Updated guidelines for gene nomenclature in wheat

S A Boden¹, R A McIntosh², C Uauy³, S G Krattinger^{4

5}, J Dubcovsky^{6

5}, W J Rogers^{7

5}, X C Xia⁸, E D Badaeva⁹, A R Bentley^{10

5}, G Brown-Guedira^{11

5}, M Caccamo^{12

5}, L Cattivelli^{13

5}, P Chhuneja¹⁴, J Cockram^{12

5}, B Contreras-Moreira¹⁵, S Dreisigacker^{10

5}, D Edwards^{16

5}, F G González^{17

5}, C Guzmán^{18

5}, T M Ikeda^{19

5}, I Karsai^{20

5}, S Nasuda²¹, C Pozniak^{22

5}, R Prins^{23

24}, T Z Sen^{25

5}, P Silva²⁶, H Simkova²⁷, Y Zhang²⁸; Wheat Initiative

Affiliations

¹ School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia. scott.boden@adelaide.edu.au.
² School of Life and Environmental Sciences, University of Sydney, Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia. Robert.mcintosh@sydney.edu.au.
³ John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. cristobal.uauy@jic.ac.uk.
⁴ Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
⁵ The Wheat Initiative, 14195, Berlin, Germany.
⁶ Department of Plant Science, University of California, Davis, CA, 95616, USA.
⁷ Departamento de Biología Aplicada, Facultad de Agronomía (CIISAS, CIC-BIOLAB AZUL, CONICET-INBIOTEC, CRESCA), Universidad Nacional del Centro de La Provincia de Buenos Aires, Av. República Italia 780, C.C. 47, (7300), Azul, Provincia de Buenos Aires, Argentina.
⁸ Institute of Crop Science, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St, Beijing, 100081, China.
⁹ N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119991.
¹⁰ International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico, D.F., Mexico.
¹¹ USDA-ARS Plant Science Research, North Carolina State University, William Hall 4114A, Raleigh, NC, 27695, USA.
¹² NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
¹³ Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, PC, Italy.
¹⁴ School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India.
¹⁵ Estación Experimental de Aula Dei (EEAD-CSIC), Zaragossa, Spain.
¹⁶ School of Biological Sciences, University of Western Australia, Perth, 6009, Australia.
¹⁷ Instituto Nacional de Tecnología Agropecuaria (INTA), EEA Pergamino, y Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Ruta 32. Km 4.5, CP 2700, Pergamino, Buenos Aires, Argentina.
¹⁸ Department of Genetics, School of Agricultural and Forest Engineering, Universidad de Córdoba, Córdoba, Spain.
¹⁹ Agroecosystem and Crop Breeding Group, Western Region Agricultural Research Center, Fukuyama, Hiroshima, 721-8514, Japan.
²⁰ Centre for Agricultural Research, ELKH, 2462, Martonvasar, Hungary.
²¹ Laboratory of Plant Breeding, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8224, Japan.
²² Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
²³ CenGen Pty Ltd., Worcester, 6850, South Africa.
²⁴ Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa.
²⁵ Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan St, Albany, CA, 94710, USA.
²⁶ Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, 70006, Colonia, Uruguay.
²⁷ Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic.
²⁸ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.

PMID: 36952017
PMCID: PMC10036449
DOI: 10.1007/s00122-023-04253-w

Updated guidelines for gene nomenclature in wheat

S A Boden et al. Theor Appl Genet. 2023.

. 2023 Mar 23;136(4):72.

doi: 10.1007/s00122-023-04253-w.

Authors

Affiliations

¹ School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia. scott.boden@adelaide.edu.au.
² School of Life and Environmental Sciences, University of Sydney, Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia. Robert.mcintosh@sydney.edu.au.
³ John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. cristobal.uauy@jic.ac.uk.
⁴ Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
⁵ The Wheat Initiative, 14195, Berlin, Germany.
⁶ Department of Plant Science, University of California, Davis, CA, 95616, USA.
⁷ Departamento de Biología Aplicada, Facultad de Agronomía (CIISAS, CIC-BIOLAB AZUL, CONICET-INBIOTEC, CRESCA), Universidad Nacional del Centro de La Provincia de Buenos Aires, Av. República Italia 780, C.C. 47, (7300), Azul, Provincia de Buenos Aires, Argentina.
⁸ Institute of Crop Science, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St, Beijing, 100081, China.
⁹ N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119991.
¹⁰ International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico, D.F., Mexico.
¹¹ USDA-ARS Plant Science Research, North Carolina State University, William Hall 4114A, Raleigh, NC, 27695, USA.
¹² NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
¹³ Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Via S. Protaso, 302, 29017, Fiorenzuola d'Arda, PC, Italy.
¹⁴ School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004, India.
¹⁵ Estación Experimental de Aula Dei (EEAD-CSIC), Zaragossa, Spain.
¹⁶ School of Biological Sciences, University of Western Australia, Perth, 6009, Australia.
¹⁷ Instituto Nacional de Tecnología Agropecuaria (INTA), EEA Pergamino, y Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Ruta 32. Km 4.5, CP 2700, Pergamino, Buenos Aires, Argentina.
¹⁸ Department of Genetics, School of Agricultural and Forest Engineering, Universidad de Córdoba, Córdoba, Spain.
¹⁹ Agroecosystem and Crop Breeding Group, Western Region Agricultural Research Center, Fukuyama, Hiroshima, 721-8514, Japan.
²⁰ Centre for Agricultural Research, ELKH, 2462, Martonvasar, Hungary.
²¹ Laboratory of Plant Breeding, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8224, Japan.
²² Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
²³ CenGen Pty Ltd., Worcester, 6850, South Africa.
²⁴ Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa.
²⁵ Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan St, Albany, CA, 94710, USA.
²⁶ Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, 70006, Colonia, Uruguay.
²⁷ Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00, Olomouc, Czech Republic.
²⁸ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.

PMID: 36952017
PMCID: PMC10036449
DOI: 10.1007/s00122-023-04253-w

Abstract

Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Fig. 1**
General process for navigating wheat gene nomenclature; based on McCouch et al. (2008). Whereas a gene may be defined as a segment of DNA with a known or predicted function or phenotype and alleles may be defined as variations in a gene sequence, we have adopted the precedence of McCouch et al. (2008) in distinguishing “alleles” based on function/phenotype from sequence variants or “haplotypes”

**Fig. 2**
Example of a gene with known phenotype (*VRN-A1*) and later cloned (*TaAP-A1*). WGC: Wheat Gene Catalogue

**Fig. 3**
Example of a gene named based on sequence homology to a gene from another plant species. Here, the gene model *TraesCS7A02G319400* is named as *TaAGL12-A1*, based on phylogenetic analyses. Sequence variants are identified in two cultivars and in two ethyl methanesulfonate (EMS) mutants from cv. Kronos; these are referred to as haplotypes as they have no phenotype associated with them

See this image and copyright information in PMC

References

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Updated guidelines for gene nomenclature in wheat

Affiliations

Updated guidelines for gene nomenclature in wheat

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources