title: Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton.
abstract: In order to construct a saturated genetic map and facilitate marker-assisted selection (MAS) breeding, it is necessary to enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants. Many ESTs are publicly available now and represent a good tool in developing EST-SSRs. From 13,505 ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by dinucleotides (30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC (4.5%). One hundred and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross [(TM-1xHai7124)TM-1]. EST-SSR markers were distributed over 20 chromosomes and 6 linkage groups in the map. These EST-SSR markers can be used in genetic mapping, identification of quantitative trait loci (QTLs), and comparative genomics studies of cotton.
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, P. R. China.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Han
authors.forename: Changbiao
authors.initials: C
authors.lastname: Wang
authors.forename: Xianliang
authors.initials: X
authors.lastname: Song
authors.forename: Wangzhen
authors.initials: W
authors.lastname: Guo
authors.forename: Jinying
authors.initials: J
authors.lastname: Gou
authors.forename: Chunhong
authors.initials: C
authors.lastname: Li
authors.forename: Xiaoya
authors.initials: X
authors.lastname: Chen
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development*; D018895:Microsatellite Repeats; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D005819:Genetic Markers