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Abstract: Shotgun survey sequences of flow‐sorted individual rye chromosomes were data mined for the presence of simple sequence repeats (SSRs). For 787,850 putative SSR loci, a total of 358,660 PCR primer pairs could be designed and 51,138 nonredundant SSR marker candidates were evaluated by in silico PCR. Of the 51,138 SSR primer candidates, 1,277 were associated with 1,125 rye gene models. A total of 2,112 of the potential SSR markers were randomly selected to represent about equal numbers for each of the rye chromosomes, and 856 SSRs were assigned to individual rye chromosomes experimentally. Potential transferability of rye SSRs to wheat and barley was of low efficiency with 4.3% (2,189) and 0.4% (223) of rye SSRs predicted to be amplified in wheat and barley, respectively. This data set of rye chromosome‐specific SSR markers will be useful for the specific detection of rye chromatin introgressed into wheat as well as for low‐cost genetic and physical mapping in rye without the need for high‐tech equipment. [ABSTRACT FROM AUTHOR]

We produced 15 dissection lines of common wheat carrying segments of chromosome 1R of wild rye (Secale montanum) (1Rm) by the gametocidal system. Using the 1Rm dissection lines and previously established 24 dissection lines of chromosome 1R from cultivated rye (Secale cereale cv. 'Imperial') (1Ri), we conducted cytological mapping of 97 markers that were amplified in the 1Ri addition line. Sixty-eight of the 97 markers were amplified in the 1Rm addition line. To reveal what structural differentiation occurred in chromosome 1R during domestication, we compared the cytological map of chromosome 1Ri with that of chromosome 1Rm, and also with the previously published cytological map of chromosome 1R from wheat cultivar 'Burgas 2' (1RB). There was one discrepancy in marker order in the satellite region between chromosomes 1Ri and 1RB, while there were four discrepancies in marker order between chromosomes 1Ri and 1Rm. These results suggested that during the domestication of rye, some intrachromosomal rearrangements had occurred in chromosome 1R, although this chromosome is regarded as the most stable chromosome in the rye genome. [ABSTRACT FROM AUTHOR]

Rye (Secale   cereale) is closely related to wheat (Triticum   aestivum) and barley (Hordeum vulgare). Due to its large genome (∼8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon , rice [ Oryza sativa ], and sorghum [ Sorghum bicolor ]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution. [ABSTRACT FROM AUTHOR]