Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper

Abstract

Root knot nematodes (Meloidogyne spp.) are significant agricultural pests on many crops, including pepper (Capsicum annuum). Host plant resistance offers the most sustainable means of controlling this pest. A cluster of genes on chromosome 9 confers resistance, with Me1 providing protection against three nematode species: M. incognita, M. javanica and M. arenaria. We describe the development of a codominant CAPS marker located 1.13 cM away from the Me1 gene. This marker should be useful for marker assisted selection of nematode resistance in pepper breeding programs.

Physical mapping of NBS-coding resistance genes to the Me-gene cluster on chromosome P9 reveals markers tightly linked to the N gene for root-knot nematode resistance in pepper

“…To date, only two of the ten RKN resistance genes on chromosome P9, Me1 and N, have been mapped because linked markers have not been identified for the rest of the genes (present work, Uncu et al 2015). Mapping of Me-1 and N to locus B and C, respectively, is consistent with resistance gene hotspots identified by CDS mapping.…”

“…In addition to CDS, two cloned RKN resistance genes (CaRKNR and CaMi) were mapped using Spidey (Chen et al 2007;Mao et al 2015). Also marker C2At2g06530 which is linked to the Me1 gene was aligned to the pepper genome using the BLAST tool of the Pepper Genome Platform (PGP) database (http://peppergenome.snu.ac.kr/blast.php) (Uncu et al 2015).…”

“…Thus, these genes are important resources for the development of resistant pepper cultivars. To date, none of these resistance genes have been isolated; however, they were mapped to a 28 cM cluster on pepper chromosome 9 (Djian-Caporalino et al 2007;Fazari et al 2012;Uncu et al 2015). Comparative mapping studies showed that this cluster is syntenic to potato and tomato chromosome 12 which contains resistance genes such as Me(s), Bs2, Mi-3/Mi-5, Lv and Gpa2/Rx (Grube et al 2000;Mazourek et al 2009).…”

PCR-based markers developed by comparison of complete chloroplast genome sequences discriminateSolanum chacoensefrom otherSolanumspecies

“…Molecular markers can effectively be developed by the application of PCR on the regions covering SNPs followed by the digestion of PCR product with the appropriate restriction enzymes that called the cleaved amplified polymorphism sequence (CAPS) marker (Konieczny and Ausubel 1993). The CAPS markers were widely used to compare with polymorphism in different genotypes of Solanum species Kim et al 2018;Park et al 2005;Smilde et al 2005;Uribe et al 2014) and other plant species (Komori and Nitta 2005;Uncu et al 2015;Wang et al 2017). Therefore, 17 primer pairs which can amplify regions including each SNPs were designed and the proper restriction enzymes had been identified.…”

Development of PCR-based markers for discriminating Solanum berthaultii using its complete chloroplast genome sequence

“…The application of PCR to SNPs can be used effectively to develop molecular markers after the PCR products are digested with the appropriate restriction enzymes on the site of the SNPs revealing polymorphisms, which is called the CAPS (cleaved amplified polymorphism sequence) marker (Konieczny and Ausubel, 1993). The CAPS is applied broadly to develop polymorphic markers that can be used to compare different genotypes on Solanum species (Park et al 2005;Smilde et al 2005;Uribe et al 2014) and other plant species (Komori and Nitta 2005;Uncu et al 2015;Wang et al 2017). Therefore, 11 primers pairs covering each SNPs site onto which the proper restriction enzymes had been identified were designed.…”