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.
Highlights
Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is important in the case of less researched crops such as cotton
The designed markers can be well used in tetraploid cotton genetic mapping
It plays a certain role in revealing transition preference and single nucleotide polymorphisms (SNPs) frequency of cotton genes
Summary
Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is 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. There are many types of molecular markers such as restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR) and SNPs. In cotton which is the world most important natural fiber crop, the most prevalent marker type as of today is SSR. SNP markers are becoming more and more important due to their abundance in the genome and very simple genetic mode (bi-allelic). Cotton researchers have tried different methods to develop SNP markers. An et al [1] reported a few SNP markers when studying R2R3-MYB transcription factors
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
