Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

“…The hexaploid nature of the wheat genome permits the engineering of wheat lines lacking specific homoeologous chromosomes, lines known as nullisomic-tetrasomics (‘nullitetras’) [57,58]. In each nullitetra line, lack (‘nulli’) of one homoeologue is compensated by an extra set of either of the remaining homoeologous chromosomes, thus restoring the hexaploid state.…”

“…We therefore obtained mRNA-Seq datasets [62] from non-normalized cDNA libraries created from shoot and root tissues of the euploid bread wheat cultivar Chinese Spring, from which the nullitetra lines are derived [58], from complete sets of chromosome 1 and 5 nullitetras, and from extant relatives of the diploid A ( Triticum urartu ) and D ( Aegilops tauschii ) genome donors, herein referred to as A and D genome diploids (Figure 1A; see Additional file 1: Table S1). In the then absence of a T. aestivum genome sequence, we exploited an extensive wheat ‘expressed sequence tags’ (ESTs) resource to construct a reference transcriptome sequence (see Additional file 2: Table S2).…”

“…In the then absence of a T. aestivum genome sequence, we exploited an extensive wheat ‘expressed sequence tags’ (ESTs) resource to construct a reference transcriptome sequence (see Additional file 2: Table S2). We selected ESTs physically mapped to segments (‘bins’) of wheat group 1 or group 5 chromosomes [58,63]. Concatenating ESTs from chromosomes 1 (1,123) and 5 (1,247), we created a wheat group 1 and 5 partial reference transcriptome consisting of 2,354 ESTs (see Methods).…”

“…First, the deletion bin mapping dataset of Qi et al [58,63], which assigned genes to homoeologous chromosomes according to the presence or absence of a restriction fragment in Southern blots from a series of aneuploid and deletion wheat lines [58,63]. Second, nullitetra analysis of our shoot and root RNA-Seq data from euploid wheat and its derived nullitetra lines to identify transcribed homoeologue-specific sequences (individual HSV sites or haplotypes).…”

“…(A) Presence of a gene on 1A, 1B, and 1D homoeologous chromosomes is inferred using nullitetra analysis of RNA-Seq data combined with deletion bin mapping data [58,63] and chromosome 1 arm-specific assemblies from Wicker et al [52]. The pie chart shows the number of genes present on one, two or three homoeologous chromosomes, while the Venn diagram shows the number of genes present on each combination of chromosomes.…”