Plant Genome Editing and the Relevance of Off-Target Changes

Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.

Plant characterization of Roundup Ready 2 Yield ® soybean, MON 89788, for use in ecological risk assessment

During the development of a genetically modified (GM) crop product, extensive phenotypic and agronomic data are collected to characterize the plant in comparison to a conventional control with a similar genetic background. The data are evaluated for potential differences resulting from the genetic modification process or the GM trait, and the differences--if any--are subsequently considered in the context of contributing to the pest potential of the GM crop. Ultimately, these study results and those of other studies are used in an ecological risk assessment of the GM crop. In the studies reported here, seed germination, vegetative and reproductive growth, and pollen morphology of Roundup Ready 2 Yield(®) soybean, MON 89788, were compared to those of A3244, a conventional control soybean variety with the same genetic background. Any statistically significant differences were considered in the context of the genetic variation known to occur in soybean and were evaluated as indicators of an effect of the genetic modification process and assessed for impact on plant pest (weed) characteristics and adverse ecological impact (ecological risk). The results of these studies revealed no effects attributable to the genetic modification process or to the GM trait in the plant that would result in increased pest potential or adverse ecological impact of MON 89788 compared with A3244. These results and the associated risk assessments obtained from diverse geographic and environmental conditions in the United States and Argentina can be used by regulators in other countries to inform various assessments of ecological risk.

Glyphosate-tolerant soybeans remain compositionally equivalent to conventional soybeans (Glycine max L.) during three years of field testing

Previous studies have shown that the composition of glyphosate-tolerant soybeans (GTS) and selected processed fractions was substantially equivalent to that of conventional soybeans over a wide range of analytes. This study was designed to determine if the composition of GTS remains substantially equivalent to conventional soybeans over the course of several years and when introduced into multiple genetic backgrounds. Soybean seed samples of both GTS and conventional varieties were harvested during 2000, 2001, and 2002 and analyzed for the levels of proximates, lectin, trypsin inhibitor, and isoflavones. The measured analytes are representative of the basic nutritional and biologically active components in soybeans. Results show a similar range of natural variability for the GTS soybeans as well as conventional soybeans. It was concluded that the composition of commercial GTS over the three years of breeding into multiple varieties remains equivalent to that of conventional soybeans.

DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationship to those of other nodulating bacteria

A 6.6-kb BamHI fragment containing the common nodulation genes of Bradyrhizobium elkanii USDA94 was identified by southern hybridization using the common nod genes of B. japonicum as a probe. This fragment was cloned and sequenced. Analysis of the sequence showed open reading frames highly homologous to nolA, nodD2, nodD1, and nodKABC from other bradyrhizobial sources. The sequence showed higher homology to the common nod genes of Bradyrhizobium sp. (Parasponia) than to those from B. japonicum. The open reading frame identified between nodD1 and nodA in the B. elkanii sequence was far more similar to nodK from Bradyrhizobium sp. (Parasponia) than to nodY from B. japonicum. The molecular phylogeny of nodD and nodAB from many sources was analyzed. The genetic distance between the nod genes is far greater than the distance between the 16S rRNA and nifH genes. The differences between the nod genes among the species of Rhizobium is as great as that between Bradyrhizobium and Rhizobium. The host range of the microsymbiont was found to be a better predictor of the similarities of the common nod genes than the 16S rRNA or nifH genes. We propose two groups of nod genes among the rhizobia and bradyrhizobia, based on molecular phylogenetic analysis: those which nodulate legumes of temperate origin in the tribes Vicieae or Trifolieae and those which nodulate legumes of tropical origin in the tribe Phaseoleae.

Common soybean inoculant strains in Brazil are members of Bradyrhizobium elkanii

The Brazilian inoculant strains 29W and 587 were found to be members of Bradyrhizobium elkanii primarily on the basis of 16S rRNA gene sequences identical to that of B. elkanii USDA76 and on the basis of reactivity with antibodies against serogroups 76 and 31, respectively. The agronomic consequences of using strains of B. elkanii as soybean inoculants are discussed.

Gibberellins and the Legume-Rhizobium Symbiosis : III. Quantification of Gibberellins from Stems and Nodules of Lima Bean and Cowpea

Lima bean (Phaseolus lunatus L.) plants inoculated with Bradyrhizobium sp. strain 127E14 displayed a period of marked internode elongation that was not observed in plants inoculated with other compatible bradyrhizobia, including strain 127E15. When strain 127E14 nodulated an alternate host, cowpea (Vigna unguiculata L. Walp), a similar, although less dramatic growth response induced by the bacteria was observed. It has been speculated that the elongative growth promotion brought about by inoculation with strain 127E14 is mediated by gibberellins (GAs). Using deuterated internal standards and gas chromatography-mass spectroscopy analysis, we have quantified the levels of GA(1), GA(20), GA(19), and GA(44) in nodules and stems of two varieties of lima bean (bush and pole) and one variety of cowpea that were inoculated with either strain 127E14 or 127E15. In nodules formed by strain 127E14 on lima bean, endogenous levels of GA(20) and GA(19) were 10 to 40 times higher (35-88 ng/g dry weight) than amounts found in nodules formed by strain 127E15 (2.2-3.9 ng/g dry weight). Relative amounts of GA(44) were also higher (4- to 11-fold) in 127E14 nodules, but this increase was less pronounced. The rhizobial-induced increase of these GAs in the nodule occurred in both pole and bush varieties and seemed to be independent of host morphology. Regardless of rhizobial inoculum, levels of the "bioactive" GA(1) in the nodule (0.3-1.1 ng/g dry weight) were similar. In cowpea nodules, a similar, although smaller, difference in GA content due to rhizobial strain was observed. The concentration of GA(1) in lima bean stems was generally higher than that observed in the nodule, whereas concentrations of the other GAs measured were lower. In contrast with the nodule, GA concentrations in lima bean stems were not greater in plants inoculated with strain 127E14, and in some cases the slower growing plants inoculated with strain 127E15 actually had higher levels of GA(20), GA(19), and GA(44). Thus, there were major differences in concentrations of the precursors to GA(1) in nodules formed by the two bacterial strains, which were positively correlated with the observed elongation growth. These results support the hypothesis that the rhizobial strain modifies the endogenous GA status of the symbiotic system. This alteration in GA balance within the plant, presumably, underlies the observed growth response.

Gibberellins and the Legume-Rhizobium Symbiosis : I. Endogenous Gibberellins of Lima Bean (Phaseolus lunatus L.) Stems and Nodules

The content of gibberellin-like substances in nodules formed by Bradyrhizobium species strain 127E14 on roots of lima bean (Phaseolus lunatus L.) has been previously found to be relatively high. The objectives of the present study were to purify and identify the endogenous gibberellins from the stems and nodules of lima bean. By sequential silica gel partition column chromatography, C(18) reverse-phase high performance liquid chromatography, and combined gas chromatography-mass spectrometry, the gibberellins A(1), A(3), A(19), A(20), A(29), and A(44) were identified from root nodules. Gibberellins A(1), A(3), A(19), A(20), and A(44) were also identified from lima bean stem tissue. These data provide the first mass spectral-based evidence that gibberellins are present in leguminous root nodules. The presence of the gibberellins identified indicates that the early 13-hydroxylation gibberellin biosynthetic pathway predominates in stem and nodule tissue. However, it is not known if the gibberellins within the nodules are produced in situ, or if they are imported from some remote host plant tissue.