On 2016 Jun 01, Kenneth Witwer commented:

These data cannot be used to conclude differential expression of miRNAs between soybean strains (only one sample per strain), but the authors are commended for publishing this study, which is interesting and potentially instructive for several reasons. Four RNA samples were prepared: one each from two soybean strains that were genetically modified using modern biotechnology and one each from the two parent strains that were genetically modified by traditional breeding approaches. A sequencing library was prepared from each RNA sample.

The first interesting aspect of the study is that the small RNA profile of soybean was overwhelmingly dominated by fragments of longer RNAs, especially the rRNAs, such that only single digit percentages of miRNAs are mapped. It would be good to compare these results with other soybean studies to determine if sample quality or processing issues contributed to degradation. To this end, it would be helpful to know more about the quality control that was mentioned. rRNA degradation fragments are variable in length and well conserved (in contrast with erroneous suggestions of species-specificity, e.g. Zhou Z, 2015), and they should not be confused with miRNAs. A study of one family, previously called "MIR2911," showed that the family does not associate with RNA regulatory machinery (Yang J, 2015) and is thus unlikely to be involved in RNA regulation, within or across organisms.

A second and more substantive contribution of the study comes from the 14 newly predicted miRNAs. Although at low abundance and not reportedly associated with "GM" strains, these may be worth some follow-up through bioinformatics and perhaps even in the lab.

As a third matter of note, the study reminds us to check data and not rely only on abstracts and conclusions in the text. Unfortunately, no conclusions can be drawn about differential expression of miRNAs between parental and "GM" strains, since there are no biological replicates. More reported differences were found between the two traditionally genetically modified "parent" strains than between parent and biotech, yet curiously this is not emphasized. The very minor reported differences, which are inconsistent between the two parent-daughter strain pairs, could be due to any number of factors that have nothing to do with biotechnology-introduced modifications, from growing, harvesting, storage, shipping, and other handling conditions (all out of the control of the authors...presumably these beans were not grown side-by-side in the same field); to a variety of technical factors introduced during isolation of RNA, library prep, and sequencing; to chance.

Finally, the study prompts reflection on the term "genetically modified," which applies to all strains examined here. The popular media definition is used in this study to refer only to molecular biotechnology-produced strains, not the parents produced by legacy methods of genetic modification.

On 2016 Jun 01, Kenneth Witwer commented:

These data cannot be used to conclude differential expression of miRNAs between soybean strains (only one sample per strain), but the authors are commended for publishing this study, which is interesting and potentially instructive for several reasons. Four RNA samples were prepared: one each from two soybean strains that were genetically modified using modern biotechnology and one each from the two parent strains that were genetically modified by traditional breeding approaches. A sequencing library was prepared from each RNA sample.

The first interesting aspect of the study is that the small RNA profile of soybean was overwhelmingly dominated by fragments of longer RNAs, especially the rRNAs, such that only single digit percentages of miRNAs are mapped. It would be good to compare these results with other soybean studies to determine if sample quality or processing issues contributed to degradation. To this end, it would be helpful to know more about the quality control that was mentioned. rRNA degradation fragments are variable in length and well conserved (in contrast with erroneous suggestions of species-specificity, e.g. Zhou Z, 2015), and they should not be confused with miRNAs. A study of one family, previously called "MIR2911," showed that the family does not associate with RNA regulatory machinery (Yang J, 2015) and is thus unlikely to be involved in RNA regulation, within or across organisms.

A second and more substantive contribution of the study comes from the 14 newly predicted miRNAs. Although at low abundance and not reportedly associated with "GM" strains, these may be worth some follow-up through bioinformatics and perhaps even in the lab.

As a third matter of note, the study reminds us to check data and not rely only on abstracts and conclusions in the text. Unfortunately, no conclusions can be drawn about differential expression of miRNAs between parental and "GM" strains, since there are no biological replicates. More reported differences were found between the two traditionally genetically modified "parent" strains than between parent and biotech, yet curiously this is not emphasized. The very minor reported differences, which are inconsistent between the two parent-daughter strain pairs, could be due to any number of factors that have nothing to do with biotechnology-introduced modifications, from growing, harvesting, storage, shipping, and other handling conditions (all out of the control of the authors...presumably these beans were not grown side-by-side in the same field); to a variety of technical factors introduced during isolation of RNA, library prep, and sequencing; to chance.

Finally, the study prompts reflection on the term "genetically modified," which applies to all strains examined here. The popular media definition is used in this study to refer only to molecular biotechnology-produced strains, not the parents produced by legacy methods of genetic modification.