A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

T Amuge,T Amuge,T Amuge,M E Ferguson,S L Goldman,M S Katari,A A Myburg,D K Berger

doi:10.1038/s41598-017-09617-z

Abstract

A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of ‘translational elongation’, ‘translation factor activity’, ‘ribosomal subunit’ and ‘phosphorelay signal transduction’, were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga’s resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.

Highlights

Cassava is among the six major crops of Africa, representing a staple food for >250 million people (FAO, 2010)
Characteristic cassava brown streak disease (CBSD) symptoms were observed in Ugandan cassava brown streak virus (UCBSV)
The challenge of Namikonga with UCBSV triggers an NBS-leucine-rich repeats (LRRs) signalling cascade, which subsequently induces a phosphorelay signal transduction pathway leading to defence

Summary

Introduction

Cassava is among the six major crops of Africa, representing a staple food for >250 million people (FAO, 2010). The disease has spread steadily since as far as DR Congo and South Sudan and together with cassava mosaic disease, causes over US$1 billion losses in production annually in Africa[1, 6, 7] Both CBSV and UCBSV are members of genus Ipomovirus, family Potyviridae[3, 4, 8]. Infected susceptible plants develop chlorosis along leaf veins, brown streaks on stems, and root necrosis (Fig. 1), with severe infection causing shoot dieback Dual infection with both virus species is common in farmers’ fields, there are no reports of synergistic virus interaction[3, 4, 8, 17], and both viruses cause similar symptoms, those of CBSV tend to be more severe than UCBSV18, 19. An understanding of the resistance mechanisms involved, including biochemical pathways, and the identification of candidate genes and biomarkers would contribute substantially to knowledge-based genomics breeding, including marker-assisted selection (MAS)

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