Mapping of the gene in tomato conferring resistance to root-knot nematodes at high soil temperature.

Root-knot nematodes (RKNs, Meloidogyne spp.) can cause severe yield losses in tomatoes. The Mi-1.2 gene in tomato confers resistance to the Meloidogyne species M. incognita, M. arenaria and M. javanica, which are prevalent in tomato growing areas. However, this resistance breaks down at high soil temperatures (>28°C). Therefore, it is imperative that new resistance sources are identified and incorporated into commercial breeding programmes. We identified a tomato line, MT12, that does not have Mi-1.2 but provides resistance to M. incognita at 32°C soil temperature. An F2 mapping population was generated by crossing the resistant line with a susceptible line, MT17; the segregation ratio showed that the resistance is conferred by a single dominant gene, designated RRKN1 (Resistance to Root-Knot Nematode 1). The RRKN1 gene was mapped using 111 Kompetitive Allele Specific PCR (KASP) markers and characterized. Linkage analysis showed that RRKN1 is located on chromosome 6 and flanking markers placed the locus within a 270 kb interval. These newly developed markers can help pyramiding R-genes and generating new tomato varieties resistant to RKNs at high soil temperatures.

Genomic-Assisted Marker Development Suitable for CsCvy-1 Selection in Cucumber Breeding.

Cucumber is a widely grown vegetable crop plant and a host to many different plant pathogens. Cucumber vein yellowing virus (CVYV) causes economic losses on cucumber crops in Mediterranean countries and in some part of India such as West Bengal and in African countries such as Sudan. CVYV is an RNA potyvirus transmitted mechanically and by whitefly (Bemisia tabaci) in a semipersistent manner. Control of this virus is heavily dependent on the management of the insect vector and breeding virus-resistant lines. DNA markers have been used widely in conventional plant breeding programs via marker-assisted selection (MAS). However, very few resistance sources against CVYV in cucumber exist, and also the lack of tightly linked molecular markers to these sources restricts the rapid generation of resistant lines. In this work, we used genomics coupled with the bulked segregant analysis method and generated the MAS-friendly Kompetitive allele specific PCR (KASP) markers suitable for CsCvy-1 selection in cucumber breeding using a segregating F2 mapping population and commercial plant lines. Variant analysis was performed to generate single-nucleotide polymorphism (SNP)-based markers for mapping the population and genotyping the commercial lines. We fine-mapped the region by generating new markers down to 101 kb with eight genes. We provided SNP data for this interval, which could be useful for breeding programs and cloning the candidate genes.

Degree of resistance of Solanum torvum cultivars to Mi-1.2-virulent and avirulent isolates of Meloidogyne incognita, Meloidogyne javanica, and Meloidogyne luci.

Root-knot nematodes (RKN) cause yield losses in eggplant-growing areas. There are no known varieties of eggplant (Solanum melongena L.) that are resistant to RKNs. However, the wild relative of eggplant, S. torvum (Sw.), provides resistance to some RKN species and is used as a rootstock for cultivated eggplants. Therefore, determination of the reproductive capacity of nematodes on eggplant rootstocks developed from S. torvum is required for effective management of RKNs that are widely present in vegetable growing areas. In the present study, the degree of reproduction of Mi-1.2-virulent and avirulent isolates of M. incognita, M. javanica, and M. luci on eggplant rootstocks, Hawk and Bogaç, was evaluated in a plant growth chamber. Hawk and Bogaç were resistant (< 10 egg masses per whole root system) to all avirulent and virulent isolates of M. incognita, M. javanica, and M. luci. This study is the first report on the resistance of S. torvum to virulent isolates of M. luci. Results indicate that S. torvum offers broad-spectrum resistance against RKNs.

First report of root-knot nematode, Meloidogyne incognita on calendula in Turkey.

Calendula officinalis L. (Asteraceae) is a traditional medicinal plant called pot marigold or English marigold. In this study, galled roots of pot marigold were collected from Balikesir province of Turkey and egg masses were picked up from the roots of each plant with fine forceps. DNA was then extracted from samples and analyzed by species-specific primers referring to the most common Meloidogyne spp. Our results showed that Meloidogyne incognita was found as the only species in all the samples taken. The determination of M. incognita on calendula was done for the first time in Turkey.

First report of root-knot nematode, Meloidogyne arenaria, on lavender in Turkey.

Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kirklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.Lavender is a medicinal and aromatic plant that is widely grown in Turkey. Gall symptoms were observed on roots of lavender (Lavandula angustifolia Mill.) collected from Kirklareli and Edirne provinces. Egg masses were collected from galled roots. DNA isolated from all samples was screened by species-specific primers belonging to the most common species of root-knot nematodes and M. arenaria was the only species that was identified in all of the samples analyzed. This is the first report of M. arenaria infecting lavender in Turkey.

Identifying molecular markers suitable for Frl selection in tomato breeding.

Modern plant breeding heavily relies on the use of molecular markers. In recent years, next generation sequencing (NGS) emerged as a powerful technology to discover DNA sequence polymorphisms and generate molecular markers very rapidly and cost effectively, accelerating the plant breeding programmes. A single dominant locus, Frl, in tomato provides resistance to the fungal pathogen Fusarium oxysporum f. sp. radicis-lycopersici (FORL), causative agent of Fusarium crown and root rot. In this study, we describe the generation of molecular markers associated with the Frl locus. An F2 mapping population between an FORL resistant and a susceptible cultivar was generated. NGS technology was then used to sequence the genomes of a susceptible and a resistant parent as well the genomes of bulked resistant and susceptible F2 lines. We zoomed into the Frl locus and mapped the locus to a 900 kb interval on chromosome 9. Polymorphic single-nucleotide polymorphisms (SNPs) within the interval were identified and markers co-segregating with the resistant phenotype were generated. Some of these markers were tested successfully with commercial tomato varieties indicating that they can be used for marker-assisted selection in large-scale breeding programmes.

Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing.

It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site-leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.

Distribution and Identification of Root-knot Nematodes from Turkey.

Root knot nematodes are causing serious losses in protected cultivation fields in the West Mediterranean region of Turkey. Correct and confident identification of the plant parasitic nematodes is important for vegetable growing and breeding. Therefore, ninety-five populations of plant parasitic nematodes were collected from regional greenhouses. Previously described species-specific primers were used to identify Meloidogyne populations. The present study indicated that SEC-1F/SEC-1R and INCK14F-INCK14R primers for identifying of M. incognita, Fjav/Rjav and DJF/DJR primers for M. javanica and Far/Rar for M. arenaria primers can be effective tools to identify the Turkish root-knot nematode species. Dissemination ratios of the population were 64.2%, 28.4% and 7.3% for Meloidogyne incognita, M. javanica and M. arenaria, respectively. The results showed that M. incognita was the prominent root-knot nematode species in the West Mediterranean coastal areas of Turkey.