BMC Genomics 2008, 9:237 http://www.biomedcentral.com/1471-2164/9/237 Background Since the beginning of the twentieth century, attempts were made to transfer useful genes from related species into cultivated wheat through interspecific hybridization. Following crosses between wheat and rye, in the first half of the twentieth century, several wheat varieties were developed; initially with the complete rye chromosome 1R substituted for wheat chromosome 1B, later substitut- ing only the 1RS chromosome arm for the short arm of chromosome 1B in a form of the 1BL.1RS translocation [45]. Other translocations were developed later, involving wheat 1AL and 1DL chromosome arms instead of the 1BL [37,46]. These translocations conferred resistance to wheat against diseases, such as powdery mildew, leaf rust, stem rust, yellow rust, and against insects such as green bug and wheat curl mite, the latter being a vector of wheat streak mosaic virus [4,28,37,46]. The 1RS chromosome is also believed to improve the adaptation and increases yield of wheat in certain genetic backgrounds [2,21]. Due to its valuable features, the 1BL.1RS translocation was integrated into wheat breeding programs all over the world, and more than 300 wheat cultivars were known to carry it at the end of the 20th century [32]. Cultivars with 1RS occupy now a considerable acreage of the wheat growing area as compared to other wheat-alien transloca- tions and the 1RS chromosome arm is by far the most widely used alien chromatin in wheat breeding [10,12]. In fact, 1RS is now part of the wheat gene pool and it would be difficult to eliminate it. A better knowledge of 1RS at the molecular level is needed to clone genes underlying the resistance phenotypes, support further improvement of existing wheat cultivars, and eliminate some negative effects of the translocation on bread making quality [15,23,33]. 1RS translocations from at least two different rye geno- types carry stem rust resistance genes. The Sr31 gene from rye cv. 'Petkus' has been used widely in CIMMYT-derived wheat cultivars to prevent wheat stem rust infection. How- ever, the recent spread of a new stem rust pathotype Ug99 [31], which is virulent on Sr31, caused concern among wheat growers worldwide because in many current wheat varieties, this gene provides the only protection against the disease. Until now, the stem rust resistance gene SrR, which is located on 1RS of cv. 'Imperial', has not been extensively used. Tests done at University of Minnesota have shown that SrR is effective against Ug99 (Jim Kol- mer, Yue Jin and R. Mago, unpublished) and so this gene could provide a useful component of stem rust resistance gene pyramids in new wheat varieties resistant to Ug99 and, at the same time, potentially provide the additional positive yield and adaptation features of 1RS from cv. 'Petkus'. We have previously shown that the region carrying SrR on 1RS of cv. 'Imperial' has synteny with the region on 1HS of barley, which carries the powdery mildew resistance gene Mla [25]. Stem rust susceptible mutants obtained in a wheat 1BL.1RS translocation stock indicated that Mla might be an ortholog of the stem rust resistance gene SrR [26]. Hybridization with a probe for barley Mla1 gene identified ~20 copies on 1RS of 'Imperial' rye. In some interstitial deletion mutants obtained by gamma irradia- tion, only three of these 20 members were lost. Thus indi- cating that these three deleted copies may be candidates for the stem rust resistance gene SrR. The analysis of the rye genome at the molecular level is hampered by its size (1C~7900 Mbp) [6], which is about 1.4-fold larger than the genomes of diploid progenitors of bread wheat. Although proportion of repeated DNA in the rye genome is not known, considering recent estimates in wheat [30], repetitive DNA may constitute at least 90% of the rye genome. The analysis at molecular level could be simplified by dissecting the genome to small parts and creating subgenomic molecular resources such as chromo- some arm-specific BAC libraries. The short arm of 1R rep- resents only 5.6 % of the whole genome [36] and hence only about 442 Mbp. The proposed approach would reduce the amount of genetic information to be studied by 18-fold and facilitate targeted investigation of this important part of the rye (and wheat) genome. We have shown previously that flow cytometry can be used to sort particular chromosomes in a range of plant species, including wheat [20,43], barley [24,41] and rye [18]. DNA of flow-sorted chromosomes has been used to construct subgenomic BAC libraries in hexaploid wheat. Until now, a composite BAC library specific for 'Chinese Spring' chromosomes 1D, 4D and 6D was created [13], as well as BAC libraries from chromosome 3B of 'Chinese Spring' [35] and 3B of 'Hope' (in preparation), and librar- ies specific for hexaploid wheat chromosome arms 1BS of 'Pavon' [14], 3AS of 'Chinese Spring' [39] and 3DS of 'Chinese Spring' (in preparation). Here we show for the first time that it is possible to sort the arm of a rye chromosome using flow cytometry. The short arm of chromosome 1R (1RS) was sorted from a 1RS wheat-rye ditelosomic addition line and used to construct the first subgenomic BAC library for rye, representing only 5.6% of the genome. The library was constructed using two restriction enzymes and provides a deep coverage of 1RS. We demonstrate its potential to speed up positional cloning of agronomically important genes such as the SrR gene by map-based cloning. Page 2 of 9 (page number not for citation purposes)