Specificity and inheritance of rBE3 and rBE4 endonuclease-induced gene modifications in rice

Journal Article / 2017

Ren, Bin; Yan, Fang; Kuang, Yongjie; Li, Na; Zhang, Dawei; Lin, Honghui; Zhou, Huanbin

The main goal of this review is to compare different approaches to constructing geometry associated with a Hecke type braiding (in particular, with that related to the quantum group U_q(sl(n))). We make an emphasis on affine braided geometry related to the so-called Reflection Equation Algebra (REA). All objects of such type geometry are defined in the spirit of affine algebraic geometry via polynomial relations on generators. We begin with comparing the Poisson counterparts of "quantum varieties" and describe different approaches to their quantization. Also, we exhibit two approaches to introducing q-analogs of vector bundles and defining the Chern-Connes index for them on quantum spheres. In accordance with the Serre-Swan approach, the q-vector bundles are treated as finitely generated projective modules over the corresponding quantum algebras. Besides, we describe the basic properties of the REA used in this construction and compare different ways of defining q-analogs of partial derivatives and differentials on the REA and algebras close to them. In particular, we present a way of introducing a q-differential calculus via Koszul type complexes. The lements of the q-calculus are applied to defining q-analogs of some relativistic wave operators. To gain more insights into the rice base editor (rBE3 and rBE4), we evaluated the mutation efficiency, off-target and inheritance of OsSERK1(D428N) and pi-ta(S918F) genes modified with rBE endonucleases. We predicted and analyzed the putative off-target sites of the sgRNA designed for OsSERK1(D428N) and pi-ta(S918F) by PCR amplification and Sanger sequencing. Then we further characterized the inheritance and stability of targeted base mutations and T-DNA segregation in the progeny of the self-fertilized T0 plants. Analysis of the DNA sequencing data of T0 plants of OsSERK1(D428N) revealed no nucleotide change at any of the four potential off-target sites. For OsSERK1(D428N) and Os08g07774 carry the same sgRNA targeting sites, base substitution at both two loci were detected at a frequency of 41.67%. The targeted base mutations could be transmitted readily to T1 progeny. Furthermore, genetic segregation caused the loss of T-DNA at a frequency between 25.0% and 40.9% in the T1 transgenic plants of OsSERK1(D428N) and pi-ta(S918F). These results demonstrated that the rBE3 and rBE4 systems could mediate specifically targeted base editing in one- or multi-site, and the targeted base editing could be stably inherited to next generation.