A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode.

Weiming Hu,Peter Digennaro,Krista Kingsbury,Shova Mishra

doi:10.3390/genes11121507

Abstract

Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyne incognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.

Highlights

Root-knot nematodes (RKN; Meloidogyne spp.) are capable of infecting more than 5000 plant species [1]
Samples not clustering based on timepoint could reflect incomplete synchronization, butnot we Samples clustering based on timepoint could reflect incomplete synchronization, but we do do notthis believe this hypothesis fully be supported with the current data
The molecular mechanisms of nematode resistance in pepper are poorly understood, multiple resistance genes that may act in a qualitative response have been discovered through breeding, the exact location and mode of action of these genes are yet unknown [45]

Summary

Introduction

Root-knot nematodes (RKN; Meloidogyne spp.) are capable of infecting more than 5000 plant species [1]. Among the numerous RKN species, M. incognita, M. arenaria, M. javanica, and M. hapla dominate as the agriculturally important nematode pathogens of bell pepper (Capsicum annuum) in the United States [2]. RKN utilize water and nutrients from the plants to complete its life cycle, resulting in decreased root and shoot growth and, a significant reduction in pepper yield. RKN management practices in the field largely rely on resistant cultivars and chemical control [3]. Hare (1957) defined resistance to M. incognita as conditioned by a single dominant gene, the N gene [5]. Backcrossing the N gene into pimiento pepper led to the subsequent release of the cultivar “Mississippi Nemaheart”

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