Hybrid Genome Assembly of a Major Quantitative Disease Resistance Locus in Soybean Toward Fusarium graminearum

Abstract

Core Ideas Quantitative disease resistance to F. graminearum was previously mapped in soybean. A major QDRL to F. graminearum characterized for putative candidate resistant genes. Hybrid genome assembly aided identification of genome rearrangement in the QDRL region. Positions of four expressed candidate genes were within the QDRL to F. graminearum. Fusarium graminearum Schwabe [teleomorph: Gibberella zeae (Schweintiz) Petch] has been identified as a pathogen of soybean [Glycine max (L.) Merr.] causing seed, seedling damping‐off and root rot in North America. A major quantitative disease resistance locus (QDRL) that contributed 38.5% of the phenotypic variance toward 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 harboring 36 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 was completed and variations in gene sequence and gene order compared with the ‘Williams 82’ reference were identified. Molecular markers were developed for genes within this region and mapped in the original population, slightly narrowing the region of interest. Analyses of the hybrid genome reassembly using three previously published bacterial artificial chromosome (BAC) sequences (BAC56G2, BAC104J7, and BAC77G7‐a) combined with RNA‐sequencing narrowed the region making candidate gene identification possible. The markers within this region may be used for marker‐assisted selection (MAS). There were 10 differentially expressed genes between resistant and susceptible lines, with four of these candidates also located within the genomic interval defined by the flanking markers. These genes included an actin‐related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3.

Understanding Root Rot Disease in Agricultural Crops

“…A subsequent study identified four differentially expressed genes that mapped to this QTL located on chromosome 8. These genes included an actin-related protein 2/3 complex subunit, an unknown protein, a hypothetical protein, and a chalcone synthase 3 [315]. This study demonstrated that removal of the seed coat of highly resistant soybean lines makes them susceptible to F. graminareum, indicating that proteins or secondary compounds in the seed coat may be involved in resistance [315].…”

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

“…Million et al . (2019) identified a major quantitative disease resistance locus on chromosome 8 that contributed 38.5% of the phenotypic variance toward F. graminearum from a cross, together with other markers, they mapped this QTL to a 305 kb region harboring 36 genes. Ye et al .…”

“…The BARCSoySNP6K assay has been applied in various genetic research, e.g., it has been used to construct linkage maps (Lee et al ., 2015), identify QTL/genes controlling a number of traits such as sudden death syndrome resistance (Wen et al ., 2014; Lightfoot et al ., 2018), aphid resistance (Bhusal et al ., 2017; Zhang et al ., 2017), charcoal rot resistance (Vinholes et al ., 2019), Phytophthora sojae , Pythium irregulare and Fusarium graminearum resistance (Stasko et al ., 2016; Million et al ., 2019), salt tolerance (Do et al ., 2018), waterlogging (Ye et al ., 2018), iron deficiency chlorosis (Merry et al ., 2019), nitrogen fixation (Huo et al ., 2019), growth period (Liu et al ., 2016), seed isoflavone content (Li et al ., 2018), oil and fatty acids (Priolli et al ., 2019), protein content (Nascimento et al ., 2018) and yield (Ye et al ., 2018). These studied not only confirmed previously identified QTL but also resulted in the discovery of new QTL, candidate genes or pathways controlling these traits.…”

Draft Genome Sequence of a New Fusarium Isolate Belonging to Fusarium tricinctum Species Complex Collected From Hazelnut in Central Italy

“…In addition, performing a hybrid assembly guarantee to take advantage, from one side, of the depth coverage and basecalling quality given by the Illumina reads and, on the other side, to increase the genome contiguity with the ONT reads ( Chen et al, 2020 ). In fact, this method proved to be very successful in fungal genome assembly, either within the Fusarium world ( Million et al, 2019 ; Degradi et al, 2021 ; Dvorianinova et al, 2021 ; Fan et al, 2021 ) or to extended species ( Faino et al, 2015 ; Saud et al, 2021 ).…”