Genome-wide Characterization Of Microsatellites And Maker Development In Bread Wheat

Bread wheat(Triticum aestivum)represents one of the best characterized example of evolution through allopolyploidy,is an allopolyploid complex of agricultural importance.Two of its three diploid progenitors have been identified: Triticum urartu(genome AA)and Aegilops tauschii(genome DD),while the origin of the B genome have been debated for years.Microsatellites are an important constituent of plant genome and distributed across entire genome.Microsatellites have been initially regarded as ?junk DNA‘ or mainly used as ?neutral‘genetic marker,while recent studies have documented that they could play crucial roles in affecting gene activity,chromatin organization and DNA metabolic processes.Besides their direct biological functions,microsatellites have been proven to be a rich source of hypervariable codominant markers because they were subjected to a high rate of single-motif insertion and deletion mutations.For the past 15 years,microsatellite markers were extensively used in many research areas such as quantitative trait loci(QTL)mapping,genetic diversity studies,marker-assisted selection and evolutionary studies.In present study,MISA program was used to search SSR using the latest version sequenced bread wheat and other Poaceae species,the frequency of SSR in different species were analyzed.Then primers flanking the identified microsatellite repeat motifs were designed in batches using the primer3_core program.The software(e-PCR-2.3.12)was used for in silico PCR analysis the amplification effectively,polymorphic and transferability of the newly development makers.A total of 21 SSR primer pairs were synthesized to test for PCR amplification in wheat and its close relatives.Results are as follows:(1)17 genome sequenced species(14 Poaceae species and three other plants),a total of 4,763,266 microsatellites were identified,with an overall frequency of 126.83 per Mb.And microsatellite characteristics were similar among the Triticeae species.(2)Aegilops tauschii was found to be the closest species to Triticum aestivum,followed by Triticum urartu,Triticum turgidum and Aegilops speltoides,while Triticum monococcum,Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity.(3)A significantly higher PCR amplification effectivity was found in chromosomes at the subgenome than its homoeologous.(4)After a rigorous screening process,a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives,which were integrated with the public available wheat markers and then anchored to the genome of wheat(CS).