Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study

Muhammad Irfan Siddique,Jelli Venkatesh,Abhinandan Surgonda Patil,Na-Young Ro,Koeun Han,Abate Mekonnen Solomon,Hea-Young Lee,Byoung-Cheorl Kang,Amornrat Changkwian,Jin-Kyung Kwon

doi:10.1038/s41598-019-46342-1

Abstract

Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.

Highlights

Pepper (Capsicum annuum) is an economically important horticultural crop grown in tropical and temperate regions that is used as a fresh vegetable and as a processed food product
Several molecular markers linked to the major quantitative trait loci (QTL), such as Phyto5NBS1 and ZL6726, have been developed and utilized for marker-assisted selection (MAS) in pepper, but their use is limited to the selection of resistant plants to highly virulent and race nonspecific P. capsici isolates[9,10]
We identified 13 significant genome-wide association study (GWAS)-SNPs linked to P. capsici root rot (PcRR) resistance at the end of the long arm (206–212 Mb) of chromosome P5 that were not detected in previous studies, emphasizing the involvement of this genomic region in PcRR resistance (Fig. 4a)

Summary

Introduction

Pepper (Capsicum annuum) is an economically important horticultural crop grown in tropical and temperate regions that is used as a fresh vegetable and as a processed food product. Resistance to PcRR is influenced by several factors, including environmental cues, the virulence of the P. capsici isolates, their physiological races, and the source of resistance[2,4]. Major resistance QTLs to PcRR have been consistently identified in close proximity on chromosome P5 in various studies irrespective of the resistance sources or P. capsici isolates[4,10,18,20,21]. Several molecular markers linked to the major QTLs, such as Phyto5NBS1 and ZL6726, have been developed and utilized for marker-assisted selection (MAS) in pepper, but their use is limited to the selection of resistant plants to highly virulent and race nonspecific P. capsici isolates[9,10]. GBS has been widely used in several crops for biparental QTL mapping and genome-wide association study (GWAS) to uncover loci controlling various traits[23,24,25]

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Conclusion