Genomics as the key to unlocking the polyploid potential of wheat

Borrill, Philippa; Adamski, Nikolai M; Uauy, Cristóbal

doi:10.1111/nph.13533

Cited by 129 publications

(126 citation statements)

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“…B, Number of genes that are differentially expressed in multiple abiotic stress and disease conditions. in SNP-and sequence-based genotyping have removed these limitations (Borrill et al, 2015). The focus has now shifted toward the understanding of gene function, which is being accelerated by the availability of a draft reference genome (International Wheat Genome Sequencing Consortium, 2014) and next-generation sequencing-enabled mapping approaches (RamirezGonzalez et al, 2015).…”

Section: Utility For Functional Genomic Research In Wheatmentioning

confidence: 99%

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

2016

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The majority of transcriptome sequencing (RNA-seq) expression studies in plants remain underutilized and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyze and visualize these data. We have developed expVIP, an expression visualization and integration platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyze public and user-specified data sets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom Web browser to visualize, sort, and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP's suitability for polyploid crops and evaluate its performance across a range of biologically relevant scenarios. To exemplify its use in crop research, we developed a flexible wheat (Triticum aestivum) expression browser (www.wheat-expression.com) that can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualization, and comparison of RNA-seq data across experiments.The global demand for staple crops is predicted to double by 2050 (FAO, 2009;Tilman et al., 2011), which will require an annual increase in yield of approximately 2.4% (Ray et al., 2013). However, currently, yields of the major crops maize (Zea mays), rice (Oryza sativa), wheat (Triticum aestivum), and soybean (Glycine max) are increasing only at 1.6%, 1%, 0.9%, and 1.3% per year, respectively (Ray et al., 2013). The advent of the genomics era represents a great opportunity to accelerate the pace of yield increase in staple crops, for example, by facilitating novel breeding strategies (Heffner et al., 2009) and providing unprecedented numbers of genetic markers (Bevan and Uauy, 2013). In particular, transcriptome sequencing (RNA-seq) is a widely adopted genomics approach in crops due to its relatively low cost (Wang et al., 2009), its suitability for nonmodel organisms (Ekblom and Galindo, 2011), and the multiple downstream applications of the data generated. These features have driven the generation of a wealth of expression data with over 9,000 RNAseq samples currently available at public repositories, such as the National Center for Biotechnology Information (NCBI)/ENA for the major agricultural crops (Table I).Although several public databases containing gene expression data for plant species exist (Lawrence et al., 2007;Ouyang et al., 2007;Dash et al., 2012), these resources do not make full use of the expression data available in SRAs, frequently relying on a subset of experiments or microarray data. Similarly, pipelines have been proposed to allow the reanalysis of expression data that provide useful functionality but limit the number of samples that can be analyzed (D'Antonio et al., 2015), have limited visualization outputs (Fonseca et al., 2014), or require t...

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Section: Utility For Functional Genomic Research In Wheatmentioning

confidence: 99%

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

2016

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“…To facilitate further expression studies the expression atlas at http://www.wheat-expression. com has been updated with the TGACv1 annotation and expression data from 424 RNA samples (Borrill et al 2015).…”

Section: Gene Expressionmentioning

confidence: 99%

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Clavijo¹,

Venturini²,

Schudoma³

et al. 2017

Genome Res.

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364

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Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

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“…However, the development of new biological tools has facilitated the genesis of functional analysis of genes in wheat [36, 37]. In addition to new advances in DNA sequencing, DNA double-strand break (DSB) technologies have provided efficient methods to obtain multiple mutant alleles in the different wheat genomes.…”

Section: Resultsmentioning

confidence: 99%

MS26/CYP704B is required for anther and pollen wall development in bread wheat (Triticum aestivum L.) and combining mutations in all three homeologs causes male sterility

et al. 2017

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Development of anthers and pollen represents an important aspect of the life cycle in flowering plants. Genes contributing to anther and pollen development have been widely studied in many plant species. Ms26/CYP704B genes play an important role in pollen development through biosynthesis of sporopollenin for pollen exine formation. To investigate the role of Ms26/CYP704B genes in anther and pollen development of bread wheat, mutations in the A-, B-, and D-homeologs of the putative Ms26/CYP704B gene were analyzed. Single and double homozygous mutants in any of the homeologs did not affect pollen development and male fertility. Triple homozygous mutants resulted in completely male sterile plants that were defective in pollen and anther development. Additionally, double homozygous-single heterozygous mutants were also male sterile although with varying levels of residual fertility. The fertility of these triple mutants was dependent upon the homeolog contributing the wild-type allele. Two heterologous Ms26/CYP704B genes, when transformed into a triple homozygous mutant background, completely restored male fertility, whereas a single gene was unable to restore fertility. Functional analysis of Ms26/CYP704B furthers the understanding of male fertility genes which can be utilized for the development of novel hybrid seed production systems in wheat.

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Genomics as the key to unlocking the polyploid potential of wheat

Cited by 129 publications

References 132 publications

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

MS26/CYP704B is required for anther and pollen wall development in bread wheat (Triticum aestivum L.) and combining mutations in all three homeologs causes male sterility

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