Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

(2018) Alice Brunazzi et al.   PLANT JOURNAL

Tracking of powdery mildew and leaf rust resistance genes in Triticum boeoticum and T. urartu, wild relatives of common wheat

(2018) N.A. Hovhannisyan et al.   Czech Journal of Genetics and Plant Breeding

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B

(2018) Jan Dvorak et al.   THEORETICAL AND APPLIED GENETICS

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

(2018) Moeko Okada et al.   BMC PLANT BIOLOGY

Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

(2018) Yuka Miki et al.   DNA RESEARCH

Natural variation in photoperiodic flowering pathway and identification of photoperiod-insensitive accessions in wild wheat, Aegilops tauschii

(2017) Kayo Koyama et al.   EUPHYTICA

Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change

(2017) Jaime Prohens et al.   EUPHYTICA

RNA-seq facilitates development of chromosome-specific markers and transfer of rye chromatin to wheat

(2017) Nan Wu et al.   MOLECULAR BREEDING

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae)

(2017) Tatiana V. Danilova et al.   PLANT JOURNAL

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Agro-morphological and molecular variability in Triticum boeoticum accessions from Zagros Mountains, Iran

(2016) Alireza Pour-Aboughadareh et al.   GENETIC RESOURCES AND CROP EVOLUTION

Fine mapping and genetic association analysis of Net2, the causative D-genome locus of low temperature-induced hybrid necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii

(2016) Kouhei Sakaguchi et al.   GENETICA

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions

(2016) Ryo Nishijima et al.   MOLECULAR GENETICS AND GENOMICS

Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilopsspp.) into chromosomes and exploring their synteny with wheat

(2016) István Molnár et al.   PLANT JOURNAL

Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring

(2016) Kang Yu et al.   THEORETICAL AND APPLIED GENETICS

Composition, variation, expression and evolution of low-molecular-weight glutenin subunit genes in Triticum urartu

(2015) Guangbin Luo et al.   BMC PLANT BIOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Comparison of gene expression profiles and responses to zinc chloride among inter- and intraspecific hybrids with growth abnormalities in wheat and its relatives

(2015) Kiyofumi Takamatsu et al.   PLANT MOLECULAR BIOLOGY

Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production

(2015) Ana Fita et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species

(2014) Laura-Jayne Gardiner et al.   PLANT JOURNAL

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

(2014) Samuel E. Fox et al.   PLoS One

Crossability of Triticum urartu and Triticum monococcum Wheats, Homoeologous Recombination, and Description of a Panel of Interspecific Introgression Lines

(2014) Agostino Fricano et al.   G3-Genes Genomes Genetics

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

A large-scale mutant panel in wheat developed using heavy-ion beam mutagenesis and its application to genetic research

(2013) Koji Murai et al.   NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

(2013) Shunichi Kosugi et al.   PLoS One

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

(2013) Julio Cesar Masaru Iehisa et al.   THEORETICAL AND APPLIED GENETICS

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

(2012) J. C. M. Iehisa et al.   DNA RESEARCH

Molecular characterization of a novel waxy allele (Wx-A u 1a) from Triticum urartu Thum. ex Gandil.

(2012) Carlos Guzmán et al.   GENETIC RESOURCES AND CROP EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum

(2009) Hai-Chun Jing et al.   BMC GENOMICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Mapping chromosomal regions affecting flowering time in a spring wheat RIL population

(2008) F. Lin et al.   EUPHYTICA