Identification and characterization of a QTL for growth of Fusarium circinatum on pine-based medium

SUPPLEMENTARY FILE S1: HPLC and GC-MS results showing the broad overview and primary metabolites identified in the pine-based media. SUPPLEMENTARY FILE S2: The primer sequences and PCR protocols used to amplify gene regions in this study. SUPPLEMENTARY FILE S3: Reference mapping of F. circinatum Illumina and MinIon raw reads mapped to the genomes of F circinatum KS17 and F. temperatum. SUPPLEMENTARY FILE S4: Genic information of the identified genes and indel region in the QTL region of F. circinatum. InterProScan and gene ontology information are provided for all genes in this region. Further information on the retrotransposons and repeats that are characteristic of the indel within the QTL region is provided.Fusarium circinatum is an economically important pathogen of pine and resides in the Fusarium fujikuroi species complex. Here we investigated the molecular processes underlying growth in F. circinatum by exploring the association between growth and the nutritional environment provided by the pine host. For this purpose, we subjected a mapping population consisting of F. circinatum X F. temperatum hybrid progeny to an analysis of growth rate on a pine-tissue derived medium. These data, together with the available genetic linkage map for F. circinatum, were then used to identify Quantitative Trait Loci (QTLs) associated with growth. The single significant QTL identified was then characterized using the available genome sequences for the hybrid progeny’s parental isolates. This revealed that the QTL localized to two non-homologous regions in the F. circinatum and F. temperatum genomes. For one of these, the F. circinatum parent contained a two-gene deletion relative to the F. temperatum parent. For the other region, the two parental isolates encoded different protein products. Analysis of repeats, G+C content, and repeat-induced point (RIP) mutations further suggested a retrotransposon origin for the two-gene deletion in F. circinatum. Nevertheless, subsequent genome and PCR-based analyses showed that both regions were similarly polymorphic within a collection of diverse F. circinatum. However, we observed no clear correlation between the respective polymorphism patterns and growth rate in culture. These findings support the notion that growth is a complex multilocus trait and raise the possibility that the identified QTL contains multiple small-effect QTLs, of which some might be dependent on the genetic backgrounds. This study improved our current knowledge of the genetic determinants of vegetative growth in F. circinatum and provided an important foundation for determining the genes and processes underpinning its ability to colonize its host environment.The South African Department of Science and Innovation’s South African Research Chair Initiative and the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria.https://www.mdpi.com/journal/jofam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog