Comparative Transcriptome Analysis to Identify Candidate Genes for FaRCg1 Conferring Resistance Against Colletotrichum gloeosporioides in Cultivated Strawberry (Fragaria × ananassa).

Vance M Whitaker,Gina Fernandez,Seonghee Lee,Natalia Salinas,Saket Chandra,Jose Guillermo Chacon,Youngjae Oh,Ashlee Anciro,Hyeondae Han

doi:10.3389/fgene.2021.730444

Vance M Whitaker, Gina Fernandez + Show 7 more

Open Access

https://doi.org/10.3389/fgene.2021.730444

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Abstract

Colletotrichum crown rot (CCR) caused by Colletotrichum gloeosporioides is a serious threat to the cultivated strawberry (Fragaria × ananassa). Our previous study reported that a major locus, FaRCg1, increases resistance. However, the genomic structure of FaRCg1 and potential candidate genes associated with the resistance remained unknown. Here, we performed comparative transcriptome analyses of resistant ‘Florida Elyana’ and susceptible ‘Strawberry Festival’ after infection and identified candidate genes potentially involved in resistance. In ‘Florida Elyana’, 6,099 genes were differentially expressed in response to C. gloeosporioides. Gene ontology analysis showed that the most upregulated genes were functionally associated with signaling pathways of plant defense responses. Three genes in the genomic region of FaRCg1 were highly upregulated: a von Willebrand Factor A domain-containing protein, a subtilisin-like protease, and a TIFY 11A-like protein. Subgenome-specific markers developed for the candidate genes were tested with a diverse panel of 219 accessions from University of Florida and North Carolina State University breeding programs. Significant and positive associations were found between the high-resolution melting (HRM) marker genotypes and CCR phenotypes. These newly developed subgenome-specific functional markers for FaRCg1 can facilitate development of resistant varieties through marker-assisted selection.

Highlights

Colletotrichum species are some of the most notorious and damaging diseases of the cultivated strawberry worldwide (Münch et al, 2008)
To investigate transcriptome profiles of the FaRCg1-mediated resistance against C. gloeosporioides, RNA-Seq was conducted from two octoploid strawberry cultivars, ‘Florida Elyana’ and ‘Strawberry Festival’
All reads from the sequencing libraries, ‘Strawberry Festival’ pathogen inoculated (Festival-PI) and ‘Florida Elyana’ pathogen inoculated (Elyana-PI), were first mapped to the coding sequences of C. gloeosporioides11 to eliminate any pathogen related short reads

Summary

Introduction

Colletotrichum species are some of the most notorious and damaging diseases of the cultivated strawberry worldwide (Münch et al, 2008). Strawberry Colletotrichum Crown Rot Resistance infections in crown tissues cause necrosis, plant collapse, and death in hot and humid conditions (MacKenzie et al, 2006; Rahman and Louws, 2017). Most commercial cultivars currently grown in the United States are susceptible to CCR and, economic losses occur nearly every season from this disease. Both curative (pyraclostrobin, strobilurins, and azoxystrobin) and preventive (captan) fungicides are commonly used to control CCR, but chemical controls are not very effective once plants become infected (MacKenzie et al, 2009; Rahman and Louws, 2017). Deciphering resistance genes and understanding their role in CCR resistance would help facilitate the development of resistant varieties

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