Abstract
Wheat production is challenged by biotic and abiotic stresses. Alien gene transfer is an effective approach to tackle such challenges. We previously showed that sea wheatgrass (SWG; Thinopyrum junceiforme (2n = 2x = 28; J(1)J(2)) is an untapped resource possessing resistance to an array of pests and abiotic stress. However, the transfer of these important traits has been hindered by the lack of genomic resources and a clear picture of its genome constitution. Using multi-color genomic in situ hybridization, we distinguished the SWG sub-genomes and corroborated that the J(1) sub-genome is closely related to the E genome of Th. elongatum and the J genome of Th. bessarabicum and the J(2) sub-genome to the V genome of Dasypyrum villosum. Meanwhile, we developed a draft SWG genome assembly and 127 SWG-specific DNA markers covering the 14 SWG chromosomes. Screening a population of 466 BC(2)F(1) and BC(2)F(2) individuals, derived from backcrosses of wheat-SWG amphiploid to wheat, by the SWG-specific markers led to selection of 72 plants putatively carrying one or two SWG chromosomes. The genome painting analysis of the 72 plants eventually identified a set of 37 wheat-SWG chromosome addition lines covering all the 14 pairs of SWG chromosomes and two compensating Robertsonian translocations (RobTs). While the wheat-SWG chromosome addition lines and RobTs are invaluable genetic resources for wheat improvement via chromosome engineering, our results showed the power of genome-specific markers in combination with genome painting in dissection of a polyploid genome and implicated the origin of a group of important polyploid grasses.