A uniform gene and chromosome nomenclature system for oat (Avena spp.)

Eric N. Jellen; Charlene P. Wight; Manuel Spannagl; Victoria C. Blake; James Chong; Matthias H. Herrmann; Catherine J. Howarth; Yung-Fen Huang; Jia Juqing; Andreas Katsiotis; Tim Langdon; Chengdao Li; Robert Park; Nicholas A. Tinker; Taner Z. Sen

doi:10.1071/CP23247

RESEARCH ARTICLE (Open Access)

Previous Next Contents Vol 75(1)

A uniform gene and chromosome nomenclature system for oat (Avena spp.)

Eric N. Jellen

^A ^* , Charlene P. Wight

^B , Manuel Spannagl ^C , Victoria C. Blake ^D ^E , James Chong ^F , Matthias H. Herrmann ^G , Catherine J. Howarth ^H , Yung-Fen Huang ^I , Jia Juqing ^J , Andreas Katsiotis ^K , Tim Langdon ^H , Chengdao Li

^L , Robert Park ^M , Nicholas A. Tinker ^B and Taner Z. Sen

^D ^N

+ Author Affiliations

- Author Affiliations

^A Department of Plant and Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT 84602, USA.

^B Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.

^C PGSB – Plant Genome and Systems Biology, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg 85764, Germany.

^D Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service, Albany, CA 94710, USA.

^E Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA.

^F Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.

^G Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, Sanitz D-18190, Germany.

^H Institute of Biological, Environmental, and Rural Sciences (IBERS), Goggerdan, Aberystwyth University, Aberystwyth SY23 3EE, UK.

^I Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da’an Dist., Taipei 10617, Taiwan.

^J College of Agronomy, Shanxi Agricultural University, Taigu 030801, China.

^K Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology, and Food Science, Limassol, Cyprus.

^L Western Crop Genetic Alliance/State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.

^M The University of Sydney, Plant Breeding Institute, Private Bag 4011, Narellan, NSW 2567, Australia.

^N Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

^* Correspondence to: rick_jellen@byu.edu

Handling Editor: Rajeev Varshney

Crop & Pasture Science 75, CP23247 https://doi.org/10.1071/CP23247

Submitted: 31 August 2023 Accepted: 1 December 2023 Published: 2 January 2024

Abstract

Context

Several high-quality reference genomes for oat (Avena sativa L. and relatives) have been published, with the prospect of many additional whole-genome assemblies emerging in the near future.

Aims

This has necessitated an effort by the International Oat Nomenclature Committee (IONC; all co-authors on this paper) to devise a universal system for naming oat genomes and subgenomes, chromosomes, genes, gene models and quantitative trait loci.

Methods

We evaluated existing naming practices, recent data from oat whole-genome sequencing, and the newly published convention for wheat nomenclature.

Key results

A framework for these rules has been posted on the GrainGenes database website (https://wheat.pw.usda.gov/GG3/oatnomenclature). The gene naming convention requires adoption of a numerical identifier for each genotype; we propose that these identifiers be assigned by contacting the GrainGenes curators, the curator of the Oat Newsletter, or a member of the IONC (as listed at the GrainGenes link above).

Conclusions

We encourage oat researchers to refer to these resources, policies, procedures and conventions, adopting them as an international nomenclature standard.

Implications

Adoption of these standards will facilitate communication and dissemination of oat research and allow programmatic access and data sharing across platforms, and will contribute to oat breeding and research worldwide.

Keywords: Avena, chromosome nomenclature, data standardisation, gene nomenclature, genome nomenclature, oat, plant breeding, QTL nomenclature.

References

Badaeva ED, Shelukhina OY, Diederichsen A, Loskutov IG, Pukhalskiy VA (2010) Comparative cytogenetic analysis of Avena macrostachya and diploid C-genome Avena species. Genome 53, 125-137.
| Crossref | Google Scholar |

Baum BR (1977) Oats: wild and cultivated. A monograph of the genus Avena L. (Poaceae). Monograph No. 14. Biosystematics Research Institute, Canada Department of Agriculture, Ottawa, ON, Canada.

Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA (2018) Haplotype-Based genotyping-by-sequencing in oat genome research. Plant Biotechnology Journal 16, 1452-1463.
| Crossref | Google Scholar |

Boden SA, McIntosh RA, Uauy C, Krattinger SG, Dubcovsky J, Rogers WJ, Xia XC, Badaeva ED, Bentley AR, Brown-Guedira G, Caccamo M, Cattivelli L, Chhuneja P, Cockram J, Contreras-Moreira B, Dreisigacker S, Edwards D, Gonzalez FG, Guzman C, Ikeda TM, Karsai I, Nasuda S, Pozniak C, Prins R, Sen TZ, Silva P, Simkova H, Zhang Y, the Wheat Initiative (2023) Updated guidelines for gene nomenclature in wheat. Theoretical and Applied Genetics 136, 72.
| Crossref | Google Scholar | PubMed |

Chaffin AS, Huang Y-F, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, Wight CP, Chao S, Oliver R, Islamovic E, Kolb FL, McCartney C, Mitchell Fetch JW, Beattie AD, Bjornstad A, Bonman JM, Langdon T, Howarth CJ, Brouwer CR, Jellen EN, Klos KE, Poland JA, Hsieh T-F, Brown R, Jackson E, Schlueter JA, Tinker NA (2016) A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. The Plant Genome 9, plantgenome2015.10.0102.
| Crossref | Google Scholar |

Dutta B, Gitaitis R, Agarwal G, Coutinho T, Langston D (2018) Pseudomonas coronafaciens sp. nov., a new phytobacterial species diverse from Pseudomonas syringae. PLoS ONE 13, e0208271.
| Crossref | Google Scholar | PubMed |

Hsam SLK, Mohler V, Zeller FJ (2014) The genetics of resistance to powdery mildew in cultivated oats (Avena sativa L.): current status of major genes. Journal of Applied Genetics 55, 155-162.
| Crossref | Google Scholar | PubMed |

Jiang W, Jiang C, Yuan W, Zhang M, Fang Z, Li Y, Li G, Jia J, Yang Z (2021) A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era. BMC Plant Biology 21, 213.
| Crossref | Google Scholar | PubMed |

Kamal N, Renhuldt NT, Bentzer J, Gundlach H, Haberer G, Juhasz A, Lux T, Bose U, Tye-Din JA, Lang D, van Gessel N, Reski R, Fu Y-B, Spegel P, Ceplitis A, Himmelbach A, Waters AJ, Bekele WA, Colgrave ML, Hansson M, Stein N, Mayer KFX, Jellen EN, Maughan PJ, Tinker NA, Mascher M, Olsson O, Spannagl M, Sirijovski N (2022) The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 606, 113-119.
| Crossref | Google Scholar | PubMed |

Kim YC (2020) First report of oat halo blight caused by Pseudomonas coronafaciens in South Korea. Plant Disease 104, 1853.
| Crossref | Google Scholar |

Ladizinsky G (2012) ‘Studies in oat evolution: a man’s life with Avena.’ (Springer: Berlin/Heidelberg, Germany)

Latta RG, Bekele WA, Wight CP, Tinker NA (2019) Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids. Scientific Reports 9, 12298.
| Crossref | Google Scholar | PubMed |

Leggett JM (2011) Further hybrids involving the perennial autotetraploid oat Avena macrostachya. Genome 35, 273-275.
| Crossref | Google Scholar |

Loskutov IG, Rines HW (2011) Avena. In ‘Wild crop relatives: genome and breeding resources’. (Ed. C Cole) pp. 109–183. (Springer: Berlin/Heidelberg, Germany)

Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN (2019) Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biology 17, 92.
| Crossref | Google Scholar | PubMed |

McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. (CSIRO Publishing: Melbourne, Vic., Australia)

Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzeda E, Prats E, Roake J, Sowa S, Ziems L, Singh D (2022) Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. Theoretical and Applied Genetics 135, 3709-3734.
| Crossref | Google Scholar |

Peng Y, Yan H, Guo L, Deng C, Wang C, Wang Y, Kang L, Zhou P, Yu K, Dong X, Liu X, Sun Z, Peng Y, Zhao J, Deng D, Xu Y, Li Y, Jiang Q, Li Y, Wei L, Wang J, Ma J, Hao M, Li W, Kang H, Peng Z, Liu D, Jia J, Zheng Y, Ma T, Wei Y, Lu F, Ren C (2022) Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nature Genetics 54, 1248-1258.
| Crossref | Google Scholar | PubMed |

Radchenko EE, Kuznetsova TL, Chumakov MA, Loskutov IG (2018) Greenbug (Schizaphis graminum) resistance in oat (Avena spp.) landraces from Asia. Genetic Resources and Crop Evolution 65, 571-576.
| Crossref | Google Scholar |

Rajhathy T (1963) A standard karyotype for Avena sativa. Canadian Journal of Genetics and Cytology 5, 127-132.
| Crossref | Google Scholar |

Rajhathy T, Thomas H (1974) ‘Cytogenetics of oats (Avena L.).’ Miscellaneous Publications of the Genetics Society of Canada, No. 2. (Genetics Society of Canada: Ottawa, Ontario)

Sanz MJ, Jellen EN, Loarce Y, Irigoyen ML, Ferrer E, Fominaya A (2010) A new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) based on FISH analysis of monosomic lines. Theoretical and Applied Genetics 121, 1541-1552.
| Crossref | Google Scholar | PubMed |

Schnable JC (2020) Genes and gene models, an important distinction. New Phytologist 228, 50-55.
| Crossref | Google Scholar | PubMed |

Simons MD, Zillinsky FJ, Jensen NF (1966) A standardized system of nomenclature for genes governing characters of oats. Bulletin 34-85. p. 22. USDA ARS, Washington, DC, USA.

Simons MD, Martens JW, McKenzie RIH, Nishiyama I, Sadanaga K, Sebesta J, Thomas H (1978) Oats: a standardized system of nomenclature for genes and chromosomes and catalog of genes governing characters. USDA Agriculture Handbook 408. (U.S. Government Printing Office: Washington, DC, USA)

Singh RJ, Tsuchiya T (1982) Identification and designation of telocentric chromosomes in barley by means of Giemsa N-banding technique. Theoretical and Applied Genetics 64, 13-24.
| Crossref | Google Scholar | PubMed |

Wang RR-C, von Bothmer R, Dvorak J, Fedak G, Linde-Laursen I, Muramatsu M (1996) Genome symbols in the Triticeae (Poaceae). In ‘Proceedings of the 2nd International Triticeae Symposium’. Logan, Utah, 1994. (Eds RR-C Wang, KB Jensen, C Jaussi) pp. 29–34. (Utah State University, Herbarium Publications: Logan, UT, USA)

Yan H, Bekele WA, Wight CP, Peng Y, Langdon T, Latta RG, Fu Y-B, Diederichsen A, Howarth CJ, Jellen EN, Boyle B, Wei Y, Tinker NA (2016) High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. Theoretical and Applied Genetics 129, 2133-2149.
| Crossref | Google Scholar | PubMed |

Yao E, Blake VC, Cooper L, Wight CP, Michel S, Cagirici HB, Lazo GR, Birkett CL, Waring DJ, Jannink J-L, Holmes I, Waters AJ, Eickholt DP, Sen TZ (2022) GrainGenes: a data-rich repository for small grains genetics and genomics. Database 2022, baac034.
| Crossref | Google Scholar |