Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping |
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| Authors: | Ximei Li Wenhui Gao Huanle Guo Xianlong Zhang David D Fang Zhongxu Lin |
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| Affiliation: | .National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China ;.College of Agronomy and Plant Protection, Qingdao Agricultural University/Shandong Key Laboratory of Dryland Farming Technology, Qingdao, 266109 Shandong China ;.Cotton Fiber Bioscience Research Unit, USDA–ARS, Southern Regional Research Center, New Orleans, LA 70124 USA |
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| Abstract: | BackgroundAvailability 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.ResultsA 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.ConclusionsIn 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1046) contains supplementary material, which is available to authorized users. |
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| Keywords: | Cotton Molecular markers SNP InDel Genetic mapping |
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