Updated guidelines for gene nomenclature in wheat
Jazyk angličtina Země Německo Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
FT210100810
Australian Research Council
DP210103744
Australian Research Council
DP210100296
Australian Research Council
DP200100762
Australian Research Council
BB/P016855/1
Biotechnology and Biological Sciences Research Council - United Kingdom
BBS/OS/NW/000016
Biotechnology and Biological Sciences Research Council - United Kingdom
BB/P010741/1
Biotechnology and Biological Sciences Research Council - United Kingdom
2022-68013-36439
National Institute of Food and Agriculture
2022-68013-36439
National Institute of Food and Agriculture
03/A215
UNCPBA
CerealMed
Partnership for Research and Innovation in the Mediterranean Area
INTA-PD-E3-I060
Instituto Nacional de Investigacion Agropecuaria, Uruguay
RYC-2017-21891
Ministerio de Ciencia e Innovación
GINOP-2.3.2-15-2016-00029
Innovation and Technology Ministry
Diversity
Genome Canada
Domestication
Genome Canada
Discovery
Genome Canada
Delivery
Genome Canada
CZ.02.1.01/0.0/0.0/16_019/0000827
European Regional Development Fund
PCI2019-103526
Programa Estatal de l+D+i Orientada a los Retos de la Sociedad
PICT 2019-03256
Agencia Nacional de Promoción de la Investigacion
2030-21000-024-00D
Agricultural Research Service
INIA_L1_CS_39
Instituto Nacional de Investigación Agropecuaria
INIA_L1_CS_35
Instituto Nacional de Investigación Agropecuaria
PR_FSA_2009_1_1369
Agencia Nacional de Investigación e Innovación
FSA_1_2013_1_12980
Agencia Nacional de Investigación e Innovación
FSA_1_2018_1_152918
Agencia Nacional de Investigación e Innovación
PubMed
36952017
PubMed Central
PMC10036449
DOI
10.1007/s00122-023-04253-w
PII: 10.1007/s00122-023-04253-w
Knihovny.cz E-zdroje
- MeSH
- fenotyp MeSH
- jedlá semena genetika MeSH
- pšenice * genetika MeSH
- rostlinné geny MeSH
- šlechtění rostlin * MeSH
- Publikační typ
- časopisecké články MeSH
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.
CenGen Pty Ltd Worcester 6850 South Africa
Centre for Agricultural Research ELKH 2462 Martonvasar Hungary
Crop Improvement and Genetics Research Unit USDA ARS 800 Buchanan St Albany CA 94710 USA
Departamento de Biología Aplicada Facultad de Agronomía Azul Provincia de Buenos Aires Argentina
Department of Genetics Stellenbosch University Matieland 7602 South Africa
Department of Plant Science University of California Davis CA 95616 USA
Estación Experimental de Aula Dei Zaragossa Spain
International Maize and Wheat Improvement Center Apdo Postal 6 641 Mexico D F Mexico
John Innes Centre Norwich Research Park Norwich NR4 7UH UK
Laboratory of Plant Breeding Graduate School of Agriculture Kyoto University Kyoto 606 8224 Japan
N 1 Vavilov Institute of General Genetics Russian Academy of Sciences Moscow Russia 119991
NIAB 93 Lawrence Weaver Road Cambridge CB3 0LE UK
School of Agricultural Biotechnology Punjab Agricultural University Ludhiana 141 004 India
School of Biological Sciences University of Western Australia Perth 6009 Australia
Zobrazit více v PubMed
Abrouk M, Athiyannan N, Müller T, Pailles Y, Stritt C, Roulin AC, Chu C, Liu S, Morita T, Handa H, Poland J, Keller B, Krattinger SG. Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color. Commun Biol. 2021;4:375. doi: 10.1038/s42003-021-01908-6. PubMed DOI PMC
Allen AM, Winfield MO, Burridge AJ, et al. Characterization of a wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum) Plant Biotech J. 2017;15:390–401. doi: 10.1111/pbi.12635. PubMed DOI PMC
Anonymous 1979 Enzyme Nomenclature (1978) Recommendations of the Nomenclature Committee of the International Union of Biochemistry. Academic Press, New York
Anonymous 1986 Enzyme Nomenclature (1986) Recommendations of the Nomenclature Committee of the International Union of Biochemistry. Academic Press, New York
Beales J, Turner A, Griffiths S, Snape JW, Laurie DA. A pseudo-response regulator is mis-expressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.) Theor Appl Genet. 2007;115:721–733. doi: 10.1007/s00122-007-0603-4. PubMed DOI
Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database. 2019;2019:baz065. PubMed PMC
Cheetham SW, Faulkner GJ, Dinger ME. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet. 2020;21:191–201. doi: 10.1038/s41576-019-0196-1. PubMed DOI
Debernardi JM, Lin H, Chuck G, Faris JD, Dubcovsky J. microRNA172 plays a crucial role in wheat spike morphogenesis and grain threshability. Development. 2017;144:1966–1975. PubMed PMC
Debernardi JM, Tricoli DM, Ercoli MF, Hayta S, Ronald P, Palatnik JF, Dubcovsky J. A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat Biotechnol. 2020;38:1274–1279. doi: 10.1038/s41587-020-0703-0. PubMed DOI PMC
Driscoll CJ, Sears ER. Mapping of a wheat-rye translocation. Genetics. 1965;51:439–443. doi: 10.1093/genetics/51.3.439. PubMed DOI PMC
Dvorak J, Deal KR, Luo MC. Discovery and mapping of wheat Ph1 suppressors. Genetics. 2006;174:17–27. doi: 10.1534/genetics.106.058115. PubMed DOI PMC
Gale M, Devos K. Comparative genetics in the grasses. Proc Natl Acad Sci U S A. 1998;95:1971–1974. doi: 10.1073/pnas.95.5.1971. PubMed DOI PMC
Gaurav K, Arora S, Silva P, Sanchez-Martin J, Horsnell R, Gao L, Brar GS, Widrig V, John Raupp W, Singh N, Wu S, Kale SM, Chinoy C, Nicholson P, Quiroz-Chavez J, Simmonds J, Hayta S, Smedley MA, Harwood W, Pearce S, Gilbert D, Kangara N, Gardener C, Forner-Martinez M, Liu J, Yu G, Boden SA, Pascucci A, Ghosh S, Hafeez AN, O’Hara T, Waites J, Cheema J, Steuernagel B, Patpour M, Justesen AF, Liu S, Rudd JC, Avni R, Sharon A, Steiner B, Kirana RP, Buerstmayr H, Mehrabi AA, Nasyrova FY, Chayut N, Matny O, Steffenson BJ, Sandhu N, Chhuneja P, Lagudah E, Elkot AF, Tyrrell S, Bian X, Davey RP, Simonsen M, Schauser L, Tiwari VK, Randy Kutcher H, Hucl P, Li A, Liu DC, Mao L, Xu S, Brown-Guedira G, Faris J, Dvorak J, Luo MC, Krasileva K, Lux T, Artmeier S, Mayer KFX, Uauy C, Mascher M, Bentley AR, Keller B, Poland J, Wulff BBH. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat Biotechnol. 2022;40:422–431. doi: 10.1038/s41587-021-01058-4. PubMed DOI PMC
Hart GE (1987) Genetic and biochemical studies of enzymes. In: Heyne EG (ed.) Wheat and Wheat Improvement. pp 199–214. American Society of Agronomy, Madison
Hewitt T, Muller MC, Molnar I, Mascher M, Holusova K, Simkova H, Kunz L, Zhang JP, Li JB, Bhatt D, Sharma R, Schudel S, Yu GT, Steurnagel B, Periyannan S, Wulff B, Ayliffe M, McIntosh R, Keller B, Lagudah E, Zhang P. A highly differentiated region of wheat chromosome 7AL encodes a Pm1a immune receptor that recognizes its corresponding AvrPm1a effector from Blumeria graminis. New Phytol. 2021;229:2812–2826. doi: 10.1111/nph.17075. PubMed DOI PMC
Igrejas G, Ikeda TM, Guzman C. Wheat quality for improving processing and human health. Switzerland: Springer Nature; 2020.
International Wheat Genome Sequencing Consortium Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361:eaar7161. PubMed
Ishida Y, Tsunashima M, Hiei Y, Komari T. Wheat transformation. In: Wang K, editor. Agrobacterium protocols: methods in molecular biology. New York: Springer; 2015. pp. 189–198. PubMed
Kihara H. Discovery of the DD analyser, one of the ancestors of Triticum vulgare (in Japanese) Agri Horti. 1944;19:889–890.
Koebner RMD, Miller TE. A note on the nomenclature for translocated chromosomes in the Triticeae. Cereal Res Commun. 1986;14:315–316.
Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J. Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci USA. 2017;114:E913–E921. doi: 10.1073/pnas.1619268114. PubMed DOI PMC
Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C. Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature. 2018;557:424–428. doi: 10.1038/s41586-018-0108-0. PubMed DOI PMC
Liu L, Ikeda TM, Branlard G, Peña RJ, Rogers WR, Lerner SE, Kolman MA, Xia XC, Wan LH, Ma WJ, Appels R, Yoshida H, Wang AL, Yan YM, He ZH. Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat. BMC Plant Biol. 2010;10:124. doi: 10.1186/1471-2229-10-124. PubMed DOI PMC
Maccaferri M, Harris NS, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, Himmelbach A, Mascher M, Bagnaresi P, Faccioli P, Cozzi P, Lauria M, Lazzari B, Stella A, Manconi A, Gnocchi M, Moscatelli M, Avni R, Deek J, Biyiklioglu S, Frascaroli E, Corneti S, Salvi S, Sonnante G, Desiderio F, Marè C, Crosatti C, Mica E, Özkan H, Kilian B, De Vita P, Marone D, Joukhadar R, Mazzucotelli E, Nigro D, Gadaleta A, Chao S, Faris JD, Melo ATO, Pumphrey M, Pecchioni N, Milanesi L, Wiebe K, Ens J, MacLachlan RP, Clarke JM, Sharpe AG, Koh CS, Liang KYH, Taylor GJ, Knox R, Budak H, Mastrangelo AM, Xu SS, Stein N, Hale I, Distelfeld A, Hayden MJ, Tuberosa R, Walkowiak S, Mayer KFX, Ceriotti A, Pozniak CJ, Cattivelli L. Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genetics. 2019;51:885–895. doi: 10.1038/s41588-019-0381-3. PubMed DOI
McCouch SR, Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative (2008) Gene nomenclature system for rice. Rice 1:72–84
McIntosh R, Yamazaki Y, Dubcovsky J, Rogers J, Morris C, Appels R, Xia XC (2013) Catalogue of gene symbols for wheat. In: 12th International wheat genetics symposium 8–13 September 2013 Yokohama, Japan
Moore G, Devos K, Wang Z, Gale M. Grasses, line up and form a circle. Curr Biol. 1995;5:737–739. doi: 10.1016/S0960-9822(95)00148-5. PubMed DOI
Morris R, Sears ER (1967) The cytogenetics of wheat and its relatives. In: Quisenberry KS & Reitz LP (eds) Wheat and wheat improvement. pp19–87. American Society of Agronomy, Madison
Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature. 1999;400:256–261. doi: 10.1038/22307. PubMed DOI
Ramirez-Gonzalez RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, International Wheat Genome Sequencing C, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Brautigam A, Uauy C (2018) The transcriptional landscape of polyploid wheat. Science 361:eaar6089 PubMed
Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. New Phytol. 2020;225:511–529. doi: 10.1111/nph.16122. PubMed DOI
Sears ER. The Cytology and genetics of the wheats and their relatives. Advanced Genetics. 1948;2:239–270. doi: 10.1016/S0065-2660(08)60470-8. PubMed DOI
Sears ER. The aneuploids of common wheat. Missouri Agric Exp Stn Res Bull. 1954;572:1–58.
Sears ER. Induced transfer of hairy neck from rye to wheat. Zeitschrift Fur Pflanzenzuchtung. 1967;57:4–25.
Shiferaw B, Smale M, Braun H-J, Duveiller E, Reynolds M, Muricho G. Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security. Food Secur. 2013;5:291–317. doi: 10.1007/s12571-013-0263-y. DOI
Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai YS, Gill BS, Faris JD. Molecular characterization of the major wheat domestication gene Q. Genetics. 2006;172:547–555. doi: 10.1534/genetics.105.044727. PubMed DOI PMC
Tsunewaki K. Prof. H. Kihara's genome concept and advancements in wheat cytogenetics in his school. In: Ogihara Y, Takumi S, Handa H, editors. Advances in wheat genetics: from genome to field. Tokyo: Springer; 2015. pp. 3–11.
Vanin EF. Processed pseudogenes: characteristics and evolution. Ann Rev Genet. 1985;19:253–272. doi: 10.1146/annurev.ge.19.120185.001345. PubMed DOI
Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo DH, Ens J, Wiebe K, N'Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnere G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ. Multiple wheat genomes reveal global variation in modern breeding. Nature. 2020;588:277–283. doi: 10.1038/s41586-020-2961-x. PubMed DOI PMC
Werner JR, Endo TR, Gill BS. Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci USA. 1992;89:11307–11311. doi: 10.1073/pnas.89.23.11307. PubMed DOI PMC
Woodhouse MR, Cannon EK, Portwood JL, Harper LC, Gardiner JM, Schaeffer ML, Andorf CM. A pan-genomic approach to genome databases using maize as a model system. BMC Plant Biol. 2021;21:385. doi: 10.1186/s12870-021-03173-5. PubMed DOI PMC
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J. Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA. 2003;100:6263–6268. doi: 10.1073/pnas.0937399100. PubMed DOI PMC