Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

Walter, N.; Walker, J.; Yang, C.-y.; Scholefield, D.; Ashling, S.; Kaithakottil, G. G.; Swarbreck, D.; Sierra-Gonzalez, A.; Hawkins, K.; Atkinson, J.; Wells, D.; Hawkesford, M. J.; Niu, J.; Quiroz-Chavez, J.; Cavalet-Giora, E.; Krattinger, S. G.; Guo, W.; King, I. P.; King, J.; Grewal, S.

doi:10.64898/2026.05.20.726494

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bioRxiv · 10.64898/2026.05.20.726494

Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

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Abstract

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum, a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

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Walter, N., Walker, J., Yang, C.-y., Scholefield, D., Ashling, S., Kaithakottil, G. G., Swarbreck, D., Sierra-Gonzalez, A., Hawkins, K., Atkinson, J., Wells, D., Hawkesford, M. J., Niu, J., Quiroz-Chavez, J., Cavalet-Giora, E., Krattinger, S. G., Guo, W., King, I. P., King, J., Grewal, S.. 2026-05-21. Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry. https://doi.org/10.64898/2026.05.20.726494

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