title: Development of novel microsatellite markers for the BBCC Oryza genome (Poaceae) using high-throughput sequencing technology.
abstract: Wild species of Oryza are extremely valuable sources of genetic material that can be used to broaden the genetic background of cultivated rice, and to increase its resistance to abiotic and biotic stresses. Until recently, there was no sequence information for the BBCC Oryza genome; therefore, no special markers had been developed for this genome type. The lack of suitable markers made it difficult to search for valuable genes in the BBCC genome. The aim of this study was to develop microsatellite markers for the BBCC genome. We obtained 13,991 SSR-containing sequences and designed 14,508 primer pairs. The most abundant was hexanuclelotide (31.39%), followed by trinucleotide (27.67%) and dinucleotide (19.04%). 600 markers were selected for validation in 23 accessions of Oryza species with the BBCC genome. A set of 495 markers produced clear amplified fragments of the expected sizes. The average number of alleles per locus (Na) was 2.5, ranging from 1 to 9. The genetic diversity per locus (He) ranged from 0 to 0.844 with a mean of 0.333. The mean polymorphism information content (PIC) was 0.290, and ranged from 0 to 0.825. Of the 495 markers, 12 were only found in the BB genome, 173 were unique to the CC genome, and 198 were also present in the AA genome. These microsatellite markers could be used to evaluate the phylogenetic relationships among different Oryza genomes, and to construct a genetic linkage map for locating and identifying valuable genes in the BBCC genome, and would also for marker-assisted breeding programs that included accessions with the AA genome, especially Oryza sativa.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Caihong
authors.initials: C
authors.lastname: Wang
authors.affiliation: College of Agricultural Sciences, Shanxi Agricultural University, Taigu, China.
authors.forename: Xiaojiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: College of Agricultural Sciences, Shanxi Agricultural University, Taigu, China.
authors.forename: Suotang
authors.initials: S
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Hanyong
authors.initials: H
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
mesh_terms: D005819:Genetic Markers; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D059372:Nucleotide Motifs; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
chemical_list: D005819:Genetic Markers