Development of co-dominant SCAR markers linked to resistant gene against the Fusarium oxysporum f. sp. radicis-lycopersici

Abstract

We developed highly reliable co-dominant SCAR markers linked to the Frl gene. FORL testing is difficult. The marker is expected to be quickly adapted for MAS by tomato breeders. Fusarium oxysporum f. sp. radicis-lycopersici causes Fusarium crown and root rot (FCR), an economically important soil-borne disease of tomato. The resistance against FCR is conferred by a single dominant gene (Frl) located on chromosome 9. The aim of this study was to develop molecular markers linked to the Frl gene for use in marker-assisted breeding (MAS) programs. The FCR-resistant 'Fla. 7781' and susceptible 'B560' lines were crossed, and F1 was both selfed and backcrossed to 'B560' to generate segregating F2 and BC1 populations. The two conserved set II (COSII) markers were found linked to the Frl gene, one co-segregated with FCR resistance in both F2 and BC1 populations and the other was 8.5 cM away. Both COSII markers were converted into co-dominant SCAR markers. SCARFrl marker produced a 950 and a 1000 bp fragments for resistant and susceptible alleles, respectively. The linkage of SCARFrl marker was confirmed in BC2F3 populations developed by backcrossing the resistant 'Fla. 7781' to five different susceptible lines. The SCARFrl marker has been in use in the tomato breeding programs in BATEM, Antalya, Turkey, since 2012 and has proved highly reliable. The SCARFrl marker is expected to aid in the development of FCR-resistant lines via marker-assisted selection (MAS).

Development of a high-resolution melting marker for selecting Fusarium crown and root rot resistance in tomato

“…In this study, we confirmed that resistance to FORL was conferred by a single dominant gene that was located on Chr. 9, as reported earlier (Vakalounakis et al 1997, Fazio et al 1999, Mutlu et al 2015, indicating that the FORL resistance in 'AV107-4' might have originated from the Frl of an S. peruvianum accession. However, the results on the genomic location of Frl were contradictory between recently published D r a f t studies and our study: by using an F 2 population, Staniaszek et al (2014) mapped the COSII marker C2_At2g38025 at 3 cM distal to Frl in line '3070'.…”

“…9 on Tomato-EXPEN 2000 map. Most recently, Mutlu et al (2015) reported two COSII markers that were flanking Frl by using F 2 and BC 1 populations. One of the COSII markers C2_At3g63200 was linked to Frl by 8.5 cM, and the other marker C2_At4g28660 was linked by 0.016 cM.…”

Identifying molecular markers suitable for Frl selection in tomato breeding

“…We then used the published tomato reference genome sequence (Tomato Genome Consortium 2012) (GenBank: GCA_000188115.2 Solyc2.50) as a reference to map sequence reads from both resistant and susceptible parents, and as well as sequences from both bulks. We concentrated on chromosome 9 around the previously published markers that were claimed to be linked to Frl (Truong et al 2011; Mutlu et al 2015). Initially, 1.2 Mb region covering some of the previous markers was taken into account and some of the identified SNVs at the flanking regions were converted to CAPS marker and were then used to map the Frl locus.…”

“…Previous mapping exercises have placed Frl on the chromosome 9 closely linked to the Tm-2 2 gene (Vakalounakis et al 1997). Several groups have used different approaches to generate PCR-based markers including RAPD (Fazio et al 1999) and SCAR (Mutlu et al 2015) markers. However, to our knowledge, the use of these markers in breeding programmes has not been reported.…”

“…This is due to the fact that it can save time, resources and efforts and selection can be done at the seedling stages (Collard and Mackill 2008). Further molecular studies resulted in the development of RAPD (Truong et al 2011) and SCAR (Mutlu et al 2015) markers that are linked to the Frl . We have tried some of these markers but none of these have proven to be close enough to be successfully used in high throughput breeding programmes as they are several cM away from the Frl locus allowing the high number of recombination events to occur, which is not desirable for commercial breeding activities.…”