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)

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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.

Introduction

The past 4 years have witnessed the publication of the first whole-genome sequence assemblies of the oat genus Avena L., classified within subfamily Pooideae of the Poaceae, tribe Poeae, subtribe Aveninae. The first oat whole-genome sequences published were for A- and C-genome diploids (Maughan et al. 2019), and rapidly progressed further to hexaploid A. sativa L. (2n = 6x = 42, AACCDD) with the online release of the hexaploid OT3098 sequence in 2020 on the GrainGenes database (Yao et al. 2022) website (https://wheat.pw.usda.gov/jb/?data=/ggds/oat-ot3098-pepsico). This release was followed by published assemblies of the OT3098 ver. 2 assembly in 2021, Swedish hulled oat cv. Sang (Kamal et al. 2022), and Chinese hulless cv. Sanfensan (Peng et al. 2022). Significantly, these whole-genome sequences permitted the assignment of each of the 21 oat chromosomes to their subgenome and homoeologous group. The group designations were based on synteny with the seven chromosomes of the non-Poeae grass barley (Hordeum vulgare L.). Whole-genome sequencing efforts are now progressing toward assemblies of multiple genotypes of common oat and closely related species in a coordinated international effort – the Oat Pangenome Project (PanOat). This has necessitated a reappraisal of the various existing oat chromosome, linkage group, gene and gene model designations and their unification into a single, universal nomenclature convention.

Oat geneticists in the 1960s were the first to suggest that A. sativa and its allohexaploid allied taxa – A. byzantina C. Koch (red oat), A. fatua L. (common wild oat) and A. sterilis L. (wild animated oat) – carried the AA, CC and DD subgenomes (Rajhathy and Thomas 1974). Their original karyotype-based nomenclature system was based on chromosome morphology without molecular cytogenetic or chromosome banding data (Rajhathy 1963), and gene nomenclature generally followed rules established in other cereal species, particularly those in the tribe Triticeae (Simons et al. 1966, 1978). We present a universal genome, chromosome, transcriptome and gene identification system approved by the International Oat Nomenclature Committee (IONC) for application to all Avena genotypes that are analysed moving forward. This system follows the convention for chromosome nomenclature established for barley (Singh and Tsuchiya 1982; Wang et al. 1996) and the new system for wheat (Boden et al. 2023).

The nomenclature rules

Genomes and subgenomes

Whole-genome sequence assemblies (Kamal et al. 2022; Peng et al. 2022) along with prior work by various authors including Yan et al. 2016 and Latta et al. (2019) have confirmed the unique identities of the A, B, C and D genomes/subgenomes of Avena. In addition, we herein propose a separate genome designator for the perennial autotetraploid oat A. macrostachya, EE, because of its uniquely long chromosomes with dense pericentromeric heterochromatin patterns, highly symmetrical karyotype (Badaeva et al. 2010), and recalcitrance to crossing with other Avena species having genomes A, B and D, albeit with somewhat greater homology to genome C (Leggett 2011). In the current proposal, the subgenomes of A. sativa are indicated with the subscript ‘s’. Diploid genomes will follow several new conventions: A_a represents the A. atlantica–strigosa biological species group, A_c is for the A. canariensis genome, A_d for A. damascena, A_l for A. longiglumis, and A_p for A. prostrata. For the CC diploids, C_e represents the genome of the A. eriantha–clauda group and C_v is used for A. ventricosa. The A. barbata group contains subgenomes A_b and B (which has not been identified in any other biological species). The C- and D-subgenomes in the Section Pachycarpa tetraploids are represented as C_i and D_i in A. insularis, C_g and D_g in A. magna (syn. A. maroccana), and C_y and D_y in A. murphyi. Use of the subscript ‘m’ is discouraged owing to potential confusion with multiple tetraploid species names beginning with the letter ‘m’.

Species/taxon designation code

For the gene models, each Avena biological species-group has a five-letter species designator beginning with ‘AVxxx’ and each genotype is to be assigned its own specific five-digit code, beginning with the first set of assembled reference genomes (Table 1). Hereafter, each new sequenced genotype should be assigned a number after consultation between the researcher and the GrainGenes curation team. Genotypes of the same species are grouped within specified numerical ranges, as follows. Numbers 00001–09999 are reserved for natural hexaploids of the A. sativa group. Tetraploids are numbered 10000–15999. Diploids are numbered 20000–26999. Synthetics will be designated with numbers in the 30000s.

Table 1.Correspondence between five-letter species designator codes, genome/subgenome formulae, and commonly accepted Avena taxa, excluding lesser used taxa identified in Baum (1977) or Loskutov and Rines (2011).

Five-letter species designator code	Ploidy	Subgenomes	Included Avena taxa	Reserved genotype identifier codes
AVAGA	4x	A’A’B’B’	agadiriana	11000–11999
AVATL	2x	AₐAₐ, sometimes AₐAₐAₐAₐ	atlantica	20000–20999
			brevis
			hirtula
			hispanica
			nuda
			nudibrevis
			strigosa
			wiestii
AVBAR	4x	A_bA_bBB	abyssinica	10000–10999
			barbata
			vaviloviana
AVCAN	2x	A_cA_c	canariensis	21000–21999
AVDAM	2x	A_dA_d	damascena	22000–22999
AVERI	2x	CₑCₑ	clauda	25000–25999
			eriantha
			pilosa
AVINS	4x	C_iC_iD_iD_i	insularis	12000–12999
AVLON	2x	AₗAₗ	longiglumis	23000–23999
AVMAG	4x	C_gC_gD_gD_g	maroccana	13000–13999
AVMAG	4x	C_gC_gD_gD_g	magna	13000–13999
AVMAC	4x	EEEE (possibly EEE’E’)	macrostachya	15000–15999
AVMUR	4x	C_yC_yD_yD_y	murphyi	14000–14999
AVPRO	2x	AₚAₚ	prostrata	24000–24999
AVESA	6x	AₛAₛCₛCₛDₛDₛ	byzantina	00001–09999
			fatua
			ludoviciana
			occidentalis
			sativa
			sativa subsp. nuda
			sterilis
AVSYN	4x-10x	Various	Synthetic allopolyploids, e.g. Amagalon	30000–30999
AVVEN	2x	C_vC_v	bruhnsiana	26000–26999
AVVEN	2x	C_vC_v	ventricosa	26000–26999

Designations generally follow biological species concept groups as outlined by Ladizinsky (2012).

Chromosome correspondences

Homoeologous chromosome groups were identified and subgenome assignments made based on common synteny within Avena and with chromosomes 1H–7H of Hordeum vulgare, along with distributions of subgenome-abundant repetitive motifs (Jiang et al. 2021; Kamal et al. 2022; Peng et al. 2022) (Table 2).

Table 2.Correspondence of chromosome, pseudochromosome, and linkage-group designation systems in Avena hexaploids and diploids A. atlantica and A. eriantha.

PepsiCo, Yao et al. (2022), Jiang et al. (2021)	Chaffin et al. (2016) Mrg consensus linkage group	Sanz et al. (2010) chromosome designation	Maughan et al. (2019) diploid oat assemblies	NEW 2x chromosome designation	NEW 6x chromosome designation
Genome A
1Aₛ(−)	Mrg18(−)	17A	AA2(+)	1Aₐ	1Aₛ
2Aₛ(+)	Mrg33(+)	15A	AA5(−)	2Aₐ	2Aₛ
3Aₛ(+)	Mrg23(+)	11A	AA3(+)	3Aₐ	3Aₛ
4Aₛ(+)	Mrg20(+)	19A	AA4(−)	4Aₐ	4Aₛ
5Aₛ(+)	Mrg24(+)	8A	AA6(−)	5Aₐ	5Aₛ
6Aₛ(+)	Mrg05(+)	16A	AA7(−)	6Aₐ	6Aₛ
7Aₛ(+)	Mrg12(+)	13A	AA1(−)	7Aₐ	7Aₛ
Genome C
1Cₛ(−)	Mrg28(−)	7C	AE5(+)	1Cₑ	1Cₛ
2Cₛ(+)	Mrg13(+)	5C	AE4(−)	2Cₑ	2Cₛ
3Cₛ(+)	Mrg15(−)	2C	AE3(−)	3Cₑ	3Cₛ
7Cₛ(+)	Mrg11(+)	1C	AE1(−)	4Cₑ	4Cₛ
5Cₛ(−)	Mrg03(−)	4C	AE6(−)	5Cₑ	5Cₛ
6Cₛ(−)	Mrg17(−)	3C	AE2(−)	6Cₑ	6Cₛ
4Cₛ(−)	Mrg09(−)	6C	AE7(−)	7Cₑ	7Cₛ
Genome D
1Dₛ(−)	Mrg01(−)	14D	–	–	1Dₛ
2Dₛ(−)	Mrg08(−)	12D	–	–	2Dₛ
3Dₛ(+)	Mrg19(+)	21D	–	–	3Dₛ
4Dₛ(+)	Mrg21(+)	20D	–	–	4Dₛ
5Dₛ(−)	Mrg06(−)	10D	–	−	5Dₛ
6Dₛ(−)	Mrg04(−)	18D	–	–	6Dₛ
7Dₛ(−)	Mrg02(−)	9D	–	−	7Dₛ

The new chromosome numbering system (bolded columns) is based on synteny with pericentromeric core chromosome regions of Hordeum vulgare. The suffixes (+) and (−) denote the orientations of chromosomes relative to the new system (Kamal et al. 2022) As new Avena species are sequenced, their chromosomes will be oriented and numbered relative to the information presented here, using the genome and subgenome designations presented in Table 1. The reference for the PepsiCo release of OT3098 is as follows: Avena sativa – OT3098 v1, PepsiCo, https://wheat.pw.usda.gov/GG3/graingenes_downloads/oat-ot3098-pepsico). Note that in this table, chromosomes 4C_s and 7C_s are switched from the designation used in the PepsiCo OT3098 (Jiang et al. 2021; Yao et al. 2022) and Sanfensan genomes (Peng et al. 2022), in keeping with the analyses reported by Kamal et al. (2022).

Quantitative trait loci, genes and proteins

Quantitative trait loci

The IONC recognises the utility of having a consistent naming system for QTL. However, many quantitative trait loci (QTLs) have been identified in oat over the years, and changing the older names could cause confusion. Therefore, the committee proposes that:

The names of previously published QTLs be kept as is, unless this would duplicate a name used elsewhere. In such cases, the name would be modified, staying close to the original.
The names of new QTLs and previously published QTLs with no names assigned be given names using the following convention, which has been derived from the standard used by the GrainGenes database (Yao et al. 2022; https://wheat.pw.usda.gov/), and informed by the new wheat nomenclature rules outlined by Boden et al. (2023):

QField1 .Field2_Field3

Field1 is the main trait name (two to five letters). If any additional trait or environment information is necessary to distinguish the QTL, then a dash followed by two to five more letters is added.

Field2 is the map name, with the year and a dash added if necessary to distinguish the work. Typically, the map name would either be an abbreviated version of the pedigree for a biparental cross, or the name given to an association mapping population.

Field3 is the linkage group name. If the group has been assigned to an ‘Mrg’ linkage group from the 2018 hexaploid oat consensus map (Bekele et al. 2018), then ‘Mrg’ is included in the name. If more than one QTL for the same trait is found on one linkage group, then a period is added, followed by a number to distinguish the QTL.

A simple example of a name created using this system would be ‘QHDNV.U8xU605_6’ (QTL for heading date using non-vernalised plants, mapped in the UFRGS 8/UFRGS 930605 (U8xU605) population on linkage group 6). A more complex example would be ‘QHD-Far11.2016-CORE_Mrg20.2’ (QTL for heading date recorded at Fargo, ND, in 2011, mapped using the CORE set of lines in 2016 on linkage group Mrg20, the second of two HD QTLs on that group). Examples of other styles of QTLs already in the literature include ‘Days to heading’, ‘KxO-11-c’ and ‘QPlumps.Aberd17.2A’ (in this last case, the chromosome number is identified).

Gene model identifiers

We recognise the importance of consistent use of gene model identifiers across Avena genotypes to facilitate analysis and interpretation across studies (Schnable 2020). It is important to emphasise that no perfect solution for gene model nomenclature exists, and each choice has advantages and disadvantages. Indeed, we are aware that different plant researcher communities adopted slightly different guidelines for their species. With this in mind, we propose the adoption of the following gene-model syntax for Avena:

Field1 . Field2 . Field3 . Field4 . Field5

Field1 is a five-character-long descriptor for species as shown in Table 1 (‘designator code’). It will be shown in all upper case letters.

Field2 is a six-character-long descriptor for oat genotypes. The first five characters will be numerical, and the last character will be alphanumeric. The currently assigned genotype identifiers are shown in Table 3. The last character (shown as ‘x’ in Table 3 as a placeholder) will be to give flexibility to account for genotype variants, or in case more than one assembly exists for the very same cultivar (e.g. assemblies done by the same or different research groups). The six-character-long identifier in this field will be assigned by the IONC and will be publicly available through GrainGenes (Yao et al. 2022) at https://wheat.pw.usda.gov/GG3/oatnomenclature. To obtain a new identifier, researchers are encouraged to reach out to the IONC through GrainGenes (feedback@graingenes.org).

Table 3.Initial oat genotype numerical assignments (in bold) for Field2 as described above and in Table 1.

Common name	Source	Avena taxa	Five-letter species designator code	Number
OT 3098	PanOat/PepsiCo	sativa	AVESA	00001 x
GMI 423	PanOat/GMI	sativa	AVESA	00002 x
Bingo	PanOat	sativa	AVESA	00003 x
FM13	PanOat	sativa	AVESA	00004 x
Hative des Alpes	PanOat	sativa	AVESA	00005 x
Bannister	PanOat	sativa	AVESA	00006 x
Bilby	PanOat	sativa	AVESA	00007 x
Clintland 60 (CIav 7234)	PanOat/USDA	sativa	AVESA	00008 x
Nicolas	PanOat/Canada	sativa	AVESA	00009 x
Sang	PanOat/Scanoat	sativa	AVESA	00010 x
OT 380	PanOat/USDA	sativa	AVESA	00011 x
Aslak	PanOat/LUKE	sativa	AVESA	00012 x
Lion	PanOat	sativa	AVESA	00013 x
Rhapsody	PanOat	sativa	AVESA	00014 x
Delfin	PanOat	sativa	AVESA	00015 x
HiFi	PanOat/Canada	sativa	AVESA	00016 x
Park	PanOat/Canada	sativa	AVESA	00017 x
GS7; 94197A1-9-2-2-2-5	PanOat/Canada	sativa	AVESA	00018 x
Leggett	AAFC	sativa	AVESA	00019 x
AC Morgan	AAFC	sativa	AVESA	00020 x
Sanfensan	Yuanying Peng	sativa subsp. nuda	AVESA	00400 x
PI 182478	PanOat/USDA	sativa subsp. nuda	AVESA	00401 x
Gehl	PanOat/Canada	sativa subsp. nuda	AVESA	00402 x
PI 258586	PanOat/IBERS	byzantina	AVESA	00500 x
Victoria	PanOat	byzantina	AVESA	00501 x
CN 25955	PanOat	fatua	AVESA	00600 x
Tn1	PanOat/IBERS	sterilis	AVESA	00700 x
Tn5	PanOat/IBERS	sterilis	AVESA	00701 x
PI 388828	PanOat/USDA	barbata	AVBAR	10000 x
PI 411152	BYU/USDA	abyssinica	AVBAR	10001 x
BYU 209	PanOat	insularis	AVINS	12000 x
CN 108634	Yuanying Peng	insularis	AVINS	12001 x
CN 58138	PanOat	longiglumis	AVLON	23000 x
CN 58139	Yuanying Peng	longiglumis	AVLON	23001 x
Amagalon	PanOat	magna X longiglumis	AVSYN	30000 x

Note that ‘x’ in the number column is only used as a placeholder (as described in the text) to account for genotype variants, or in case more than one assembly exists for the same cultivar.

Field3 is a two-character-long descriptor for the annotation release version for a given assembly. The first release will be r1, the second r2, and so forth. One example could be the same group working on the same assembly creating a second set of annotations.

Field4 is a 10-character-long descriptor. The first two characters are alphanumeric and designate the chromosome (e.g. 4D). The third character is ‘g’ for gene locus, even for transcripts or proteins. The lower case, as opposed to upper case, ‘g’ was selected to increase the readability of the preceding chromosome descriptor. The following seven characters are the gene model identifier based on the position ordering from the 5’ to 3’ DNA sequence for each chromosome (i.e. first predicted gene loci on the 1A chromosome will be 1Ag0000001, 1Ag0000002, and so forth; first predicted gene locus on the 2A chromosome will be 2Ag0000001). There is a caveat for researchers: these numbers are dependent on the annotation pipelines/assemblies, and therefore, the same gene identifier may not point to the same gene locus for different releases or between different genotypes. To obtain orthologous relationships between the individual gene models of all genotypes included in PanOat, we will provide an orthologous gene framework with the pan-genome analysis.

Field5 is a flexible-length descriptor to show transcripts, isoforms/splice variants, and proteins. Field5 will be blank for gene loci. For gene models, gene transcripts, isoforms and proteins, the field will be numbered as 1, 2, and so forth.

As an example, the following is an acceptable instance for Avena sativa (therefore ‘AVESA’) OT3098 genotype’s (‘00001’) ver. 1 assembly (‘a’; if this was ver. 2 assembly, it would have been ‘b’) and ver. 2 annotation set (‘r2’), on the 1A chromosome (‘1A’), for the first gene locus (‘0000001’):

Gene locus: AVESA.00001a.r2.1Ag0000001
Gene models/transcripts/isoforms/proteins: AVESA.00001a.r2.1Ag0000001.1, AVESA.00001a.r2.1Ag0000001.2, and so on.

Functional gene names

Existing oat gene names will continue to be used, but moving forward, the guidelines developed for wheat gene nomenclature detailed in Boden et al. (2023) will be followed.

Pathogenic disease reaction

The system for designating loci controlling reaction to biotic agents that attack oat proposed by Simons et al. (1978) (Table 4) will continue to be followed but with the omission of the hyphen in designations (e.g. ‘Pc1’ rather than ‘Pc-1’) to reflect the more common usage of the former in publications since 1978. It should be noted that the chromosomal locations of many of the loci that have been catalogued to date remain unknown, and that some of these may prove to be allelic once this is resolved. If this arises, it will be necessary to change the numbering of the locus/loci involved, and possibly delete others from the catalogue, as has occurred in wheat (e.g. the deletion of Sr1 due to synonymy with Sr9d, and of Sr3 and Sr4 due to a lack of single gene stocks; McIntosh et al. 1995) (Park et al. 2022).

Table 4.Locus designations for genes controlling pathogenic disease reaction in Avena.

Pathogen	Disease	Gene designation	Notes
Blumeria graminis f. sp. avenae (syn. Erysiphe graminis)	Powdery mildew	Pm	Formerly Eg (Hsam et al. 2014)
Ditylenchus dipsaci	Stem nematode	Dd
Heterodera avenae	Cereal cyst nematode	Ha
Helminthosporium (Cochliobolus) victoriae	Victoria blight	Hv
Puccinia coronata f. sp. avenae	Crown rust	Pc
Puccinia graminis f. sp. avenae	Stem rust	Pg
Pseudomonas coronafaciens pv. coronafaciens	Halo blight	Psc	Kim (2020)
Pseudomonas coronafaciens pv. striafaciens	Stripe blight	Pcs	Dutta et al. (2018)
Schizaphis graminum	Greenbug	Grb	Radchenko et al. (2018)
Ustilago kolleri	Covered smut	U
Ustilago avenae	Loose smut	U

Proteins

The protein notation for gene models is specified in the Gene model Identifiers section above. For the protein names associated with gene loci, Boden et al. (2023) will be followed.

Discussion

The rules and guidelines outlined above represent an effort to accommodate over 100 years of gene, genome and chromosome nomenclature in Avena, while providing for standardisation, not only within the oat research community, but also extending to the broader cereal grass research community working on barley, wheat, rye and triticale. The time is ripe for this standardised nomenclature system, given the rapid expansion of oat and Triticeae genome sequencing efforts. It is our expectation that genome sequence information from other cereal grass genera will be essential resources to leverage in identifying economically important gene homologs within the A. sativa genome. We strongly encourage all oat researchers to familiarise themselves with this nomenclature and with the online resources and personnel at GrainGenes (https://wheat.pw.usda.gov/GG3/; Yao et al. 2022) and to adhere to the policies above through consultation with the GrainGenes team.

Data availability

Data sharing is not applicable because no new data were generated or analysed during this study.

Conflicts of interest

Robert Park is an Associate Editor of Crop & Pasture Science. To mitigate this potential conflict of interest, he was blinded from the review process. The authors declare no other conflicts of interest.

Declaration of funding

VCB and TZS were supported by the US Department of Agriculture, Agricultural Research Service, Project No. 2030-21000-056-00D.

Acknowledgements

USDA is an equal opportunity provider and employer.

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 |