Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor

Iehisa, Julio C. M.; Shimizu, Akifumi; Sato, Kazuhiro; Nasuda, Shuhei; Takumi, Shigeo

doi:10.1093/dnares/dss028

Cited by 30 publications

(32 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The gene order within this region is highly conserved among grasses (Mayer et al, 2011). Based on the synteny among grasses, a hypothetical gene order (GenomeZipper) was established in barley (Mayer et al, 2011) that let us develop markers to the narrow target region in wheat (Iehisa et al, 2012). Using this strategy, we have developed genic markers in the 3AL region and have reevaluated the genotype-phenotype association for early flowering (Mizuno et al, in preparation).…”

Section: Introductionmentioning

confidence: 99%

A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat

et al. 2012

View full text Add to dashboard Cite

An X-ray mutant showing an early flowering phenotype has been identified in einkorn wheat (Triticum monococcum L.), for which a major QTL for heading time was previously mapped in the telomeric region on the long arm of chromosome 3A. Recent advances in Triticeae genomics revealed that the gene order in this region is highly conserved between wheat and barley. Thus, we adopted a hypothetical gene order in barley, the so-called GenomeZipper, to develop DNA markers for fine mapping the target gene in wheat. We identified three genes tightly linked to the early heading phenotype. PCR analysis revealed that early-flowering is associated with the deletion of two genes in the mutant. Of the two deleted genes, one is an ortholog of the LUX ARRHYTHMO (LUX)/PHYTOCLOCK 1 (PCL1) gene found in Arabidopsis, which regulates the circadian clock and flowering time. We found distorted expression patterns of two clock genes (TOC1 and LHY) in the einkorn pcl1 deletion mutant as was reported for the Arabidopsis lux mutant. Transcript accumulation levels of photoperiod-response related genes, a photoperiod sensitivity gene (Ppd-1) and two wheat CONSTANS-like genes (WCO1 and TaHd1), were significantly higher in the einkorn wheat mutant. In addition, transcripts of the wheat florigen gene (WFT) accumulated temporally under shortday conditions in the einkorn wheat mutant. These results suggest that deletion of WPCL1 leads to abnormally higher expression of Ppd-1, resulting in the accumulation of WFT transcripts that triggers flowering even under short-day conditions. Our observations from gene mapping, gene deletions, and expression levels of flowering related genes strongly suggest that WPCL1 is the most likely candidate gene for controlling the early flowering phenotype in the einkorn wheat mutant.

show abstract

Section: Introductionmentioning

confidence: 99%

A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat

et al. 2012

View full text Add to dashboard Cite

show abstract

“…The four Xctg loci of CAPS markers represented high-confidence SNPs derived from the Ae. tauschii RNA-seq-derived SNP information (Iehisa et al, 2012(Iehisa et al, , 2014a. The map length of 7DS was 50.0 cM with an average spacing of 2.78 cM between loci.…”

Section: Resultsmentioning

confidence: 99%

“…tauschii accessions that represent two major lineages, and more than 16,000 high-confidence single nucleotide polymorphisms (SNPs) were found in 5,808 contigs (Iehisa et al, 2012(Iehisa et al, , 2014a. Contig sequences with the SNPs were used with the BlastN algorithm to search the Ae.…”

Section: Phenotype Evaluation As a Quantitative Traitmentioning

confidence: 99%

“…Scaffolds without genes were anchored based on respective results from BlastN searches against the barley genome. First, high-confidence SNPs (Iehisa et al, 2012(Iehisa et al, , 2014a) plotted on barley 7HS were used for marker development to refine the Hch1 region. Next, SciRoKo software was used with the search mode setting Fine mapping of wheat hybrid chlorosis gene "mismatched; fixed penalty" to identify additional SSR markers in sequence data of candidate scaffolds.…”

Section: Phenotype Evaluation As a Quantitative Traitmentioning

confidence: 99%

“…tauschii genome that covers 4 Gb is also available (Luo et al, 2013). In addition, barley genome information efficiently helps to assign wheat genomic and transcript sequences in silico to the barley physical map (Iehisa et al, 2012(Iehisa et al, , 2014a. Thus, the scaffold sequence data of the Ae.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Fine mapping of Hch1, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and Aegilops tauschii

et al. 2015

View full text Add to dashboard Cite

Hybrid chlorosis, one of the reproductive barriers between tetraploid wheat and its D-genome progenitor, Aegilops tauschii, inhibits normal growth of synthetic wheat hexaploids. Hybrid chlorosis appears to be due to an epistatic interaction of two loci from the AB and D wheat genomes. Our previous study assigned the causal D-genome gene for hybrid chlorosis, Hch1, to the short arm of chromosome 7D. Here, we constructed a fine map of 7DS near Hch1 using 280 F 2 individuals from a cross of two wheat synthetic lines, one showing normal growth and the other showing hybrid chlorosis. The hybrid chlorosis phenotype was controlled by a single dominant allele of the Hch1 locus in the synthetic hexaploids. Hch1 was closely linked to four new markers within 0.2 cM, and may be localized near or within the two Ae. tauschii scaffolds containing the linked markers on 7DS. Comparative analysis of the Hch1 chromosomal region for Ae. tauschii, barley and Brachypodium showed that a local inversion occurred in the region proximal to Hch1 during the divergence between barley and Ae. tauschii, and that the Hch1 region on wheat 7DS is syntenic to Brachypodium chromosome 1. These observations provide useful information for further studies toward map-based cloning of Hch1.

show abstract

Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii

et al. 2013

View full text Add to dashboard Cite

13,347 high-confidence SNPs were discovered through transcriptome sequencing of Aegilops tauschii, which are useful for genomic analysis and molecular breeding of hexaploid wheat. In organisms with large and complex genomes, such as wheat, RNA-seq analysis is cost-effective for discovery of genome-wide single nucleotide polymorphisms (SNPs). In this study, deep sequencing of the spike transcriptome from two Aegilops tauschii accessions representing two major lineages led to the discovery of 13,347 high-confidence (HC) SNPs in 4,872 contigs. After removing redundant SNPs detected in the leaf transcriptome from the same accessions in an earlier study, 10,589 new SNPs were discovered. In total, 5,642 out of 5,808 contigs with HC SNPs were assigned to the Ae. tauschii draft genome sequence. On average, 732 HC polymorphic contigs were mapped in silico to each Ae. tauschii chromosome. Based on the polymorphic data, we developed markers to target the short arm of chromosome 2D and validated the polymorphisms using 20 Ae. tauschii accessions. Of the 29 polymorphic markers, 28 were successfully mapped to 2DS in the diploid F2 population of Ae. tauschii. Among ten hexaploid wheat lines, which included wheat synthetics and common wheat cultivars, 25 of the 43 markers were polymorphic. In the hexaploid F2 population between a common wheat cultivar and a synthetic wheat line, 23 of the 25 polymorphic markers between the parents were available for genotyping of the F2 plants and 22 markers mapped to chromosome 2DS. These results indicate that molecular markers that developed from polymorphisms between two distinct lineages of Ae. tauschii might be useful for analysis not only of the diploid, but also of the hexaploid wheat genome.

show abstract

Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor

Cited by 30 publications

References 40 publications

A wheat homologue of <i>PHYTOCLOCK 1</i> is a candidate gene conferring the early heading phenotype to einkorn wheat

A wheat homologue of <i>PHYTOCLOCK 1</i> is a candidate gene conferring the early heading phenotype to einkorn wheat

Fine mapping of <i>Hch1</i>, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and <i>Aegilops tauschii</i>

Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii

Contact Info

Product

Resources

About