Development Of Specific Markers For Chromosome Arms Of Rye(Secale Cereale L.)

Rye?Secale cereal L.?,a relative of common bread wheat?Triticum aestivum L.?,has played an important role in wheat breeding programs as a valuable reservoir of genes.Fast and accurate identification and characterization of rye chromatin in wheat backgrounds can improve the application efficiency of elite rye genes in wheat breeding.Many molecular markers of rye have been developed.However,the rye-specific markers that are based on PCR and agarose gel electrophoresis?AGE?are limited.Therefore,more rye chromosome-specific and PCR-based markers,especially those suited to agarose gel electrophoresis?AGE?are needed for identification of rye chromatin in wheat backgrounds.In the present study,new PCR and AGE-based and rye-specific markers have been developed by using specific length amplified fragment sequencing?SLAF-seq?technology.Wheat-rye monosomic addition and monotelosomic addition lines were used to locate these markers on specific rye arm.In addition,the generality of these markers were tested using two sets of wheat-rye disomic addition lines CS-Imperia and Holdfast-King ?.The results are as follows:1.From the progeny of common wheat Mianyang11?MY11?×rye Kustro,a set of wheat-rye monosomic addition lines,MA1R^Ku-7RKu,and 13 monotelosomic addition lines including MTA1RSKu?MTA1RLKu?MTA2RSKu?MTA2RLKu?MTA3RSKu?MTA4RSKu?MTA4RLKu?MTA5RSKu?MTA5RLKu?MTA6RSKu?MTA6RLKu?MTA7RSKu and MTA7RLKu were identified.2.Genomic DNA of Kustro was sequenced by using the SLAF-seq method.The pair-end reads were compared with wheat genomic DNA sequences and rye-specific reads were obtained.From the rye-specific pair-end reads,a total of 1104 reads were randomly selected for designing primers.578 primers amplified specific bands from rye Kustro,but not from common wheat MY11,Chinese Spring?CS?and Holdfast.The 578 pairs of primers were regarded as new rye-specific markers.3.Using rye Kustro,Imperial,and King ? to test the polymorphism of the 578 rye-specific markers,76 markers displayed polymorphism among rye Kustro,Imperial,and King II.4.427 of the 578 markers were located on 7 individual chromosomes of Kustro by using monosomic addition lines MAIRKu-7RKu.5.387 of the 427 markers were located on 13 individual chromosome arms of Kustro by using monotelosomic addition lines MTA1RSKu?MTA1RLKu?MTA2RSKu?MTA2RLKu?MTA3RSKu?MTA4RSKu?MTA4RLKu?MTA5RSKu?MTA5RLKu?MTA6RSKu?MTA6RLKu?MTA7RSKu and MTA7RLKu.6.Two sets of wheat-rye disomic addition lines,which were derived from CSxImperial and HoldfastxKing II were used to test the generality of the 427 markers,and 281 markers have generality among the three set of wheat-rye materials.The PCR-based and rye-specific markers developed in this study have generality among three kinds of rye and they can be used to identify rye chromatin in wheat backgrounds.Furthermore,some markers that displayed polymorphism can be used to study the genetic diversity of different rye sources.The markers developed in this study can accelerate the utilization of elite genes on rye chromosomes in wheat breeding programs.