-10 gene. Furthermore, these analyses suggest that Solyc01g007130.3 is a potential candidate to be regarded as Cf-10 gene.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1616-7) contains supplementary material, which is available to authorized users.

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato

“…The tomato-C. fulvum interaction follows a typical gene-for-gene relationship, and the products of C. fulvum-resistance genes (Cf genes) in tomato specifically recognize the products encoded by the AVR genes in C. fulvum, leading to HR [18,19]. At least 24 Cf genes have been reported since the discovery of the Cf-1 gene in the 1930s [20,21], and these genes have been introduced into cultivated tomatoes [22][23][24][25][26][27][28][29][30].…”

PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

“…If a gene does not contribute to the trait phenotype, its alleles would be randomly segregated in both bulks; whereas if a gene is responsible for the trait phenotype, its alleles would be enriched in either bulk, e.g., one bulk has more allele A while the other bulk has more allele a. BSA was primarily used to develop genetic markers for detecting gene-trait association at its early stage [1,2]. The application of nextgeneration sequencing technology to BSA has eliminated the time-consuming and labor-intensive marker development and genetic mapping steps and has dramatically sped up the detection of gene-trait associations [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. This technique was termed either QTL-seq or BSA-Seq in different publications [5,6,21]; we adapted the latter here because it can be applied to study both qualitative and quantitative traits.…”

Mapping and candidate gene screening of Cladosporium fulvum resistance gene Cf‐12 in tomato (Solanum lycopersicum) by high‐throughput sequencing

“…The most efficient control method for C. fulvum is to introduce Cf resistance genes into cultivated tomato (Rivas & Thomas, 2005). Several Cf genes such as Cf ‐ 1 to Cf ‐ 5 , Cf ‐ 9 , Cf ‐ 10 , Cf ‐ 19 , Cf ‐ Ecp1 , Cf ‐ Ecp2 , Cf ‐ Ecp4 , Cf ‐ Ecp5 and Cf ‐ Ecp6 have been identified in recent years (De Jonge et al, 2010; De Kock, Brandwagt, Bonnema, de Wit, & Lindhout, 2005; De Wit, Joosten, Thomma, & Stergiopoulos, 2009; Liu et al, 2019; Zhao et al, 2016). The Cf and Cf‐Ecp resistance proteins specifically recognize C. fulvum effector Avr and Ecp proteins and trigger incompatible interaction, inducing a hypersensitive response (HR; Bolton et al, 2008; Stergiopoulos & Wit, 2009).…”

“…The Cf‐4 and Cf‐9 haplotypes each contain five tandemly duplicated transcription units ( Hcr9 ‐ 9A to 9 E and Hcr9 ‐ 4A to 4 E ; Parniske et al, 1997; Thomas et al, 1997). The Cf ‐ 10 and Cf ‐ 19 genes were also located in the Hcr9s locus on chromosome 1 (Liu et al, 2019; Zhao et al, 2016). The Cf ‐ 2 and Cf ‐ 5 genes belong to the Hcr2s gene family and were mapped on the short arm of chromosome 6 (Dickinson, Jones, & Jones, 1993; Jones et al, 1993).…”