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

Background: Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae.

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

The wild species in the Triticeae tribe are tremendous resources for crop breeding due to their abundant natural variation. However, their huge and highly repetitive genomes have hindered the establishment of physical maps and the completeness of their genome sequences. To develop molecular markers for the efficient utilization of their valuable traits while avoiding their genome complexity, we assembled RNA sequences of ten representative accessions of Aegilops tauschii, the progenitor of the wheat D genome, and estimated single nucleotide polymorphisms (SNPs) and insertions/deletions (indels).

Improvement of barley genome annotations by deciphering the Haruna Nijo genome.

Full-length (FL) cDNA sequences provide the most reliable evidence for the presence of genes in genomes. In this report, detailed gene structures of barley, whole genome shotgun (WGS) and additional transcript data of the cultivar Haruna Nijo were quality controlled and compared with the published Morex genome information. Haruna Nijo scaffolds have longer total sequence length with much higher N50 and fewer sequences than those in Morex WGS contigs.

454 sequencing of pooled BAC clones on chromosome 3H of barley.

Background: Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000 Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones.