The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms

Abstract

In the year 2018, the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.

Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome

“…In the A and D diploid genome donors, similar TE content was observed (81.4% and 84.4% of the genome in Triticum urartu and Aegilops tauschii , respectively), with high proportion of LTR-retrotransposons (70.5% and 65.9% in Triticum urartu and Aegilops tauschii , respectively) ( Luo et al., 2017 ; Ling et al., 2018 ). While the overall TE content is similar between different Triticum and Aegilops species from different ploidy levels and between the sub-genomes of allopolyploid wheats (see Guan et al. (2020) for detailed comparison of TE content among wheat species), there is evidence for rapid TE turnover and waves of TE amplification during wheat evolution.…”

“…Although wheat is a highly important crop, the challenges in wheat genomics have led to a relatively slow advancement in this field during the beginning of the next generation sequencing (NGS) era as reviewed by Guan et al. (2020) .…”

“…(2007) ]. The repetitive nature of the wheat genome, together with its huge size – 17 Gbp, have delayed the generation of the bread wheat genome draft when many other organisms (both animals and plants) have already been sequenced ( Bolger et al., 2014 ; Uauy, 2017 ; Guan et al., 2020 ).…”

“…Although wheat is a highly important crop, the challenges in wheat genomics have led to a relatively slow advancement in this field during the beginning of the next generation sequencing (NGS) era as reviewed by Guan et al (2020). The major obstacle in creating a reference genome draft for bread wheat was the assembly of contigs made from mostly (over 80%) repetitive sequences.…”

“…Each class of TEs can be further divided into subclass, orders, super-families, families, and subfamilies, and includes both autonomous and non-autonomous TEs [for more details on the classification system for eukaryotic TEs see Wicker et al (2007)]. The repetitive nature of the wheat genome, together with its huge size -17 Gbp, have delayed the generation of the bread wheat genome draft when many other organisms (both animals and plants) have already been sequenced (Bolger et al, 2014;Uauy, 2017;Guan et al, 2020).…”