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Thinopyrum distichum(Thunb.) Á. Löve (2n= 4x= 28; J1dJ1dJ2dJ2d) inhabits harsh, dry saline coastal dunes. Its adaptive genes can be of value to cultivated cereals; therefore, single‐chromosome additions were previously developed in hexaploid triticale (×TriticosecaleWittm. ex A. Camus) and common wheat (Triticum aestivumL.); however, their homoeology to triticale and wheat chromosomes remained largely unknown. Here we used genotyping‐by‐sequencing (GBS) to supplement conventional markers and determine the synteny of the Th. distichumaddition chromosomes. Twenty‐seven triticale lines with single Th. distichumaddition chromosomes were analyzed. Genotyping‐by‐sequencing yielded 2.75 million unique sequences that included 134,506 Th. distichum‐specific tags absent in the wheat, durum wheat [Triticum turgidumL. subsp. Durum(Desf.) van Slageren], ×Triticosecalespp., and rye (Secale cerealeL.) controls. The Th. distichum‐specific tags were then sorted into 125,262 informative, single‐pair tags (from one homoeologous group) and 9,244 uninformative, multi‐group tags associated with more than one homoeologous group. Presence–absence patterns produced by the single‐pair tags suggested the presence of 11 different Th. distichumaddition chromosomes whose associated sequence tags were then aligned to the Th. elongatum(Host) D. R. Dewey and Chinese Spring (CS) genomic databases to reveal their homoeology. Five prominent translocations were detected among the 11 Th. distichumaddition chromosomes and three chromosomes appeared to be extensively restructured. The extra chromosomes in 10 additions to common wheat represented five different Th. distichumchromosomes that were also represented in the triticale set. The 11 distinct Th. distichumaddition chromosomes constitute a useful genetic resource for continued dissection of the Th. distichumgenomes.

Leaf rust resistance gene Lr62was transferred from Aegilops neglectaReq. ex Bertol. to chromosome 6A of common wheat (Triticum aestivumL.) in 2008. After homoeologous chromosome pairing induction, smaller translocations that retained Lr62were derived from it. This study compared the original translocation and the four apparently shortest recombinants to determine which would be the best suited for breeding. The translocations were analyzed using chromosome 6A and 6B simple sequence repeat (SSR) markers and genomic in situ hybridization. Recombined translocations 133, 135, and 136 were found to occur at the 6AS telomere. In addition to the wheat Xdupw217aestSSR locus on chromosome arm 6BS, the three recombinants also expressed an Ae. neglecta–derived homoeo‐locus (Xdupw217negl) that could be used to detect the presence of the Ae. neglectachromosomal segment. The Lr62‐129 translocation was relocated to 6BS in an allosyndetic recombination event that replaced the Xdupw217aestlocus with Xdupw217negl. Lr62‐129 retained the least Ae. neglectachromatin and is therefore recommended for use in wheat breeding.