Updated guidelines for gene nomenclature in wheat

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.EEA PergaminoFil: Boden, S. A. University of Adelaide. Waite Research Institute. School of Agriculture, Food and Wine; AustraliaFil: McIntosh, R .A. University of Sydney. School of Life and Environmental Sciences. Plant Breeding Institute; AustraliaFil: Uauy, C. Norwich Research Park. John Innes Centre; Reino UnidoFil: Krattinger, S. G. King Abdullah University of Science and Technology. Biological and Environmental Science and Engineering Division. Plant Science Program; Arabia SauditaFil: Krattinger, S. G. The Wheat Initiative; AlemaniaFil: Dubcovsky, J. University of California. Department of Plant Science; Estados UnidosFil: Dubcovsky, J. The Wheat Initiative; AlemaniaFil: Rogers, W.J. Universidad Nacional del Centro de La Provincia de Buenos Aires. Facultad de Agronomía (CIISAS, CIC-BIOLAB AZUL, CONICET-INBIOTEC, CRESCA). Departamento de Biología Aplicada; ArgentinaFil: Rogers, W.J. The Wheat Initiative; AlemaniaFIL: Xia, X. C. Chinese Academy of Agricultural Sciences. National Wheat Improvement Centre. Institute of Crop Science; ChinaFil: Badaeva, E. D. Russian Academy of Sciences. N.I. Vavilov Institute of General Genetics; RusiaFil: Bentley, A. R. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Bentley, A. R. The Wheat Initiative; AlemaniaFil: Brown-Guedira, G. North Carolina State University. USDA-ARS Plant Science Research; Estados UnidosFil: Brown-Guedira, G. The Wheat Initiative; AlemaniaFil: González, Fernanda G. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Sección Ecofisiología; ArgentinaFil: González, Fernanda G. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA); ArgentinaFil: González, Fernanda G. The Wheat Initiative; AlemaniaFil: Zhang, Y. Fudan University. School of Life Sciences. Institute of Plant Biology. Collaborative Innovation Center of Genetics and Development. State Key Laboratory of Genetic Engineering; Chin

Updated guidelines for gene nomenclature in wheat.

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.S. A. Boden, R. A. McIntosh, C. Uauy, S. G. Krattinger, J. Dubcovsky, W. J. Rogers, X. C. Xia, E. D. Badaeva, A. R. Bentley, G. Brown, Guedira, M. Caccamo, L. Cattivelli, P. Chhuneja, J. Cockram, B. Contreras, Moreira, S. Dreisigacker, D. Edwards, F. G. González, C. Guzmán, T. M. Ikeda, I. Karsai, S. Nasuda, C. Pozniak, R. Prins, T. Z. Sen, P. Silva, H. Simkova, Y. Zhang, the Wheat Initiativ

Origin and evolution of the bread wheat D genome

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.

Background: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate Vigil quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale.Results: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%.Conclusions: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies

From shade to light : fonio, an african orphan crop, towards renewed challenges

The FAO recently estimated that demand for food will increase by 70% by 2050. The challenge will not only be on increasing the food supply but also on improving its nutritional value under an accelerating rate of environmental and social changes. One solution would be the wider use of underutilized crops to diversify alimentation and develop sustainable and low-input agriculture. Are orphan crops commodities for the future, and how can they be promoted. In this regard, fonio (Digitaria exilis Stapf) appears to be a promising crop. It is an indigenous staple cereal from Western Africa playing a crucial role in food security. Additionally, it is a model crop in important up-to-date concepts such as resilience, agroecology, population health, climatic changes, poverty reduction, and women's empowerment. Nevertheless, fonio has received limited attention from mainstream research compared to other dryland cereals, such as pearl millet and sorghum. Increasingly available genomic resources promise to promote advanced breeding strategies in fonio. This paper presents the past, present, and future of fonio research. We argue the need for interdisciplinarity and multistakeholder research approaches for increasing fonio production, conservation, and sustainable uses

Updated guidelines for gene nomenclature in wheat

Key message: Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. Abstract: 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.Fil: Boden, S. A.. University of Adelaide; AustraliaFil: McIntosh, R. A.. University of Sydney; AustraliaFil: Uauy, C.. Norwich Research Park; Reino UnidoFil: Krattinger, S.G.. King Abdullah University of Science and Technology; Arabia SauditaFil: Dubcovsky, Jorge. University of California at Davis; Estados UnidosFil: Rogers, William John. Universidad Nacional del Centro de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Cientifico Tecnolológico Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología. Laboratorio de Biología Funcional y Biotecnología; ArgentinaFil: Xia, X. C.. Chinese Academy of Sciences; República de ChinaFil: Badaeva, E.D.. Russian Academy Of Sciences; RusiaFil: Bentley, A.R.. Centro Internacional de Mejoramiento de Maiz y Trigo; MéxicoFil: Brown Guedira, G.. North Carolina State University; Estados UnidosFil: Cáccamo, Mario José. The Wheat Initiative; AlemaniaFil: Cattivelli, L.. Research Centre For Genomics And Bioinformatics; Italia. The Wheat Initiative; AlemaniaFil: Chhuneja, P.. Punjab Agricultural University; IndiaFil: Cockram, J.. The Wheat Initiative; AlemaniaFil: Contreras Moreira, B.. Consejo Superior de Investigaciones Científicas; EspañaFil: Dreisigacker, S.. The Wheat Initiative; Alemania. Centro Internacional de Mejoramiento de Maiz y Trigo; MéxicoFil: Edwards, D.. University of Western Australia; Australia. The Wheat Initiative; AlemaniaFil: González, Fernanda Gabriela. The Wheat Initiative; Alemania. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria; ArgentinaFil: Guzmán, C.. Universidad de Córdoba; España. The Wheat Initiative; AlemaniaFil: Ikeda, T. M.. Western Region Agricultural Research Center; Japón. The Wheat Initiative; AlemaniaFil: Karsai, I.. The Wheat Initiative; Alemania. Centre For Agricultural Research; HungríaFil: Nasuda, S.. Kyoto University; JapónFil: Pozniak, C.. University of Saskatchewan; Canadá. The Wheat Initiative; AlemaniaFil: Prins, R.. Stellenbosch University; SudáfricaFil: Sen, T .Z.. United States Department of Agriculture. Agriculture Research Service; Estados Unidos. The Wheat Initiative; AlemaniaFil: Silva, P.. Instituto Nacional de Investigación Agropecuaria Inia Uruguay; UruguayFil: Simkova, H.. Czech Academy of Sciences. Institute of Botany; República ChecaFil: Zhang, Yunlin. School Of Life Sciences Fudan University; Chin