Recombinant DNA molecules and constructs useful for modulating gene expression in plants, including molecules derived from Medicago truncatula sequences, are provided. Plants, plant cells, plant parts, and seeds comprising recombinant DNA molecules operably linked to heterologous transcribable DNA molecules are further provided, as are methods of their use.

Compositions and methods are provided for an inducible, high efficiency intra-genomic homologous recombination (IGHR) system in plants, that can be used for non-chimeric, heritable gene targeting. The advantage of IGHR approach to targeted integration is that every cell contains donor DNA and nuclease-encoding sequences, so that there are many potentially homology-directed targeting events that can occur during plant development.

The present invention relates to novel strategies for gradually decreasing the expression of genes by modifying the promoter sequence. Provided are methods for gradually decreasing the expression level of a nucleic acid molecule of interest in a cell, preferably in a plant cell, comprising the step of introducing at least one modification into a promoter sequence, wherein the modification disrupts a core promoter consensus sequence. Furthermore, the invention also provides methods for producing a cell or an organism, preferably a plant cell or a plant, having a decreased expression level of a nucleic acid molecule of interest. The invention also relates to a cell and an organism, preferably a plant cell and a plant, obtained by a method according to the invention.

This invention provides recombinant DNA constructs, transgenic plant nuclei and cells with such recombinant DNA construct for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.

The invention relates to binary vectors based on compatible and autonomous origins, specifically based on the pBBR1 and RK2 replication origins. These binary vectors are useful for having a wide range of hosts, for their maintenance in Agrobacterium sp. and Escherichia coli, and as a new tool for plant synthetic biology as well as a flexible framework for assembly, transfer and characterization of multiple DNA elements. The binary vectors disclosed are small, preferably less than 3.8 kb in size, stable, include an origin compatible with the most commonly used binary T-DNA vectors, comply with current standards for plant synthetic biology, and allow the administration of multiple T-DNA cassettes by means of the multiplexing of the vectors. The present invention also relates to methods for transferring and expressing nucleic acid sequences using said binary vectors, and to the uses of the same.

Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NOs: 710-1153 and 9276-15726, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-709 and 1157-9275, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

Described herein are methods of introducing variation into plants. Also described herein are methods of producing a plant and/or seed, methods of breeding plants, methods of generating a commercially relevant trait or allele in a plant, and methods of generating a plant and/or seed library. Products produced from such methods (e.g., plants and/or seeds) are also described herein.

A method of inducing genetic recombination, including: allowing a protein having DNA double-stranded cleavage activity to act in cells of a eukaryotic organism which is a polyploidy inherently possessed by a eukaryotic organism. In eukaryotic organisms, various genetic recombination generates new genome set composition. This is done to obtain a population of eukaryotic organisms that hold the modified genomic set.

It was now found that the expression of a nucleotide sequence as described in the method of the invention in a plant cell results in much higher rates of indels compared to those seen in cells transformed with a control nucleic acid molecule. Thus, the invention is directed to codon-optimized Cas9 endonuclease-encoding polynucleotide. Accordingly, the present invention provides a method for modifying a target site in the genome of a plant cell, the method comprising providing one or more guide RNA and a Cas endonuclease to said plant cell, wherein said guide RNA and Cas endonuclease are capable of forming a complex that enables the Cas endonuclease to introduce a double strand break at said target site, and wherein the Cas9 endonuclease is expressed in the plant cell from a polynucleotide comprising an codon-optimized Cas9 endonuclease encoding nucleic acid molecule with a nucleotide sequence selected from the disclosed nucleotide sequences.

The invention provides recombinant DNA molecules and constructs, and their nucleotide sequences, useful for modulating gene expression in plants. The invention also provides transgenic plants, plant cells, plant parts, and seeds comprising a recombinant DNA molecule comprising a DNA molecule operably linked to a heterologous transcribable DNA molecule, as well as methods of their use.