Risk assessment of transgenic apomictic tetraploid bahiagrass, cytogenetics, breeding behavior and performance of intra-specific hybrids

Multi-allelic gene editing in an apomictic, tetraploid turf and forage grass (Paspalum notatum Flüggé) using CRISPR/Cas9

Polyploidy is common among grasses (Poaceae) and poses challenges for conventional breeding. Genome editing technology circumvents crossing and selfing, enabling targeted modifications to multiple gene copies in a single generation while maintaining the heterozygous context of many polyploid genomes. Bahiagrass (Paspalum notatum Flüggé; 2n=4x=40) is an apomictic, tetraploid C4 species that is widely grown in the southeastern United States as forage in beef cattle production and utility turf. The chlorophyll biosynthesis gene magnesium chelatase (MgCh) was selected as a rapid readout target for establishing genome editing in tetraploid bahiagrass. Vectors containing sgRNAs, Cas9 and nptII were delivered to callus cultures by biolistics. Edited plants were characterized through PCR-based assays and DNA sequencing, and mutagenesis frequencies as high as 99% of Illumina reads were observed. Sequencing of wild type (WT) bahiagrass revealed a high level of sequence variation in MgCh likely due to the presence of at least two copies with possibly eight different alleles, including pseudogenes. MgCh mutants exhibited visible chlorophyll depletion with up to 82% reductions in leaf greenness. Two lines displayed progression of editing over time which was linked to somatic editing. Apomictic progeny of a chimeric MgCh editing event were obtained and allowed identification of uniformly edited progeny plants among a range of chlorophyll depletion phenotypes. Sanger sequencing of a highly edited mutant revealed elevated frequency of a WT allele, probably due to frequent homology-directed repair (HDR). To our knowledge these experiments comprise the first report of genome editing applied in perennial, warm-season turf or forage grasses. This technology will accelerate bahiagrass cultivar development.

Reproductive Systems in Paspalum: Relevance for Germplasm Collection and Conservation, Breeding Techniques, and Adoption of Released Cultivars

The objective of this review is to analyze and describe the impact that mode of reproduction in Paspalum has on germplasm conservation, genetic improvement, and commercialization of cultivars. Germplasm collection and conservation can now be rethought considering the newly available information related to how diversity is allocated in nature and how it can be transferred between the sexual and apomictic germplasm using novel breeding approaches. An inventory of species and accessions conserved around the world is analyzed in relation to the main germplasm banks. Because of the importance of apomixis in Paspalum species different breeding approaches have been used and tested. Knowledge related to the inheritance of apomixis, variable expressivity of the trait and techniques for early identification of apomicts has helped to improve the efficiency of the breeding methods. Novel breeding techniques are also being developed and are described regarding its advantages and limitations. Finally, the impact of reproductive mode on the adoption of the released cultivars is discussed.

Harnessing apomictic reproduction in grasses: what we have learned from Paspalum

BACKGROUND

Apomixis is an alternative route of plant reproduction that produces individuals genetically identical to the mother plant through seeds. Apomixis is desirable in agriculture, because it guarantees the perpetuation of superior genotypes (i.e. heterotic hybrid seeds) by self-seeding without loss of hybrid vigour. The Paspalum genus, an archetypal model system for mining apomixis gene(s), is composed of about 370 species that have extremely diverse reproductive systems, including self-incompatibility, self-fertility, full sexual reproduction, and facultative or obligate apomixis. Barriers to interspecific hybridization are relaxed in this genus, allowing the production of new hybrids from many different parental combinations. Paspalum is also tolerant to various parental genome contributions to the endosperm, allowing analyses of how sexually reproducing crop species might escape from dosage effects in the endosperm.

SCOPE

In this article, the available literature characterizing apomixis in Paspalum spp. and its use in breeding is critically reviewed. In particular, a comparison is made across species of the structure and function of the genomic region controlling apomixis in order to identify a common core region shared by all apomictic Paspalum species and where apomixis genes are likely to be localized. Candidate genes are discussed, either as possible genetic determinants (including homologs to signal transduction and RNA methylation genes) or as downstream factors (such as cell-to-cell signalling and auxin response genes) depending, respectively, on their co-segregation with apomixis or less. Strategies to validate the role of candidate genes in apomictic process are also discussed, with special emphasis on plant transformation in natural apomictic species.

Gene use restriction technologies for transgenic plant bioconfinement

The advances of modern plant technologies, especially genetically modified crops, are considered to be a substantial benefit to agriculture and society. However, so-called transgene escape remains and is of environmental and regulatory concern. Genetic use restriction technologies (GURTs) provide a possible solution to prevent transgene dispersal. Although GURTs were originally developed as a way for intellectual property protection (IPP), we believe their maximum benefit could be in the prevention of gene flow, that is, bioconfinement. This review describes the underlying signal transduction and components necessary to implement any GURT system. Furthermore, we review the similarities and differences between IPP- and bioconfinement-oriented GURTs, discuss the GURTs' design for impeding transgene escape and summarize recent advances. Lastly, we go beyond the state of the science to speculate on regulatory and ecological effects of implementing GURTs for bioconfinement.

Co-infection patterns and geographic distribution of a complex pathosystem targeted by pathogen-resistant plants

Increasingly, pathogen-resistant (PR) plants are being developed to reduce the agricultural impacts of disease. However PR plants also have the potential to result in increased invasiveness of nontarget host populations and so pose a potential threat to nontarget ecosystems. In this paper we use a new framework to investigate geographical variation in the potential risk associated with unintended release of genetically modified alfalfa mosaic virus (AMV)-resistant Trifolium repens (white clover) into nontarget host populations containing AMV, clover yellow vein virus (ClYVV), and white clover mosaic virus (WCIMV) in southeastern Australia. Surveys of 213 sites in 37 habitat types over a 300 000-km2 study region showed that T. repens is a significant weed of many high-conservation-value habitats in southeastern Australia and that AMV, ClYVV, and WClMV occur in 15-97% of nontarget host populations. However, T. repens abundance varied with site disturbance, habitat conservation value, and proximity to cropping, and all viral pathogens had distinct geographic distributions and infection patterns. Virus species frequently co-infected host plants and displayed nonindependent distributions within host populations, although co-infection patterns varied across the study region. Our results clearly illustrate the complexity of conducting environmental risk assessments that involve geographically widespread, invasive pasture species and demonstrate the general need for targeted, habitat- and pathosystem-specific studies prior to the process of tiered risk assessment.

Cloning plants by seeds: Inheritance models and candidate genes to increase fundamental knowledge for engineering apomixis in sexual crops

Apomixis is desirable in agriculture as a reproductive strategy for cloning plants by seeds. Because embryos derive from the parthenogenic development of apomeiotic egg cells, apomixis excludes fertilization in addition to meiotic segregation and recombination, resulting in offspring that are exact replicas of the parent. Introgression of apomixis from wild relatives to crop species and transformation of sexual genotypes into apomictically reproducing ones are long-held goals of plant breeding. In fact, it is generally accepted that the introduction of apomixis into agronomically important crops will have revolutionary implications for agriculture. This review deals with the current genetic and molecular findings that have been collected from model species to elucidate the mechanisms of apomeiosis, parthenogenesis and apomixis as a whole. Our goal is to critically determine whether biotechnology can combine key genes known to control the expression of the processes miming the main components of apomixis in plants. Two natural apomicts, as the eudicot Hypericum perforatum L. (St. John's wort) and the monocot Paspalum spp. (crowngrass), and the sexual model species Arabidopsis thaliana are ideally suited for such investigations at the genomic and biotechnological levels. Some novel views and original concepts have been faced on this review, including (i) the parallel between Y-chromosome and apomixis-bearing chromosome (e.g., comparative genomic analyses revealed common features as repression of recombination events, accumulation of transposable elements and degeneration of genes) from the most primitive (Hypericum-type) to the most advanced (Paspalum-type) in evolutionary terms, and (ii) the link between apomixis and gene-specific silencing mechanisms (i.e., likely based on chromatin remodelling factors), with merging lines of evidence regarding the role of auxin in cell fate specification of embryo sac and egg cell development in Arabidopsis. The production of engineered plants exhibiting apomictic-like phenotypes is critically reviewed and discussed.

Transgene introgression in crop relatives: molecular evidence and mitigation strategies

Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.

Advances in plant molecular farming

Plant molecular farming (PMF) is a new branch of plant biotechnology, where plants are engineered to produce recombinant pharmaceutical and industrial proteins in large quantities. As an emerging subdivision of the biopharmaceutical industry, PMF is still trying to gain comparable social acceptance as the already established production systems that produce these high valued proteins in microbial, yeast, or mammalian expression systems. This article reviews the various cost-effective technologies and strategies, which are being developed to improve yield and quality of the plant-derived pharmaceuticals, thereby making plant-based production system suitable alternatives to the existing systems. It also attempts to overview the different novel plant-derived pharmaceuticals and non-pharmaceutical protein products that are at various stages of clinical development or commercialization. It then discusses the biosafety and regulatory issues, which are crucial (if strictly adhered to) to eliminating potential health and environmental risks, which in turn is necessary to earning favorable public perception, thus ensuring the success of the industry.

Apomixis and ploidy barrier suppress pollen-mediated gene flow in field grown transgenic turf and forage grass (Paspalum notatum Flüggé)

Bahiagrass (Paspalum notatum Flüggé) is the predominant forage grass in the southeastern US. The commercially important bahiagrass cultivar 'Argentine' is preferred for genetic transformation over sexual diploid cytotypes, since it produces uniform seed progeny through apomixis. Pseudogamous apomictic seed production in Argentine bahiagrass may contribute to transgene confinement. It is characterized by embryo development which is independent of fertilization of the egg cell, but requires fertilization with compatible pollen to produce the endosperm. Pollen-mediated gene transfer from transgenic, glufosinate-resistant apomictic bahiagrass as pollen donor at close proximity (0.5-3.5 m) with non-transgenic sexual or apomictic bahiagrass cultivars as pollen receptors was evaluated under field conditions. Hybridization frequency was evaluated by glufosinate herbicide resistance in >23,300 seedlings derived from open-pollinated (OP) pollen receptor plants. Average gene transfer between transgenic apomictic, tetraploid and sexual diploid bahiagrass was 0.03%. Herbicide-resistant hybrids confirmed by immuno-chromatographic detection of the PAT protein displayed a single copy bar gene identical to the pollen parent. Hybrids resulting from diploid pollen receptors were confirmed as triploids or aneu-triploids with significantly reduced vigor and seed set as compared to the parents. Transmission of transgenes to sexual bahiagrass is severely restricted by the ploidy difference between tetraploid apomicts and diploid sexual bahiagrass. Average gene transfer between transgenic apomictic tetraploid and non-transgenic, apomictic tetraploid bahiagrass was 0.17%, confirming a very low frequency of amphimixis in apomictic bahiagrass cultivars. While not providing complete transgene containment, gene transfer between transgenic apomictic and non-transgenic bahiagrass occurs at a much lower frequency than reported for other cross-pollinating or facultative apomictic grasses.