Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Genotypes That Are Susceptible, Resistant, and Hypersensitive to Reniform Nematode (Rotylenchulus reniformis).

Ruijuan Li,Narendra K Singh,Aaron M Rashotte,Kathy S Lawrence,Robert D Locy,David B Weaver,John Jones

doi:10.1371/journal.pone.0143261

Abstract

Reniform nematode is a semi-endoparasitic nematode species causing significant yield loss in numerous crops, including cotton (Gossypium hirsutum L.). An RNA-sequencing analysis was conducted to measure transcript abundance in reniform nematode susceptible (DP90 & SG747), resistant (BARBREN-713), and hypersensitive (LONREN-1) genotypes of cotton (Gossypium hirsutum L.) with and without reniform nematode infestation. Over 90 million trimmed high quality reads were assembled into 84,711 and 80, 353 transcripts using the G. arboreum and the G. raimondii genomes as references. Many transcripts were significantly differentially expressed between the three different genotypes both prior to and during nematode pathogenesis, including transcripts corresponding to the gene ontology categories of cell wall, hormone metabolism and signaling, redox reactions, secondary metabolism, transcriptional regulation, stress responses, and signaling. Further analysis revealed that a number of these differentially expressed transcripts mapped to the G. raimondii and/or the G. arboreum genomes within 1 megabase of quantitative trait loci that had previously been linked to reniform nematode resistance. Several resistance genes encoding proteins known to be strongly linked to pathogen perception and resistance, including LRR-like and NBS-LRR domain-containing proteins, were among the differentially expressed transcripts mapping near these quantitative trait loci. Further investigation is required to confirm a role for these transcripts in reniform nematode susceptibility, hypersensitivity, and/or resistance. This study presents the first systemic investigation of reniform nematode resistance-associated genes using different genotypes of cotton. The candidate reniform nematode resistance-associated genes identified in this study can serve as the basis for further functional analysis and aid in further development of reniform a nematode resistant cotton germplasm.

Highlights

Reniform nematodes (RN, Rotylenchlus reniformis) are semi-endoparasitic nematode species causing significant yield loss in cotton [1]
A relative increase of root biomass was observed for susceptible genotypes under higher RN inoculum levels, a reduction of root volume was observed for hypersensitive genotype LONREN-1 with increased RN inoculum levels, while the root mass of resistant genotype BARBREN-713 remained constant at different RN inoculum levels (Fig 1)
To obtain a global view of gene expression in different genotypes of cotton infested with RN, six paired-end (100bp) cDNA libraries were generated from cotton roots

Summary

Introduction

Reniform nematodes (RN, Rotylenchlus reniformis) are semi-endoparasitic nematode species causing significant yield loss in cotton [1]. At present genetic sources of resistance to RN in cotton are limited, and there are no RN tolerant/resistant commercial varieties available. Successful RN parasitism is contingent on establishment of a syncytium, which serves as the sole nutrient source on which RN live. Nematode secretions injected through their stylet, a specialized needle-like mouthpart, are essential in syncytium initiation and maintenance [2, 3]. Several peptide sequences homologous to other sedentary plant parasitic nematode effectors have been identified from RN expressed sequence tag (EST) assemblies [4]. None of these have been experimentally studied

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