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

Citation

Copetti, Dario (2020), Gene annotation of the Fhb1 locus on the assembly of bread wheat variety Norin 61, Dryad, Dataset, https://doi.org/10.5061/dryad.z08kprrbg

Abstract

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.

Methods

The gene models were predicted with MAKER-P using ab initio (Augustus) and homology-based (Chinese Spring, transcriptomes) methods. Models encoding transposable element proteins were removed

Funding

JST CREST, Award: JPMJCR16O3

Swiss National Science Foundation, Award: 31003A_182318,CRSII5_183578

Genome Prairie

NCCR Evolving Language, Award: 51NF40_180888

European Union's Horizon 2020 research and innovation programme

Marie Sklodowska-Curie, Award: 847585

MEXT KAKENHI The Birth of New Plant Species, Award: JP16H06469,JP16H06464,JP16H06466,JP16K21727

National Agriculture and Food Research Organization (NARO) Vice President Fund

NBRP Genome Information Upgrading Project 2017, AMED

University of Zurich Research Priority Program Evolution in Action

German Federal Ministry of Food and Agriculture, Award: 2819103915

Canadian Triticum Applied Genomics research project (CTAG2) funded by Genome Canada

Western Grains Research Foundation, Government of Saskatchewan, Saskatchewan Wheat Development Commission, Alberta Wheat Commission, Viterra and Manitoba Wheat and Barley Growers Association