title: Genome-wide mining, characterization, and development of microsatellite markers in gossypium species.
abstract: Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping.
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2].
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2].
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Jiedan
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Zhanfeng
authors.initials: Z
authors.lastname: Si
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Sen
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Lijing
authors.initials: L
authors.lastname: Chang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Wangzhen
authors.initials: W
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D005787:Gene Frequency; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D003368:Gossypium / Q000235:genetics*; D018895:Microsatellite Repeats; D059372:Nucleotide Motifs; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers