Completion of Centromere Map for 14 Chromosomes in Wild Emmer Wheat, Revealing Genome Reconfiguration Pathways Driven by Polyploidization
Background
Wheat is a key food crop providing nearly 20% of the calories consumed by humanity worldwide. Modern bread wheat (Triticum aestivum) possesses a complex genome formed through natural hybridization and polyploidization of different wild ancestral species. In this process, three types of subgenomes—A, B, and D—combined to complete a massive and complex allohexaploid structure. Among them, wild emmer wheat (Triticum turgidum subsp. dicoccoides) is a tetraploid species composed of A and B subgenomes, serving as a source of genetic diversity for modern wheat and a key material for studying climate adaptation traits.
The problem has been that wheat genome sequencing has been blocked by the wall of repetitive sequences. Wheat chromosomes are not only enormous in size but are also covered by more than 80% retrotransposons (mobile genetic elements) and extremely repetitive satellite DNA. In particular, the centromere region, where spindle fibers attach during cell division to ensure normal distribution of genetic material, is so highly repetitive that assembly was impossible with existing short-read sequencing technologies. On the genome map, centromeres always remained as empty gaps, making it difficult to reveal how centromeres of different subgenomes stabilized and restructured their architecture following polyploidization.
Key Discoveries
An international collaborative research team, by combining the latest long-read sequencing and chromosome structure capture technologies, has constructed a high-quality genome map that completely decodes the centromeric regions of the 14 chromosomes of wild emmer wheat. This is a result of achieving a near-complete assembly that connects from the chromosome ends to the centromeric cores without gaps. For the first time, complex repetitive sequence blocks, inversions, and inverted repeats within the centromeres have been revealed for each chromosome.
The analysis results show interesting facts. It was confirmed that the centromeres of the A and B subgenomes followed vastly different evolutionary trajectories after polyploidization. While the two subgenomes coexist within the same nucleus, they not only maintained unique ratios of centromeric repetitive sequence composition but also exhibited distinct asymmetries in the insertion cycles and expansion patterns of retrotransposons. In certain chromosome centromeres, specific satellite repeat units expanded rapidly, while in others, the rearrangement of retroelements drove centromeric dynamics.
This subgenome-specific centromere reconfiguration is interpreted as an evolutionary adaptation mechanism that enabled the two genomes to perform meiosis stably without colliding after the formation of the allopolyploid. The sequence composition and epigenetic marks of the centromeres have acted as a shield to maintain the chromosome segregation homeostasis unique to each subgenome.
Significance and Outlook
This achievement allows for the rewriting of the chromosomal evolutionary history of complex polyploid crops at the molecular level. In particular, it is evaluated as establishing a physical reference point for the precise analysis of the structural diversity and epigenetic mechanisms of plant centromeres, which were previously referred to as a
Nature Genetics, Published online: 22 October 2026; doi:10.1038/s41588-026-02808-3A near-complete genome assembly of wild emmer wheat with resolved centromeric regions across 14 chromosomes highlights subgenome-associated patterns of centromere remodeling during wheat polyploid evolution.
The completion of the wild emmer wheat centromere map provides an immediate turning point for precision crop breeding in response to the climate crisis. Modern wheat varieties have significantly depleted genetic diversity due to centuries of artificial selection. Breeders have attempted to introduce wild genes from wild emmer wheat that possess superior disease resistance and drought tolerance, but frequent issues with chromosome segregation abnormalities or infertility during interspecific hybridization have hindered progress.
With the centromeric structure of the 14 chromosomes clearly identified, researchers can now predict and prevent centromere loss or abnormal translocation during the chromosome recombination process between wild and cultivated species. By utilizing centromere-linked markers, it becomes possible to perform chromosome-manipulation breeding, specifically targeting and stably introducing only the superior useful traits of wild embar wheat into modern wheat. A bridge has been secured between wild genetic resources and advanced molecular breeding technologies.