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Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Highly fertile F 1 hybrids were made between Triticum turgidum L. ssp. turgidum (2n = 28, AABB) and Aegilops tauschii Coss. (2n = 14, DD) without embryo rescue and hormone treatment. The F 1 plants had an average seed set of 25%. Approximately 96% of the F 2 seeds were able to germinate normally and about 67% of the F 2 plants were spontaneous amphidiploid (2n = 42, AABBDD). Cytological analysis of male gametogenesis of the F 1 plants showed that meiotic restitution is responsible for the high fertility. A mitosis-like meiosis led to meiotic restitution at either of the two meiotic divisions resulting in unreduced gametes. Test crosses of the T. t. turgidum-Ae. tauschii amphidiploid with Ae. variabilis and rye suggested that the mitosis-like meiosis is controlled by one or more nuclear genes that continue to function in derived lines. This discovery indicates a potential application of such genes in producing double haploids.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a global threat to wheat production. Aegilops tauschii , one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst -resistant allele YrAS2388R has duplicated 3’ untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P . striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii -derived synthetic wheat; it is absent in 100% ( n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species.

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Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

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