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.

Keywords: Common wheat; Homoeologous genomes; Polyploid; Sequencing; Triticum aestivum.

Figure 1

A chart depicting the progress of wheat genome sequencing The International Wheat Genome Sequencing Consortium (IWGSC) was formed in 2005. IWGSC agreed to use the bread wheat (Triticum aestivum L.) variety Chinese Spring (CS) as a consensus accession to build a reference wheat genome due to numerous genetic stocks available for this variety. T. urartu is the donor of the wheat A subgenome (AA, 2 N = 2 × = 14), while Ae. tauschii is the donor of the wheat D subgenome (DD, 2 N = 2 × = 14). First draft assemblies of Ae. tauschii and T. urartu were reported in 2013 , . Two reference quality assemblies of Ae. tauschii, 1 and 2, were published in 2017 , , while the reference quality assembly of T. urartu was reported in 2018 . The domesticated form of wild emmer wheat (WEW), T. turgidum (AABB, 2 N = 4 × = 28), is the putative tetraploid donor of common wheat, and durum wheat (DW) is a cultivated emmer wheat to make spaghetti (AABB, 2 N = 4 × = 28). The two tetraploid wheat WEW and DW were sequenced in 2017 and 2019, respectively , . CS (CSS) is a draft CS genome sequence assembed with various short chromosome survey sequences available in 2014 , together with the first continous chromosome, the chromosome 3B (Chr 3B) of CS . CS (TAGCv1) is an improved CS genome assembly with larger and more continuous scaffolds and better annotations published in 2017 , while CS (RefSeq v1.0) is the first reference quality genome assembly published in 2018 , which has been continuously improved since then (http://www.wheatgenome.org/).