EST-SSR markers derived from transcribed regions of DNA were show

EST-SSR markers derived from transcribed regions of DNA were shown to produce high rates of transferability in cotton species [17] and other related plant groups Selleck ATR inhibitor [18] and [19]. In this study, a total of 707 SSR markers developed from G. arboreum (A genome), G. raimondii (D genome), and G. hirsutum (AD genome) were chosen to amplify DNA from G. hirsutum, G. anomalum, and the synthetic. All 707 primer pairs yielded microsatellite products in G. hirsutum and the synthetic, but 14 failed to produce a band in G. anomalum. However the transferability rate from the three species to G. anomalum was very high (98.0%). D-genome-derived SSR markers showed slightly lower rates of transferability than A- and AD-genome species-derived

markers. Although all selected SSR markers expressed high levels of transferability and polymorphism, almost half of the markers (47.24%) were dominant in G. hirsutum. Since G. hirsutum will be used as the recurrent parent in future backcrossing programs, those dominant markers in G. hirsutum cannot be used to monitor the introgression of TGF-beta inhibitor G. anomalum-specific segments in backcross populations. However, the A-genome-derived markers produced more codominant loci (56.38%) than the D-genome-derived

markers (42.59%), indicating that the A-genome-derived markers were more powerful for distinguishing genomic differences between G. hirsutum and G. anomalum. In addition, the A-genome-derived SSR markers have a higher level of transferability between G. hirsutum and G. anomalum than the D-genome-derived SSR markers. These phenomena suggest that SSR markers developed from close relatives of the wild species are more applicable to the analysis of the transfer of chromosome segments from the wild species to cultivated cotton than other types of markers. Although hybrids are expected to have additive banding profiles of the two parents, previous work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis in crops such as wheat [20] and [21] and rapeseed [22]. However, there is no evidence for structural genomic

changes or de novo DNA methylation modifications in newly synthesized allopolyploid cotton [23]. In this study, 9 SSR primer pairs failed to amplify G. anomalum-specific oxyclozanide bands in hexaploid plants. Possible explanations for this include chromosome loss, heterozygosity at some loci in a parental plant, chromosome rearrangement, and sequence discrepancy between the different species. Loss of chromosomes was not the causative factor because the synthetic plants had the expected chromosome number (2n = 78). The presence of heterozygous loci in a parental plant was also unlikely since there was no evidence of variation among the tested parental plants. We also ruled out the possibility of chromosome rearrangement since one SSR marker (NAU2954) that failed to amplify G.

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