Gene annotation of the Fhb1 locus on the assembly of bread wheat variety Norin 61

In the areas with wet climate of Eastern Asia, Fusarium head blight (FHB)
is a major threat to bread wheat production. A source of FHB resistance
(Fhb1) was identified in the Asian wheat germplasm and through classical
breeding it was introduced in several varieties
(https://doi.org/10.1186/s40066-017-0139-z ). The molecular determinant
was identified as a deletion in an  histidine-rich
calcium-binding-protein gene on chromosome 3BS.
(https://doi.org/10.1038/s41588-019-0426-7). The allele is common in many
East Asia wheat varieties, but not in the reference assembly Chinese
Spring (CS).  The whole-genome assembly of the Japanese variety
Norin 61 allowed to confirm the sequence and structure of the haplotype
surrounding Fhb1. Given the low amount of sequence conservation with CS at
the locus, we noticed that the annotation based on projections of CS gene
models (https://doi.org/10.1038/s41586-020-2961-x) did not identify all
genes in the Norin 61 haplotype. To describe the complete set of coding
regions in the Fhb1 allele, we de novo annotated the Norin 61 ~340 kb Fhb1
region with homology- and ab initio-based evidence. MAKER v2.31.9 was run
on the Norin 61 genomic interval, with the Uniprot Liliopsida proteome,
and the annotation from https://doi.org/10.1038/s41586-020-2961-x.
Augustus was run with wheat as a species, and the output was parsed
removing models that had >40% similarity over >50% of their
length to TE proteins via BLASTP. Our annotation identified 70
protein-coding genes, 50 more than the ones identified by homology only.A
deletion in the start codon (third exon) of TaHRC gene was confirmed as
the causal mutaiton conferring resistance, and it was present in other
vaireties having the same resistance. This resource highlights the
importance of an appropriate characterization of the sequence in a
non-reference genotype, especially when considering new variants with
traits important for modern breeding programs.