Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

Rye has been used worldwide as a source for the genetic improvement of wheat. In this study, 2 stable wheat-rye primary T1RS.1BL translocation lines were selected from the progeny of the crossing of the wheat cultivar Mianyang11-1 and a Chinese local rye variety, Weining. These 2 novel translocation lines were identified by molecular cytogenetic analysis. PCR results, multi-color fluorescence in situ hybridization (MC-FISH), and acid polyacrylamide gel electrophoresis (A-PAGE) indicated that both new translocation lines harbor a pair of T1RS.1BL translocation chromosomes, and have been named RT828-10 and RT828-11, respectively. The cytogenetic results also indicated that the pSc119.2 signals of 5AL were absent in both lines along with the pSc119.2 signals of 4AL of RT828-11. When inoculated with different stripe rust and powdery mildew isolates, both lines expressed high resistance to Puccinia striiformis f. sp. tritici and Blumeria graminis f. sp. tritici pathotypes, which are prevalent in China and are virulent on Yr9 and Pm8. The line RT828-11 also exhibited excellent agronomic traits in the field. The present study indicates that this rye variety may carry untapped variations that could potentially be used for wheat improvement.

WRKY transcription factors have been found in most plants and play an important role in regulating organ growth and disease response. Outlining the profile of WRKY genes is a very useful project for studying morphogenesis and resistance formation. In the present study, a total of 63 WRKY genes consisting of 13 class I, 41 class II, and 9 class III genes were identified from the newly published A. trifoliata genome, of which 62 were physically distributed on all 16 chromosomes. Structurally, two AkWRKY genes (AkWRKY6 and AkWRKY52) contained four domains, and AkWRKY17 lacked the typical heptapeptide structure. Evolutionarily, 42, 16, and 5 AkWRKY genes experienced whole genome duplication (WGD) or fragmentation, dispersed duplication, and tandem duplication, respectively; 28 Ka/Ks values of 30 pairs of homologous genes were far lower than 1, while those of orthologous gene pairs between AkWRKY41 and AkWRKY52 reached up to 2.07. Transcriptome analysis showed that many of the genes were generally expressed at a low level in 12 fruit samples consisting of three tissues, including rind, flesh, and seeds, at four developmental stages, and interaction analysis between AkWRKY and AkNBS genes containing W-boxes suggested that AkWRKY24 could play a role in plant disease resistance by positively regulating AkNBS18. In summary, the WRKY gene family of A. trifoliata was systemically characterized for the first time, and the data and information obtained regarding AkWRKY could be very useful in further theoretically elucidating the molecular mechanisms of plant development and response to pathogens and practically improving favorable traits such as disease resistance.