A method for increasing the efficiency of homologous recombination-based gene editing in a plant according to an embodiment of the present invention includes optimizing temperature and photoperiod conditions during tissue culture of plant cells, expressing factors required for homology-directed DNA repair (HDR) and factors for increasing the HDR efficiency by using a multiple replicon, or regulating the HDR pathway or non-homologous end joining (NHEJ) pathway.

Aspects of the disclosure relate to plants containing one or more of a mutant sler (Solyc08g061560) gene or a homolog thereof, a mutant sp5g (Solyc05g053850) gene or a homolog thereof and a mutant sp (Solyc06g074350) gene or a homolog thereof, as well as methods of producing such plants. In some aspects, such plants have one or more improved traits, such as modified stem length and modified time for flowering and fruit production.

Provided are a parthenogenetic haploid induction gene DMP and an application thereof. The parthenogenetic haploid induction genes AtDMP8 and AtDMP9 are cloned from Arabidopsis thaliana. Experiments have shown that mutations of AtDMP8 and AtDMP9 can produce parthenogenetic haploid inducibility, to enable dicotyledonous crops to be induced to produce haploids via parthenogenetic means. The present invention was further verified in tomatoes, and it was also found in tomatoes that the mutation of SlDMP can produce parthenogenetic haploid inducibility. The invention lays an important foundation for broadening the application of haploid breeding technology on dicotyledonous plants and revealing the biological mechanism of parthenogenetic haploid production. Given the universality of the utilization of haploid breeding technology in the current breeding industry, the invention has very wide application space and market prospects.

A genetically modified plant that exhibits an increase in seed yield relative to a progenitor plant is disclosed. The genetically modified plant includes (a) a first homeolog of the SUGAR-DEPENDENT1 (SDP1) gene being homozygous for a wild-type allele; and (b) a second homeolog of the SDP1 gene being homozygous for a mutant allele. The wild-type allele encodes an active SDP1 triacylglycerol lipase and is identical to an allele of the first homeolog from the progenitor plant. The mutant allele does not encode an active SDP1 triacylglycerol lipase and includes one or more additions, deletions, or substitutions of one or more nucleotides relative to an allele of the second homeolog from the progenitor plant. The genetically modified plant expresses about 20% to 80% of SDP1 triacylglycerol lipase activity in seeds relative to the progenitor. The increase in seed yield is at least 10%.

The present invention relates to methods and compositions for modifying a target site in the genome of a cell. Fusion proteins including one or more DNA binding domains and one or more heterologous domains, such as DNA modifying domains, connected by improved linker sequences are provided. Codon optimized polynucleotides encoding fusion proteins including one or more DNA binding domains and one or more heterologous domains connected by improved linker sequences are provided.

A method for introducing a genome editing enzyme into a plant cell includes: treating the cell with plasma; and then bringing the cell into contact with the genome editing enzyme in the presence of a di- or higher-valent metal cation.

The present disclosure provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides small Cas proteins and their use in modifying target sequences. In one aspect, the present disclosure provides a non-naturally occurring or engineered system comprising: a Cas protein that comprises a RuvC domain and a HNH domain, and is less than 850 amino acids in size; and a guide sequence capable of forming a complex with the Cas protein and directing the complex to bind to a target sequence.

The invention provides compositions and methods useful for modulating protein expression in eukaryotic cells. The invention also provides transgenic plants, edited plant cells, plant parts, and seeds comprising depleted or optimized Kozak sequences and methods of their use.

The present disclosure provides methods for transfecting plants and for expressing RNA or polypeptide molecules in plants. In particular, plants having reduced POLQ expression and/or activity are transfected in order to reduce random integration events. The disclosure further provides transfected plants and plant progeny produced by the methods disclosed herein.

A more efficient breeding against infestation with beet cyst nematode, or the development of new resistant lines, is enabled via the provision of the Heterodera resistance-mediating nucleic acid molecule according to the invention; in particular, a dominant resistance effect in the target plant is evoked by the property of the identified nucleic acid molecule. The Heterodera resistance-mediating nucleic acid molecule, and embodiments of the present invention that are described in the preceding, offer additional applications, e.g., the use of the resistant gene allele in cis-genetic or trans-genetic approaches, with the goal of developing new resistant cultivars.