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Wild Wheat Genome Gives Peek Into Wheat Domestication

NEW YORK (GenomeWeb) – The wild emmer wheat genome has provided a glimpse into the genomic changes that occurred in its domesticated wheat descendants.

The allotetraploid wild emmer wheat, Triticum turgidum ssp. dicoccoides, is a direct progenitor of economically important wheat like durum and bread wheat. Using a combination of whole-genome shotgun sequencing and three-dimensional chromosome conformation capture sequencing, a Tel Aviv University-led team generated a 10.1-gigabase assembly of the wild emmer wheat genome. As the team reported in Science today, it uncovered mutations in two genes that likely contributed to the loss of spike shattering, an important domestication trait.

"From a biological and historical viewpoint, we have created a 'time tunnel' we can use to examine wheat from before the origins of agriculture," Tel Aviv University's Assaf Distelfeld said in a statement. "Our comparison to modern wheat has enabled us to identify the genes involved in domestication — the transition from wheat grown in the wild to modern-day varieties."

Distelfeld and his colleagues performed whole-genome shotgun sequencing on the wild emmer wheat accession Zavitan. They validated the scaffolds they generated using 3D HiC data, which further placed them into 14 pseudomolecular sequences that reflected the 14 wild emmer wheat chromosomes, along with a set of unassigned scaffolds. This resulted in a 10.5 Gb assembly, 10.1 Gb of which is contained among the 14 pseudomolecular sequences, researchers reported.

At the same time, the team generated RNA sequencing reads from various wild emmer wheat tissues at different developmental stages. From this, it identified 65,012 high-confidence gene models. Homology analysis of the wild emmer wheat subgenomes further indicated that nearly three-quarters of the genes had a homologous pair.

Distelfeld and his colleagues homed in on the brittle spike trait of domesticated wheat. Spikes in wild wheat break at maturity to disseminate its seeds, but the spikes in domesticated wheat don't break, allowing for an easier harvest.

By crossing Zavitan and a domesticated durum wheat strain, the researchers uncovered genomic regions that regulate the brittle spike phenotype, including two major ones on the wild emmer wheat chromosomes 3A and 3B. In particular, they identified the wheat genes TtBtr1-A and TtBtr2-A on chromosome 3A and TtBtr1-B and TtBtr2-B on chromosome 3B.

Domesticated wheat harbors TtBtr1-A and TtBtr1-B allele variants that are predicted to affect protein function and lead to a loss of function, the authors wrote. By examining the effect of TtBtr1-A and TtBtr1-B in an isogenic wheat line, they found that the two homozygous recessive mutations appear to be necessary to generate the non-shattering spike trait.

The researchers further identified regions of the wild emmer wheat genome that have been under domestication selection by comparing DNA variation found within the exomes of wild emmer and domesticated emmer wheat accessions. Regions that appeared to be under selection — ones that harbored increased levels of SNPs — were enriched for involvement in the response to auxin stimulus, according to a gene ontology analysis.

"This new resource allowed us to identify a number of other genes controlling main traits that were selected by early humans during wheat domestication and that served as foundation for developing modern wheat cultivars," co-author and Kansas State University researcher Eduard Akhunov said in a statement. "These genes provide an invaluable resource for empowering future breeding efforts. Wild emmer is known as a source of novel variation that can help to improve the nutritional quality of grain as well as tolerance to diseases and water-limiting conditions."