Hybrid genome assembly of a major quantitative disease resistance locus in soybean toward fusarium graminearum

Authors: GEDLING, CASSIDY - The Ohio State University; WIJERATNE, S - The Ohio State University; CASSONE, BRYAN - The Ohio State University; LEE, SUNGWOO - North Carolina State University; Mian, Rouf; MCHALE, LEAH - The Ohio State University; DORRANCE, ANNE - The Ohio State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2019
Publication Date: 5/9/2019
Citation: Gedling, C., Wijeratne, S., Cassone, B., Lee, S., Mian, R.M., Mchale, L., Dorrance, A. 2019. Hybrid genome assembly of a major quantitative disease resistance locus in soybean toward fusarium graminearum. The Plant Genome. 12:1-17.
DOI: https://doi.org/10.3835/plantgenome2018.12.0102

Interpretive Summary: Soybean seedling and root rot, caused by Fusarium graminearum, is a serious disease in some major soybean growing states in the U.S. A major quantitative disease resistance locus (QDRL) which contributed 38.5% of the phenotypic variance towards F. graminearum in soybean was previously identified through mapping of a recombinant inbred line (RIL) population derived from a cross between Wyandot and PI 567301B. This major QDRL mapped to soybean chromosome 8 to a predicted 305 kilobase region with 37 genes. This locus maps near the Rhg4 locus for soybean cyst nematode (SCN) and the I locus contributing to seed coat color. Long read sequencing of the region with oxford nanopore technology was completed and variations in gene sequence and gene order compared to the Williams 82 reference were identified. Analyses of the hybrid genome reassembly using three previously published BAC sequences (56G2, 104J7, and 77G7-a) combined with RNA-sequencing narrowed the region making candidate gene identification possible. DNA markers were developed for genes within this region. Using a total of 50 Near Isogenic Line individuals and 14 DNA markers spanning the region, we were able to fine map the newly assembled region within 2.5 centiMorgan. The markers within this region may be used for marker-assisted selection (MAS). The region associated with resistance was narrowed to 10 differentially expressed putative candidate genes for resistance and susceptibility with three of these candidates located within the markers flanking the 2.5 cM region. These genes included a subtilisin-like protease, an actin-related protein 2/3 complex subunit, and an unknown protein. In addition to providing reliable DNA makers for MAS, this research should also lead to cloning of the causal gene for resistance to F. graminearum at this locus.

Technical Abstract: Fusarium graminearum has been identified as a pathogen of soybean causing seedling and root rot in North America. A major quantitative disease resistance locus (QDRL) which contributed 38.5% of the phenotypic variance towards F. graminearum in soybean was previously identified through mapping of a recombinant inbred line (RIL) population derived from a cross between Wyandot and PI 567301B. This major QDRL mapped to chromosome 8 to a predicted 305 kb region with 37 genes. This locus maps near the Rhg4 locus for soybean cyst nematode (SCN) and the I locus contributing to seed coat color. Long read sequencing of the region with oxford nanopore technology was completed and variations in gene sequence and gene order compared to the Williams 82 reference were identified. Analyses of the hybrid genome reassembly using three previously published BAC sequences (56G2, 104J7, and 77G7-a) combined with RNA-sequencing narrowed the region making candidate gene identification possible. KASP markers were developed for genes within this region. Using a total of 50 NIL individuals and 14 markers spanning the region, we were able to fine map the newly assembled region within 2.5 cM. The markers within this region may be used for marker-assisted selection (MAS). The region associated with resistance was narrowed to 10 differentially expressed putative candidate genes for resistance and susceptibility with three of these candidates located within the markers flanking the 2.5 cM region. These genes included a subtilisin-like protease, an actin-related protein 2/3 complex subunit, and an unknown protein.