title: Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.
abstract: BACKGROUND
  Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzed in silico to identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton.
  
  
  RESULTS
  A total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, mining G. hirsutum unigenes, and analyzing 3' untranslated region (3'UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1 population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between the in silico predicted sequences and the actual sequencing results.
  
  
  CONCLUSIONS
  In silico analysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low.
authors.forename: Ximei
authors.initials: X
authors.lastname: Li
authors.forename: Wenhui
authors.initials: W
authors.lastname: Gao
authors.forename: Huanle
authors.initials: H
authors.lastname: Guo
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
authors.forename: David D
authors.initials: DD
authors.lastname: Fang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China. linzhongxu@mail.hzau.edu.cn.
authors.forename: Zhongxu
authors.initials: Z
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D056426:Genetic Loci; D003368:Gossypium / Q000235:genetics*; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D057891:Tetraploidy