Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

Abstract

Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.

Figure 1. Biparametric flow karyotype of chromosomes isolated from T. dicoccoides.

Prior to the analysis, GAA microsatellites were labeled by FITC and chromosomal DNA was stained by DAPI. FITC fluorescence was acquired at logarithmic scale, while DAPI fluorescence was measured at linear scale. This approach permitted separation from other chromosomes in the karyotype, including its homoeolog 5A. Insets: Images of flow-sorted chromosomes 5A and 5B. The chromosomes were identified after FISH with probes for GAA microsatellites (yellow-green) and for Afa family repeats (red).

Figure 2. Repetitive element composition of Tdic5B.

a. Repeat fractions by superfamily (left) and the cumulative sizes covered by the most abundant repeat families (right) of Tdic5B. b. Repeat fractions of T. aestivum 5A and 5D chromosomes by superfamily as in (a). DTC = DNA transposon, CACTA; RLG = retroelement, LTR, Gypsy; RLC = retroelement, LTR, Copia.

Figure 3. Venn diagram exhibiting Tdic5B sequence reads matching Brachypodium (Bd: Brachypodium distachyon), sorghum (Sb: Sorghum bicolor), rice (Os: Oryza sativa), and barley (Hv: Hordeum vulgare) proteins.

Figure 4

Gene-Ontology annotations of Tdic5B conserved and non-conserved genes in terms of, a. Biological Process, b. Molecular Function, c. Cellular Component.

Figure 5. Predicted miRNA repertoires of T. aestivum 5A & 5D (Ta5A & Ta5D) and Tdic5B.