Agriculture : Plant biotech


New Software Algorithm Advances Measurement Technology in Agribusiness

UW–Madison researchers have developed a new scanning algorithm for use in assessing yield and quality of crop production.

To determine characteristics such as kernel loading on an ear of corn and ear size, researchers scan up to three ears at a time using a common flatbed scanner. To measure 100 kernel weight, another common yield measurement, researchers weigh a handful of individual kernels and scatter them on the scanner. The resulting images are then analyzed using the algorithm to quickly provide yield data.

The algorithm uses a thresholding technique to separate the ears from the background and a Fourier transform to more accurately estimate kernel length. It also corrects for individual kernels clustering together.

New Protein Production Strategy for Plants

UW–Madison researchers have identified a new plant viral IRES that can facilitate the efficient expression of multiple proteins from a single mRNA. The researchers discovered the new IRES in the Triticum mosaic virus (TriMV), a wheat virus that expresses 10 proteins from a single mRNA strand.

Gene Controls Flowering Time in Corn

The researchers now have found a gene in maize that affects flowering time. By modulating this gene, GRMZM2G171650, the onset of flowering in maize may be delayed or accelerated. Standard vector and transgenic methods can be employed to overexpress or suppress the gene, or introduce it into new crop lines.

The gene was identified by studying more than 500 different maize lines. The researchers mapped single nucleotide polymorphisms (SNPs) correlating to early or late flowering traits. A large concentration of such SNPs was located in GRMZM2G171650, a transcription factor on chromosome 3. The gene was of previously unknown function in corn.

Extending Juvenile Stage of Plants for Biofuels and Feedstock

UW–Madison researchers have developed methods for locking plants in a juvenile state by modifying genes related to maturation.

The genes – GRMZM2G362718 or GRMZM2G096016 – have been analyzed by the researchers and shown to influence growth transition in corn. To alter plant development, these genes and their homologs could be knocked out or inhibited by small molecules or biologics. The process could involve additional genes known to affect juvenile to adult growth development.

Increasing Resistance to Soybean Cyst Nematode with Polypeptides

UW–Madison researchers and others have developed methods to increase the expression of polypeptides that help root cells resist SCN. They also have developed ways to detect naturally occurring genetic configurations that may confer improved SCN resistance.

The polypeptides are Glyma18g02580, Glyma18g02590 and Glyma18g2610. Their expression in plants, including soybean, potato, sugar beet and corn, can be increased using strong or tissue-specific promoters or by introducing extra copies of the polynucleotides into cells.

A Method of Modifying Lignin to Improve Biomass Utilization

Wisconsin researchers have developed a method of structurally altering lignin by modifying its monomer complement to allow biomass polysaccharides to be more efficiently and sustainably utilized. The method comprises performing a lignin-producing polymerization reaction in the presence of various gallic acid or flavan-3-ol derivatives. Cell walls containing these modified lignins are inherently more fermentable by rumen microflora and can be more readily delignified by mild pretreatments and enzymatically saccharified to sugars for industrial fermentations.

Late Blight Resistance Gene from Wild Potato

Wisconsin researchers have identified and cloned a gene, known as RBver, from the wild potato species S. verrucosum, which is naturally resistant to P. infestans. When expressed in S. tuberosum, this gene confers late blight resistance on the foliage of the plants.

Peptide Extension for Enhancement of Transgene Expression in Chloroplasts

UW-Madison researchers have developed a method of modifying the chloroplast genome to enable increased expression of a desired protein. The method starts with a peptide extension consisting of two to 50 contiguous amino acids from the amino terminus of the well-expressed chloroplast protein PsbA. A nucleic acid sequence encoding the peptide extension is fused to a gene of interest. When this construct is inserted into the chloroplast genome, the peptide extension increases expression of the target protein.

Singlet Oxygen-Resistant Technologies

UW-Madison researchers have developed a method of altering the response of cells to 1O2 by modulating the interaction between an anti-sigma factor, ChrR, and σE, or by altering the expression of a gene product required for viability in the presence of 1O2. The growth of phototrophic bacteria exposed to 1O2 may be inhibited by administering an anti-sigma agent, such as ChrR, to reduce the availability of σE On the other hand, a bacterium or other organism may be protected from damage from 1O2 by modifying the genes in the σE regulon or by modifying ChrR to alter binding between it and σE.

Vernalization-Related Molecules and Methods for Inducing Permanent Changes in Plant Gene Expression

UW-Madison researchers have identified a novel polypeptide, VIN3, that plays a role in vernalization. During exposure to cold, VIN3 represses FLC, one of the two main genes responsible for flowering in plants. High FLC expression levels inhibit flowering; thus, by repressing FLC, VIN3 helps promote flowering. During vernalization, VIN3 likely represses FLC by hypoacetylating FLC chromatin, triggering histone modifications that result in a stable, repressed heterochromatin state.

This VIN3-mediated process can be applied in other organisms to cause a permanent change in gene expression. The components of the process, including VIN3, can be used to transform a host organism in which a selected gene has been modified to contain certain FLC sequences. These components are preferably under the control of an inducible promoter, which allows the user to trigger at will the development of stable repressed or active chromatin at the target gene. This, in turn, results in an alteration in gene expression that is stable through subsequent plant cell mitotic cycles.

Yeast Genes That Affect Viral Replication

UW-Madison researchers have used their knowledge of essential host genes to offer a promising new way to prevent the replication of positive strand RNA viruses. Through the development of a system in which brome mosaic virus (BMV) is able to replicate in yeast (Saccharomyces cerevisiae), they have discovered that mutations in four novel yeast genes (MAB1, MAB2, MAB3 and OLE1) severely inhibit RNA-dependant RNA replication of BMV. 

The researchers have developed methods for creating virus-resistant organisms that contain mutated MAB1, MAB2, MAB3 and OLE1 transgenes, or transgenes that alter the expression of the MAB and OLE genes. Their discovery also may be used to screen libraries of chemicals for potential antiviral agents that affect the expression, stability and activity of MAB and OLE genes and proteins.

Dominant Gene That Delays Flowering

UW-Madison researchers have developed a powerful tool for delaying flowering in plants, allowing plant breeders to control the growth and development of agriculturally and horticulturally important species. They isolated a gene from Arabidopsis thaliana that when expressed at higher than normal levels causes a substantial delay in flowering. Overexpression of this gene also appears to render the plant insensitive to factors that normally induce flowering, such as treatment with the hormone gibberellin or exposure to flower-promoting light conditions. Tests are underway to introduce this gene into other species.

Dwarfism Genes and Dwarf Plants

UW-Madison researchers have identified the function, cDNA sequences and expressed amino acid sequences of a gene that affects gibberellic acid levels in plants. This dominant gene may be used to alter the height of a plant or to alter the size of a specific plant organ. When over-expressed in a plant, this gene reduced the level of bioactive GA, resulting in a plant that produced the same amount of seed as a wild-type plant, but was more compact.

Floral Induction Gene Affects Flowering Time and Plant Production

UW-Madison researchers have identified an Arabidopsis gene, FPA, which can be manipulated to affect flowering time. An FPA polynucleotide sequence capable of up-regulating or down-regulating FPA activity is introduced into the genome of a plant. Suppression of FPA activity results in delayed flowering, while overexpression of FPA leads to earlier floral induction. This may be used to manage flowering time for optimal flower, fruit and seed production.

Methods for Enhancing Plant Health Using Lysophospholipids

UW-Madison researchers now have discovered that these compounds may also: 1) prevent damage to growing plants and seeds caused by abiotic and biotic stressors, 2) accelerate plant recovery from stress and 3) enhance seed germination and seedling vigor. In a series of experiments, they showed that plants sprayed with a lysophospholipid solution were both protected and recovered more quickly from chilling, drought, wound-damage, pesticide application and microbial infection.

Alteration of Flowering Time in Plants

UW-Madison researchers have developed a unique tool for altering the timing of flowering in plants, allowing plant breeders to control the growth and development of agriculturally and horticulturally important species. The researchers characterized novel genes, the flowering locus C (FLC) gene and relatives of FLC, from Arabidopsis thaliana and Brassica rapa, which play a significant role in the delay of flowering. In experiments with Arabidopsis, genetically modified plants lacking FLC activity or activity of an FLC relative flowered significantly earlier than wild-type. In addition, plants over-expressing the FLC gene or relatives took substantially longer to flower or did not flower at all, and showed large (i.e. 10-fold) increases in biomass.

Cultivar Specificity Gene from the Rice Pathogen Magnaporthe grisea

UW-Madison researchers have cloned a novel avirulence gene from M. grisea, termed AVR1-CO39. This gene encodes a signal that triggers a strong defense response in rice cultivar CO39, which carries the corresponding resistance gene. Open reading frame 3 (ORF 3) of the AVR1-CO39 avirulence gene appears to play a key role in inducing cultivar-specific defense against the pathogen.

Transforming or treating rice cultivar CO39 with the AVR1-CO39 gene or its products may broaden the scope of the cultivar’s resistance to additional M. grisea races/pathotypes and to pathogens other than M. grisea. Also, the resistance gene from cultivar CO39, which must be present in a plant for induction of disease resistance using AVR1-CO39, can be introduced into other susceptible rice cultivars.

Trans-Dominant Inhibition of Geminiviral DNA Replication by Geminivirus Rep Gene Mutants

UW-Madison researchers have developed a genetic construct that when inserted into a plant cell, is able to dramatically reduce replication of geminivirus. The construct contains a plant promoter operably connected to a trans-dominant inhibitor of the geminiviral rep gene. The inhibitor is a mutant rep gene, which expresses a protein that interferes with the wild-type rep gene. The rep gene, which encodes a complex, multifunctional protein that acts as a rolling circle initiator protein, is the only geminiviral gene necessary for viral replication. The construct interferes with the function of the rep gene and inhibits replication of geminivirus in plants.

Measuring Lignin in Corn Stalks

UW–Madison researchers have developed an automated method to scan and analyze corn stalks. The algorithm extracts information about rind thickness, vascular bundles, density and size. The new method uses a flatbed scanner to image samples. The images are acquired as RGB color at a resolution of 800 dpi. Thresholding techniques are used to assess the outer ring boundaries and vasculature.

New Tools for Student Training and Gene Discovery/Trait Improvement in Plants

UW–Madison researchers used a selective breeding program to create a self-compatible (can propagate via self-pollination) analog of a self-incompatible variety of B. rapa.

Seeds of the self-incompatible variety are used by educators in 88 countries around the world (estimated sales ~15 million seeds/year) to provide students with a hands-on, inquiry-based approach to enhance their understanding of plant biology and general biological principles. However, the obligatory outcrossing reproductive habit of existing plants essentially precludes extension of the biology curriculum to the realms of molecular biology and genomics.

The new self-compatible and highly inbred (hence true-breeding) variety circumvents those limitations while providing a familiar classroom model system whose growth habits—compact stature, rapid progression from seed to progeny seeds, vigorous growth with minimal material inputs—are of high value to educators and plant breeders alike.

With the reference strain in hand, UW researchers have developed a suite of derivative lines and genetic/genomic resources that include:
  1. A diverse collection of mutant derivatives whose phenotypes are provocative and clearly distinct from the parental strain, and whose transmission from parental to progeny generations epitomizes fundamental Mendelian genetic principles of inheritance;
  2. PCR-based molecular genetic markers that enable localization and molecular characterization of mutant/variant alleles;
  3. A DNA sequence assembly that describes the nucleotide sequences of the ~40,000 genes encoded by the B. rapa genome;
  4. Several RNA-Seq data sets useful to understand genome-wide patterns of gene expression; and
  5. Advance Intercross Recombinant Inbred Lines with demonstrated utility for identification of B. rapa genes that modify the expression of quantitative genetic traits.

As an integrated collection of resources, this plant model system will be of considerable use to both educators and agricultural biotechnology firms interested in identifying lead gene candidates for enhancement of agronomically important traits.

A Saturating Population of Insertionally Mutagenized Arabidopsis thaliana Plants

UW-Madison researchers have established a large population of Arabidopsis seed lines that have been insertionally mutagenized using T-DNA and are available in very small pools. This collection provides an excellent means of obtaining knockout plants to determine the role of plant genes. The seed collection is comprised of 8000 tubes, each containing seeds from nine independently isolated plants. Each plant line has approximately 1 to 1.4 insertional mutations. The population is three- to four-fold saturated, which confers a greater than 85 percent probability of obtaining a knockout plant for an average gene size of 3-5 kb. This feature also confers a greater than 70 percent chance of getting two or more independent knockout alleles of the same gene.