Updated guidelines for gene nomenclature in wheat

Boden, Scott A.; McIntosh, R. A.; Uauy, Cristóbal; Krattinger, Simon G.; Dubcovsky, Jorge; Rogers, William J.; Xia, X. C.; Бадаева, Е. Д.; Bentley, Alison R.; Brown‐Guedira, Gina; Cáccamo, Mario; Cattivelli, L.; Chhuneja, Parveen; Cockram, James; Contreras‐Moreira, Bruno; Dreisigacker, Susanne; Edwards, David; González, Fernanda G; Guzmán, Carlos; Ikeda, Tatsuya; Karsaï, I.; Nasuda, Shuhei; Pozniak, Curtis; Prins, R.; Sen, Taner Z.; Silva, Paula; Šimková, Hana; Zhang, Y

doi:10.1007/s00122-023-04253-w

Cited by 41 publications

(27 citation statements)

References 36 publications

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“…(TraesCS4D02G094400) (Supplementary Table 4), in accordance with guidelines on wheat gene nomenclature based on homology (Boden et al, 2023). NAC5-A1…”

Section: Resultsmentioning

confidence: 99%

Wheat NAC transcription factorNAC5-1is a positive regulator of senescence

Evans,

Mogg,

Soraru

et al. 2024

Preprint

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Wheat (Triticum aestivum L.) is an important source of both calories and protein in global diets, but there is a trade-off between grain yield and protein content. The timing of leaf senescence could mediate this trade-off as it is associated with both decline in photosynthesis and nitrogen remobilisation from leaves to grain. NAC transcription factors play key roles in regulating senescence timing. In rice, OsNAC5 expression is correlated with earlier senescence, but the role of the wheat ortholog in senescence had not been characterised. We verified that NAC5-1 is the ortholog of OsNAC5 and that it is expressed in senescing flag leaves in wheat. To characterise NAC5-1, we combined missense mutations in NAC5-A1 and NAC5-B1 from a TILLING mutant population and overexpressed NAC5-A1 in wheat. Mutation in NAC5-1 was associated with delayed onset of flag leaf senescence, while overexpression of NAC5-A1 was associated with slightly earlier onset of leaf senescence. DAP-seq was performed to locate transcription factor binding sites of NAC5-1. Analysis of DAP-seq and comparison with other studies identified putative downstream target genes of NAC5-1 which could be associated with senescence. This work showed that NAC5-1 is a positive transcriptional regulator of leaf senescence in wheat. Further research is needed to test the effect of NAC5-1 on yield and protein content in field trials, to assess the potential to exploit this senescence regulator to develop high-yielding wheat while maintaining grain protein content.

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“…(TraesCS4D02G094400) (Supplementary Table 4), in accordance with guidelines on wheat gene nomenclature based on homology (Boden et al, 2023). NAC5-A1…”

Section: Resultsmentioning

confidence: 99%

Wheat NAC transcription factorNAC5-1is a positive regulator of senescence

Evans,

Mogg,

Soraru

et al. 2024

Preprint

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“…Furthermore, the AP2L-D5 allele of ANK-15 is different from N67 by a G to A transition on exon 10. We designated the wild-type AP2L-D5 allele of N67 as AP2L-D5a (same as AP2L-D5 in Chinese Spring) and the ANK-15 allele carrying the point mutation as AP2L-D5b based on the wheat gene nomenclature guidelines (Boden et al 2023).…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel SNP in the miR172 binding site ofQhomoeologAP2L-D5is associated with spike compactness and agronomic traits in wheat (Triticum aestivumL.)

Zeng,

Uauy,

Chen

2023

Preprint

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Spike architecture is a key determinant of wheat yield, a crop which supports much of the human diet but whose yield gains are stagnating. Spike architecture mutants offer opportunities to identify genetic factors contributing to inflorescence development. Here, we investigate the locus underlying the compact spike phenotype of mutant line ANK-15 by conducting mRNA-sequencing and genetic mapping using ANK-15 and its non-compact spike near-isogenic line Novosibirskaya 67 (N67). Previous literature has placed the compact spike locus of ANK-15 to chromosome 2B. However, based on the single nucleotide polymorphisms (SNPs) identified using mRNA-seq data, we were unable to detect polymorphisms between N67 and ANK-15 in the putative chromosome 2B region. We performed differential expression analysis of developing rachis and found thatAP2L-D5, the D homoeolog of the domesticationQgene, is upregulated in ANK-15 in comparison to N67. ANK-15 carries a SNP in the microRNA172 binding site ofAP2L-D5, which is predicted to lead to higher expression ofAP2L-D5due to decreased miRNA172-mediated degradation. Furthermore, we performed genetic mapping using an ANK-15 x N67 F2population and found a single quantitative trait locus on chromosome 5D coinciding with the position ofAP2L-D5. This result suggests thatAP2L-D5is likely the underlying causal gene for the compact spike phenotype in ANK-15. We performed a field trial to investigate the effect of theAP2L-D5allele on agronomic traits and found that theAP2L-D5allele from ANK-15 is associated with a significant reduction in height, increased thousand grain weight, and increased grain width.

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“…Gene models were generated from the T. timopheevii assembly using REAT - Robust and Extendable eukaryotic Annotation Toolkit (https://github.com/EI-CoreBioinformatics/reat) and Minos (https://github.com/EI-CoreBioinformatics/minos) which make use of Mikado 49 (https://github.com/EI-CoreBioinformatics/mikado), Portcullis (https://github.com/EI-CoreBioinformatics/portcullis) and many third-party tools (listed in the above repositories). A consistent gene naming standard 50 was used to make the gene models uniquely identifiable.…”

Section: Methodsmentioning

confidence: 99%

“…Gene models were generated from the T. timopheevii 50 was used to make the gene models uniquely identifiable.…”

Section: Genome Annotationmentioning

confidence: 99%

Chromosome-scale genome assembly of bread wheat’s wild relativeTriticum timopheevii

Grewal,

Yang,

Scholefield

et al. 2024

Preprint

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Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world.Triticum timopheevii(2n = 4x = 28) is an allotetraploid wheat wild relative species containing the Atand G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly ofT. timopheeviiaccession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb, and 166,325 predicted gene models. DNA methylation analysis showed that the G genome had on average more methylated bases than the Atgenome. The G genome was also more closely related to the S genome ofAegilops speltoidesthan to the B genome of hexaploid or tetraploid wheat. In summary, theT. timopheeviigenome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

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Updated guidelines for gene nomenclature in wheat

Cited by 41 publications

References 36 publications

Wheat NAC transcription factorNAC5-1is a positive regulator of senescence

Wheat NAC transcription factorNAC5-1is a positive regulator of senescence

Identification of a novel SNP in the miR172 binding site ofQhomoeologAP2L-D5is associated with spike compactness and agronomic traits in wheat (Triticum aestivumL.)

Chromosome-scale genome assembly of bread wheat’s wild relativeTriticum timopheevii

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