10.5061/DRYAD.Z08KPRRBG
Copetti, Dario
0000-0002-2680-2568
University of Zurich
Gene annotation of the Fhb1 locus on the assembly of bread wheat variety
Norin 61
Dryad
dataset
2020
JST CREST
JPMJCR16O3
Swiss National Science Foundation
https://ror.org/00yjd3n13
31003A_182318,CRSII5_183578
Genome Prairie
https://ror.org/013s3gf12
NCCR Evolving Language
51NF40_180888
European Union's Horizon 2020 research and innovation programme
Marie Sklodowska-Curie
847585
MEXT KAKENHI The Birth of New Plant Species
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
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
2020-12-28T00:00:00Z
2020-12-28T00:00:00Z
en
https://doi.org/10.1093/pcp/pcaa152
https://doi.org/10.1038/s41586-020-2961-x
117698 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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