Method for improved plant breeding

{
  "publication_number": "US8991098B2",
  "country": "US",
  "kind": "B2",
  "title": "Method for improved plant breeding",
  "abstract": "An improved plant breeding system for high throughput analysis of plant phenotype and genotype is provided. A method for analyzing the impact of genetic modifications on plants and selecting a plant with a genetic modification of interest is also provided. Also provided is a method for developing marketable information for improved plant breeding and a method for collecting data on a selected plant phenotype for rapid analysis of the effect of a genetic modification on the selected phenotype.",
  "claims": [
    "1. A method for analyzing the impact of genetic modifications on plants and selecting a plant with a genetic modification of interest, the method comprising: a) providing a plurality of plants growing in one or more containers under controlled environmental conditions, each plant being associated with a machine-readable identification that distinguishes the plant from other plants; b) moving the plants on transport belts in an automated transporter system at one or more intervals during their growing cycle so as to avoid extended exposure to a particular micro-environment, thereby reducing the influence of micro-environment variations on the phenotype of the plants; c) transporting one or more plants at one or more intervals during its growing cycle through an imaging system for imaging of the plant, wherein the imaging system is made to image the plant while the plant is being moved forward continuously through said imaging system and comprises a turning mechanism and an imaging device, and wherein the turning mechanism turns the plant or the imaging device in a controlled manner; d) imaging one or more characteristic of the plant while the plant is being moved forward through the imaging system; e) analyzing the images for the one or more characteristic of the plant by computer processing and associating the resulting information with the machine-readable identification information for the plant; f) analyzing the resulting information for the one or more characteristic of the one or more plant to determine the impact of the genetic modification; and g) either selecting one or more plants with a genetic modification of interest or communicating information from analyzing steps e) and/or f) to others for selecting one or more plants with a genetic modification of interest.",
    "2. The method of claim 1, where the turning mechanism comprises time-belts, wherein the time-belts and/or the containers are coated with a high friction material.",
    "3. The method of claim 2, wherein the time-belts are positioned in order to grip sides of the container.",
    "4. The method of claim 2, wherein the time-belts have different speed settings allowing the container to turn in a controlled way while being transported over the transport belts.",
    "5. The method of claim 2, where the position of a container containing a plant is detected by sensors which trigger the action of the imaging system.",
    "6. The method of claim 1, wherein the imaging system comprises one or more high speed and/or high resolution cameras.",
    "7. The method of claim 6, wherein the camera is capable of taking high resolution pictures within 75 milliseconds.",
    "8. The method of claim 1, wherein the one or more characteristic comprises one or more of an observable physical manifestation of the plant, color, greenness, yield, growth, biomass, maturity, flowering, nutrient use, water use, or effects of disease, pests, and/or stress.",
    "9. The method of claim 1, the one or more characteristic comprises one or more of leaf area, height, width, leaf angle, number of leaves, presence and/or number of inflorescences, number of shoots, and branching pattern.",
    "10. The method of claim 1, wherein the one or more plants comprises one or more transgenic plants.",
    "11. The method of claim 1, wherein the one or more plants is selected for further use in a plant breeding or advancement experiment or for introducing further modifications.",
    "12. The method of claim 1, wherein the images and/or information are taken of above ground plant parts and/or of plant roots.",
    "13. The method of claim 12, wherein the above ground plant parts comprise shoots, leaves, tillers, inflorescence, flowers, seed, or any combination thereof.",
    "14. The method of claim 1, further comprising processing seed from the plant obtained from step g) or processing seed in preparation for growing a transgenic plant with a seed dehulling device comprising a recipient-block combination each having a flat surface with high friction on which the seeds are put, where either recipient or block is moved under pressure, in such a way to release the hulls and to minimize damage to the seeds.",
    "15. The method of claim 14, wherein the speed of movement of recipient or block and pressure are regulated or controlled automatically.",
    "16. The method of claim 14, wherein the movement of the recipient or block comprises rotating, rolling, or rubbing.",
    "17. The method of claim 14, wherein the seeds comprise oblong seeds.",
    "18. The method of claim 14, wherein the seeds are automatically transported to or from the seed dehulling device.",
    "19. The method of claim 14, wherein the seeds and hulls are transported from the dehulling device to a system to separate seeds from hulls in an automatic way.",
    "20. The method of claim 19, further comprising counting, imaging, and/or evaluating physical and/or biochemical parameters of the seed.",
    "21. The method of claim 20, wherein the counting, imaging, and/or evaluating of the seed is done in an automatic way.",
    "22. The method of claim 14, wherein after the seeds and hulls are removed from the seed dehulling device, the recipient and block are inspected visually or with an imaging device to ensure that no seeds remain to prevent cross-contamination between batches of seed.",
    "23. The method of claim 1, further comprising extracting DNA from seed, plants, or plant parts, from the plant obtained from step g) or in preparation for growing a transgenic plants utilizing a modified sample extraction system comprising a double seal vial system comprising one or more of a first cap comprising a pierceable slit and one or more of a second cap which fits inside the first cap.",
    "24. The method of claim 1, further comprising isolating DNA from seed, plants, or plant parts, from the plant obtained from step g) or in preparation for growing a transgenic plants utilizing a double magnet in a modified bead mediated extraction system comprising magnetic beads which are capable of binding to a molecular compound, a first magnet positioned inside a reaction vial lid, and a second magnet positioned below the reaction vial.",
    "25. A method for developing marketable information for improved plant breeding, the method comprising: (a) providing a plurality of plants growing under controlled environmental conditions, each plant being associated with a machine-readable identification that distinguishes the plant from other plants; (b) reducing the influence of micro-environment variations on the phenotype of the plants by moving the plants in an automated transporter system at one or more intervals during their growing cycle so as to avoid extended exposure to a particular micro-environment, thereby; (c) continuously transporting one or more plants at one or more intervals during its growing cycle through an imaging system containing a turning mechanism for turning the plant or the imaging device in a controlled manner; (d) taking images of one or more characteristic of the plant while the plant is being moved forward continuously through the imaging system and storing the images on a computer or processing device; (e) analyzing the images for the one or more characteristic of the plant by computer processing and associating the resulting information with the machine-readable identification information for the plant; and (f) analyzing the resulting information for the one or more characteristic of the one or more plant, wherein the images and/or resulting information provide marketable information for making decisions on plant identification and/or selection in a plant breeding system, and wherein said imaging system is made to image the plant while the plant is being moved forward continuously through said imaging system.",
    "26. A method for collecting data on a selected plant phenotype for rapid analysis of the effect of a genetic modification on the selected phenotype, the method comprising: (a) providing a plurality of plants growing under controlled environmental conditions, each plant being associated with a machine-readable identification that distinguishes the plant from other plants; (b) reducing the influence of micro-environment variations on the phenotype of the plants by moving the plants in an automated transporter system at one or more intervals during their growing cycle so as to avoid extended exposure to a particular micro-environment, thereby; (c) continuously transporting one or more plants at one or more intervals during its growing cycle through an imaging system containing a turning mechanism for turning the plant or the imaging device in a controlled manner; (d) taking images of one or more characteristic of the plant while the plant is being moved forward continuously through the imaging system and storing the images on a computer or processing device; (e) analyzing the images for the one or more characteristic of the plant by computer processing and associating the resulting information with the machine-readable identification information for the plant; and (f) analyzing the resulting information for the one or more characteristic of the one or more plant; and (g) collecting the information from steps e) and/or f) on a selected plant phenotype for rapid analysis of the effect of a genetic modification on the selected phenotype, wherein said imaging system is made to image the plant while the plant is being moved forward continuously through said imaging system."
  ],
  "description_excerpt": "The invention relates generally to an improved plant breeding system. More particularly, this invention relates to a method for automated, high throughput analysis of plant phenotype and plant genotype in a breeding program.\n\nPlant breeding programs require analyses of phenotypes for a large number of plants. These analyses involve measurement of a wide array of plant characteristics including plant morphology, disease and environmental stress tolerance, seed quality, and yield. In addition to the evaluation of phenotype, breeding programs often necessitate determination of genotype, for example, to identify a DNA marker associated with a specific phenotype or to confirm the presence of a transgene in a transgenic plant. Therefore extraction of plant genomic DNA may also be necessary. Traditionally, analysis of phenotype in a breeding program has been conducted through visual evaluation and manual measurement of morphological characteristics. However, due to the large number of plants that must be evaluated and to the small differences when plants are evaluated early, this process is extremely time consuming, thus limiting the number of plants that can be analyzed. Initial attempts have been made to automate this process by developing evaluation methods for the model plant Arabidopsis thaliana. For example, Granier et al. describe a system composed of steel frame supporting trays with holes to support pots and a mechanical arm able to move according to a software program (Granier et al., 2002, New Phytologist 169: 623-635).",
  "cpc": [
    "A01H 1/04",
    "A01C 1/00",
    "A01G 9/02",
    "B65G 15/005",
    "B65G 15/14",
    "B65G 43/00",
    "C12N 15/1013",
    "G05B 15/02",
    "G06T 2207/30188",
    "G06T 7/0012"
  ],
  "ipc": [
    "A01G 31/02",
    "A01H 1/04",
    "B65G 15/00",
    "B65G 15/14"
  ],
  "assignees": [
    "LEJEUNE PIERRE",
    "LEYNS FREDERIK",
    "VANDAELE CEDRICK",
    "VAN CAENEGHEM WIM",
    "BASF PLANT SCIENCE GMBH"
  ],
  "inventors": [
    "LEJEUNE PIERRE",
    "LEYNS FREDERIK",
    "VANDAELE CEDRICK",
    "VAN CAENEGHEM WIM"
  ],
  "filing_date": "2009-09-16",
  "publication_date": "2015-03-31",
  "grant_date": "2015-03-31",
  "priority_date": "2008-09-16",
  "application_number": "US-200913063217-A",
  "family_id": "41350628",
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