Genomics-enabled analysis of the emergent disease cotton bacterial blight.

Anne Z Phillips,Rebecca S Bart,Terry Wheeler,Tom W Allen,Jeffrey C Berry,Jillian Burke,J Imani Bunn,Anupama Vijayaraghavan,Mark C Wilson,Gitta Coaker

doi:10.1371/journal.pgen.1007003

Abstract

Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen Xcm isolates and analyzed along with 4 previously published Xcm genomes. These genomes encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different clade III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal important insights into the Xcm-G. hirsutum disease complex and strategies for future development of resistant cultivars.

Highlights

Upland cotton (Gossypium hirsutum L.) is the world’s leading natural fiber crop
We compare diverse pathogen isolates and cotton varieties to further understand the virulence mechanisms employed by Xanthomonas citri pv. malvacearum (Xcm) and to identify promising
PCR amplification of the 16S rRNA gene confirmed that the causal agent was a member of the Xanthomonas genus

Summary

Introduction

Upland cotton (Gossypium hirsutum L.) is the world’s leading natural fiber crop. Cotton is commercially grown in over 84 countries, and in the United States, is responsible for $74 billion annually [1, 2]. Numerous foliar diseases affect cotton throughout the world’s cotton growing regions. One of the most significant foliar diseases has been bacterial blight, caused by Xanthomonas citri pv. Cotton bacterial blight significantly limited cotton yield in the late 20th century. In the 1940’s and 1950’s, breeders identified and introgressed multiple resistance loci into elite germplasm [3,4,5]. This strategy proved durable for over half a century. In 2011, cotton bacterial blight (CBB) returned and caused significant losses to farmers in the southern United States, including in Arkansas and Mississippi. Modern molecular and genomic technologies can be employed expeditiously to deduce the underlying cause of the disease re-emergence and pinpoint optimized routes towards the development of durable resistance

Methods

Results

Discussion

Conclusion