Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of these tocochromanol forms in barley, seven of which were within 2 cM of sequences homologous to cloned genes associated with tocochromanol production in barley and/or other plants. These associations confirmed a prior report based on bi-parental QTL mapping. This knowledge will aid future efforts to better understand the role of tocochromanols in barley, with specific reference to abiotic stress resistance. It will also be useful in developing barley varieties with higher tocochromanol concentrations, although at current recommended daily consumption amounts, barley would not be an effective sole source of vitamin E. However, it could be an important contributor in the context of whole grains in a balanced diet

Tools for building de novo transcriptome assembly

The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. The transcriptome data from a species can be analyzed in the context of its sequenced genomes or closely related genome to score biological sample-specific transcript isoforms, novel transcribed regions and to refine gene models including identification of new genes, in addition to the differential gene expression analysis. However, many plant species of importance currently lack a sequenced genome or a closely related reference genome and thus, rely on the de novo methods for generating transcript models and transcriptome assemblies. Here we describe various tools used for de novo transcriptome assembly and discuss the data management practices and standards

Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (<i>WAK91</i>) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance

Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome_SupportingInformation.zip

BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. PRINCIPAL FINDINGS: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ,22,000 simple sequence repeat (SSR) sites. CONCLUSIONS: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf

BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. PRINCIPAL FINDINGS: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ,22,000 simple sequence repeat (SSR) sites. CONCLUSIONS: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers

Simple_Sequence_Repeats_data.tar.gz

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. For more details on the Triticum monococcum transcriptome project data, visit: http://jaiswallab.cgrb.oregonstate.edu/genomics/whea

Transcriptome_expression_analysis.tar.gz

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. For more details on the Triticum monococcum transcriptome project data, visit: http://jaiswallab.cgrb.oregonstate.edu/genomics/whea

BLAT_Alignments.tar.gz

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. For more details on the Triticum monococcum transcriptome project data, visit: http://jaiswallab.cgrb.oregonstate.edu/genomics/whea

Single_Nucleotide_Polymorphism_data.tar.gz

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. For more details on the Triticum monococcum transcriptome project data, visit: http://jaiswallab.cgrb.oregonstate.edu/genomics/whea

readme_Triticum_monococcum_dataset.txt

Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. For more details on the Triticum monococcum transcriptome project data, visit: http://jaiswallab.cgrb.oregonstate.edu/genomics/whea