Development of Clustered Resistance Gene Analogs-Based Markers of Resistance to Phytophthora capsici in Chili Pepper.

Nayoung Kim,Jundae Lee,Won-Hee Kang,Seon-In Yeom

doi:10.1155/2019/1093186

Abstract

The soil-borne pathogen Phytophthora capsici causes severe destruction of Capsicum spp. Resistance in Capsicum against P. capsici is controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers on Capsicum chromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between two Capsicum germplasms that are resistant and susceptible, respectively, to P. capsici. 11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL for P. capsici resistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61 Capsicum accessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes against P. capsici in pepper.

Highlights

Hot pepper (Capsicum spp.) is an economically important crop that belongs to the Solanaceae family along with tobacco, potato, and tomato
The sequences of previously developed markers were screened to extend the major QTL region on Capsicum chromosome 5 and the resistance gene analogs (RGAs) were reanalyzed within that region to identify candidate resistance genes
The following DNA sequences and QTL information were used in this study: cleaved amplified polymorphic sequence (CAPS) markers mapped to the Pc.5.2, Pc.5.3 region of ‘H3’ × ‘Vania’ (HV), and ‘Perenial’ × ‘Yolo Wonder’ (PY) [40]; single nucleotide polymorphisms (SNPs) markers within the Pc5.1 region of ‘Early Jalapeno’ × ‘CM334’ (EC), the Phyto5 region of ‘YCM334’ × ‘Tean,’ and the Pc5.2 region of ‘CM334’ × ‘Chilsungcho’ (CC) and ‘NB1’ × ‘Bhut Jolokia’ [41,42,43,44]; and simple sequence repeat (SSR) markers mapped to the Pc5.1 region of ‘Manganji’ × ‘CM334’ [45]

Summary

Introduction

Hot pepper (Capsicum spp.) is an economically important crop that belongs to the Solanaceae family along with tobacco, potato, and tomato. High-quality de novo sequenced Capsicum genomes, including the ‘CM334’ genome, were reported [16, 17] This genomic information from the hot pepper could be applied to plant breeding and the selection of crops with specific traits such as disease resistance or large fruit size [16, 18, 19]. The sequences of previously developed markers were screened to extend the major QTL region on Capsicum chromosome 5 and the RGAs were reanalyzed within that region to identify candidate resistance genes. A total of 61 Capsicum accessions were used to validate the newly developed RGA-based markers through high-resolution melting (HRM) analysis These markers could be useful to validate the genotyping of germplasms and to further characterize resistance genes against P. capsici

Materials and Methods

Results and Discussion

E: CaNB-5530

Conclusion