A roadmap for gene functional characterisation in wheat

Adamski, Nikolai M; Borrill, Philippa; Brinton, Jemima; Harrington, Sophie A; Marchal, Clémence; Uauy, Cristóbal

doi:10.7287/peerj.preprints.26877v1

Cited by 4 publications

(4 citation statements)

References 35 publications

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“…One of the more tangible results of the improved genome assemblies and gene annotations is the increased ease with which knowledge from other species can be transferred into wheat (Adamski et al ., ). High‐quality gene annotations based on the new assemblies are now included in platforms such as Ensembl Plants, which identify putative orthologous genes in other species.…”

Section: Hypothesis Generation In Wheatmentioning

confidence: 97%

“…In summary, the last decade has brought about a revolution in the resources and approaches used for wheat research and breeding. We now have a wide range of resources that provide opportunities to improve our understanding of wheat gene functions, many of which are easily accessible for researchers moving into wheat from other species (Adamski et al ., ). One of the key challenges moving forwards will be predicting which genes will be most valuable within breeding programmes in diverse and changing environmental conditions.…”

Section: Looking Forwardmentioning

confidence: 97%

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Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

2018

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Summary Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in‐field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome‐level assembly of the wheat genome now facilitates a step‐change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene‐editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.

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Section: Hypothesis Generation In Wheatmentioning

confidence: 97%

Section: Looking Forwardmentioning

confidence: 97%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

2018

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“…Screening of the assembled mutants collection using a detached-leaf bioassay identified two independent T-DNA insertion mutants in the AtMin7 gene, which encodes an ADP ribosylation factor (ARF) guanine nucleotide exchange factor (GEF) protein, that displayed striking hyper-susceptibility to F. graminearum strain PH-1 infection compared to the parental wild-type A. thaliana ecotype Col-0. Utilizing a recently released high-quality fully annotated wheat genome reference sequence assembly (International Wheat Genome Sequencing Consortium (IWGSC), 2018) and well established bioinformatics tools enabling identification of putative gene orthologs from different plant species (Adamski et al, 2019) we identified the three homoeologous TaMin7 genes in hexaploid wheat ( Triticum aestivum ). Knock-down of these genes using Virus-induced gene silencing (VIGS) (Lee et al, 2012) significantly promoted FHB disease formation in this crop species.…”

Section: Introductionmentioning

confidence: 99%

The vesicular trafficking system component MIN7 is required for minimizing Fusarium graminearum infection

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Grimwade-Mann

et al. 2020

Preprint

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Plants have developed intricate defense mechanisms, referred to as innate immunity, to defend themselves against a wide range of pathogens. Plants often respond rapidly to pathogen attack by the synthesis and delivery of various antimicrobial compounds, proteins and small RNA in membrane vesicles to the primary infection sites. Much of the evidence regarding the importance of vesicular trafficking in plant-pathogen interactions comes from the studies involving model plants whereas this process is relatively understudied in crop plants. Here we assessed whether the vesicular trafficking system components previously implicated in immunity in Arabidopsis thaliana play a role in the interaction with Fusarium graminearum, a fungal pathogen notoriously famous for its ability to cause Fusarium head blight (FHB) disease in wheat. Among the analyzed vesicular trafficking mutants, two independent T-DNA insertion mutants in the AtMin7 gene displayed a markedly enhanced susceptibility to F. graminearum. Earlier studies identified this gene, encoding an ARF-GEF protein, as a target for the HopM1 effector of the bacterial pathogen Pseudomonas syringae pv. tomato, which destabilizes AtMIN7 leading to its degradation and weakening host defenses. To test whether this key vesicular trafficking component may also contribute to defense in crop plants, we identified the candidate TaMin7 genes in wheat and knocked-down their expression through Virus induced gene silencing. Wheat plants in which TaMIN7 were silenced displayed significantly more FHB disease. This suggests that disruption of MIN7 function in both model and crop plants compromises the trafficking of innate immunity signals or products resulting in hyper-susceptibility to various pathogens.One sentence summaryDisruption of an ARF-GEF protein encoding gene AtMin7 in Arabidopsis thaliana and silencing of the orthologous gene in wheat result in hyper susceptibility to the fungal pathogen Fusarium graminearum.

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“…Several important crops are polyploid, including bread and durum wheat, oilseed rape, and cotton [67]. Uauy et al [68,69] found that despite this ostensible disadvantage, the numerous mutations of every gene made polypoid species suitable for TILLING, because the technique has the capability to bear very high mutation densities.…”

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confidence: 99%

TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies

et al. 2020

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A substantial increase in yield of food crops is crucial to feeding the burgeoning global population. There is a need to introduce new breeding strategies that will accelerate the average phenotypic values of crop plants. The use of induced mutations coupled with modern genomics tools is an effective strategy for identifying and manipulating genes for crop improvement. High-throughput TILLING (Targeting Induced local Lesions IN Genomes) methodology, detects mutations in mutagenized populations, and EcoTILLING identifies single nucleotide polymorphisms (SNPs) within a natural population and associates these variations with traits of breeding interest. The main advantage of these techniques as a “reverse genetics” strategy is that they can be applied to any species regardless of genome size and ploidy level. In cereals, several space-induced and EMS-induced mutant populations have been used to identify mutants with important traits including salinity tolerance, grain size, and recombinant crossovers via TILLING by sequencing (TbyS). Genes such as TaSSIV, which plays an important role in starch granule formation, and Pin a and Pin b, which have been associated with kernel hardness in wheat, have been exploited in cereals via the EcoTILLING approach. This review focused on the functions and challenges of TILLING and the relation of TILLING to next-generation sequencing (NGS) technologies which help to exploit the induced mutations and their potential applications in cereal crops.

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A roadmap for gene functional characterisation in wheat

Cited by 4 publications

References 35 publications

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

The vesicular trafficking system component MIN7 is required for minimizing Fusarium graminearum infection

TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies

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