Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Abstract

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization. Introduction Wheat, a major cereal food crop, is rich in carbohydrates, proteins and minerals and is grown on over 220 million hectares of land worldwide (Henry et al., 2016; Mayer et al., 2014). However, yield trends show increasing instability worldwide, particularly across developing regions, where wheat represents a staple food source (Iizumi et al., 2014). The formation of T. aestivum occurred through at least two spontaneous hybridizations accompanied by whole-genome duplications. Several hundred thousand years ago, a spontaneous hybridization between the diploid A-genome progenitor, Triticum urartu (2n = 2x = 14, AA), and the unknown B-genome progenitor, a close relative of extant Aegilops speltoides (BB), led to the formation of allotetraploid Triticum turgidum (2n = 4x = 28, AABB), which eventually gave rise to bread wheat after a subsequent hybridization with the diploid D-genome progenitor Aegilops tauschii (2n = 2x = 14, DD) (Marcussen et al., 2014). While the allotetraploid wheat was also domesticated and is being cultivated as durum wheat, wild populations that diverged into subspecies continue to exist. Among these wild populations is wild emmer wheat, Triticum turgidum ssp. dicoccoides (2n = 4x = 28, AABB), the wild relative of durum wheat. T. dicoccoides populations show remarkable genetic diversity for traits such as grain micronutrient content, abiotic stress tolerance and biotic stress resistance (Budak et al., 2013b; Ergen and Budak, 2009; Ergen et al., 2009). For instance, T. dicoccoides genotype TR39477.