Comparative proteomic analysis of kernel proteins of two high amylose transgenic durum wheat lines obtained by biolistic and Agrobacterium-mediated transformations

•Comparison of two different methods of genetic transformation.•Changes in abundance of granule bound starch proteins between wt and GM wheat are investigated.•Changes in abundance of metabolic proteins between wt and GM wheat are investigated.•Minimal differences have been found between biolistic and Agrobacterium-mediated method.

In this work, we compared the proteome of mature and immature kernels of transgenic and untransformed durum wheat lines in which genes of the starch branching enzymes of class II (SBEIIa) were silenced by RNA interference using two different methods of genetic transformation. The comparative analysis of granule bound and metabolic protein fractions of Svevo and Ofanto and their derived transgenic lines highlighted twenty four and thirty three differentially accumulated spots, respectively, in the line MJ16-112 (obtained by biolistic transformation of Svevo) and in the line A431_4p1a (obtained by Agrobacterium-mediated transformation of Ofanto).The comparative analysis of GM vs wild type plants highlighted subtle differences, most of which were considered as "predictable unintended effects" due to the primary effect of the transgene on the starch biosynthetic pathway. In particular, increased levels of SBEI isoforms in RNAi lines probably represent a compensatory effect due to the absence of SBEIIa enzymes. Other proteins involved in starch synthesis, namely SSII, GBSS and phosphorylase enzymes, also showed significant changes in their relative abundance.These results were detectable in both lines obtained with the two different transformation procedures, thus showing that the transgenic event is the main factor responsible for the effect on protein expression.