Source: http://www.google.com/patents/US7832143?dq=Xerox+%2B+%22centroid
Timestamp: 2014-08-23 04:41:53
Document Index: 346491337

Matched Legal Cases: ['Application No. 61', 'Application No. 60', 'Application No. 60', 'Application No. 60', 'Application No. 61', 'Application No. 60', 'Application No. 60', 'Application No. 60']

Patent US7832143 - High throughput methods for sampling seeds - Google PatentsSearch Images Maps Play YouTube News Gmail Drive More »Sign in<nobr>Advanced Patent Search</nobr>PatentsA high-throughput method is provided for analyzing individual seeds in a population of seeds. The method generally includes removing a tissue sample from at least one or more seeds in the population of seeds while preserving germination viability of the at least one or more seeds from which the tissue...http://www.google.com/patents/US7832143?utm_source=gb-gplus-sharePatent US7832143 - High throughput methods for sampling seedsAdvanced Patent SearchPublication numberUS7832143 B2Publication typeGrantApplication numberUS 12/358,985Publication dateNov 16, 2010Filing dateJan 23, 2009Priority dateAug 26, 2004Fee statusPaidAlso published asUS20090215060Publication number12358985, 358985, US 7832143 B2, US 7832143B2, US-B2-7832143, US7832143 B2, US7832143B2InventorsKevin L. Deppermann, Michael W. Petersen, Allen T. Christian, James J. Schaefer, Chad Allen StendalOriginal AssigneeMonsanto Technology LlcExport CitationBiBTeX, EndNote, RefManPatent Citations (103), Non-Patent Citations (63), Referenced by (15), Classifications (16), Legal Events (4) External Links: USPTO, USPTO Assignment, EspacenetHigh throughput methods for sampling seedsUS 7832143 B2Abstract A high-throughput method is provided for analyzing individual seeds in a population of seeds. The method generally includes removing a tissue sample from at least one or more seeds in the population of seeds while preserving germination viability of the at least one or more seeds from which the tissue sample is taken, depositing the tissue sample into an individual compartment of a sample tray, contacting the tissue sample with an extraction buffer to remove DNA from the sample, and analyzing the extracted DNA for the presence or absence of a transgene of interest. The extraction buffer may be present in the individual compartment of the sample tray before the tissue sample is deposited into the individual compartment.
1. A high-throughput method for analyzing individual seeds in a population of seeds, the method comprising:
removing a tissue sample from at least one or more seeds in a population of seeds while preserving germination viability of the at least one or more seeds from which the tissue sample is removed;
depositing the tissue sample into an individual compartment of a sample tray;
contacting the tissue sample with an extraction buffer to remove DNA from the tissue sample; and
analyzing the extracted DNA for the presence or absence of a transgene of interest.
2. The method as set forth in claim 1, wherein the extraction buffer is present in the individual compartment of the sample tray before depositing the tissue sample into the individual compartment of the sample tray.
3. The method as set forth in claim 1, further comprising adding the extraction buffer to at least one or more compartments of the sample tray before depositing the tissue sample into an individual compartment of the sample tray.
4. The method as set forth in claim 3, wherein depositing the tissue sample into a compartment of the sample tray includes depositing the tissue sample into a compartment of the sample tray having extraction buffer within said compartment for contacting the tissue sample.
5. The method as set forth in claim 1, wherein the sample tray comprises a 384-well microtiter plate.
6. The method as set forth in claim 1, further comprising generally sealing said compartment of the sample tray after the tissue sample is deposited in said compartment and storing the tissue sample prior to analyzing the extracted DNA.
7. The method as set forth in claim 6, wherein storing the tissue sample includes cooling the tissue sample to at least about −80 degrees Celsius.
8. The method as set forth in claim 1, further comprising selecting at least one or more individual seeds from the population of seeds based on the results of the analysis; and cultivating at least one or more plants from the at least one or more selected seeds.
9. The method as set forth in claim 1, wherein the population of seeds includes seeds selected from the group consisting of alfalfa seed, apple seed, banana seed, barley seed, bean seed, broccoli seed, cabbage seed, carrot seed, cauliflower seed, celery seed, castor bean seed, citrus seed, clover seed, coconut seed, coffee seed, maize seed, cotton seed, cucumber seed, Douglas fir seed, eggplant seed, Eucalyptus seed, Loblolly pine seed, linseed seed, lettuce seed, melon seed, millet seed, oat seed, olive seed, palm seed, pea seed, peanut seed, pepper seed, poplar seed, pumpkin seed, Radiata pine seed, radish seed, rapeseed seed, rice seed, rye seed, spinach seed, sorghum seed, Southern pine seed, soybean seed, squash seed, strawberry seed, sugarbeet seed, sugarcane seed, sunflower seed, sweetgum seed, switchgrass seed, tea seed, tobacco seed, tomato seed, triticale seed, turf seed, watermelon seed, wheat seed, and Arabidopsis thaliana a seed.
10. The method as set forth in claim 1, wherein removing the tissue sample from at least one or more seeds in a population of seeds and depositing the tissue sample into an individual compartment of a sample tray are done by an automated seed sampler system.
11. The method of claim 1, further comprising removing a tissue sample from each seed in a population of seeds and depositing each tissue sample into an individual compartment of a sample tray having an extraction buffer present therein using an automated system; and analyzing the extracted DNA from each tissue sample for the presence or absence of a transgene of interest. Description
CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No. 61/023,765, filed Jan. 25, 2008. This application is also a continuation-in-part of U.S. patent application Ser. No. 11/680,611, filed Feb. 28, 2007, which claims priority to U.S. Provisional Application No. 60/778,828, filed on Mar. 2, 2006, and which is a continuation-in-part of U.S. patent application Ser. No. 11/213,435, filed on Aug. 26, 2005, claiming priority from U.S. Provisional Application No. 60/604,604, filed on Aug. 26, 2004 and U.S. Provisional Application No. 60/691,100, filed on Jun. 15, 2005. The entire disclosures of U.S. patent application Ser. No. 11/680,611, U.S. patent application Ser. No. 11/213,435, U.S. Provisional Application No. 61/023,765, U.S. Provisional Application No. 60/778,828, U.S. Provisional Application No. 60/604,604, and U.S. Provisional Application No. 60/691,100 are incorporated herein by reference in their entirety.
FIELD The present disclosure relates generally to the field of plant breeding. More specifically, this disclosure provides methods for augmenting and economizing germplasm improvement activities using high throughput and nondestructive seed sampling techniques.
Apparatus and methods for the high-throughput, non-destructive sampling of seeds have been described which would overcome the obstacles of statistical samples by allowing for individual seed analysis. For example, U.S. patent application Ser. No. 11/213,430 (filed Aug. 26, 2005); U.S. patent application Ser. No. 11/213,431 (filed Aug. 26, 2005); U.S. patent application Ser. No. 11/213,432 (filed Aug. 26, 2005); U.S. patent application Ser. No. 11/213,434 (filed Aug. 26, 2005); U.S. patent application Ser. No. 11/213,435 (filed Aug. 26, 2005); and U.S. patent application Ser. No. 11/680,180 (filed Feb. 28, 2007), which are incorporated herein by reference in their entirety, disclose apparatus and systems for the automated sampling of seeds as well as methods of sampling, testing and bulking seeds.
The present disclosure addresses needs in the art for improved breeding methods using high-throughput, non-destructive seed sampling systems.
The present disclosure relates generally to high-throughput methods for analyzing individual seeds in populations of seeds. In one example embodiment, a method generally includes removing a tissue sample from at least one or more seeds in a population of seeds while preserving germination viability of the at least one or more seeds from which the tissue sample is removed, depositing the tissue sample into an individual compartment of a sample tray, contacting the tissue sample with an extraction buffer to remove DNA from the tissue sample, and analyzing the extracted DNA for the presence or absence of a transgene of interest.
The terminology used herein is for the purpose of describing particular example embodiments only and is not intended to be limiting. As used herein, the singular forms �a�, �an� and �the� may be intended to include the plural forms as well, unless the context clearly indicates otherwise. The terms �comprises,� �comprising,� �including,� and �having,� are inclusive and therefore specify the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof. The method steps, processes, and operations described herein are not to be construed as necessarily requiring their performance in the particular order discussed or illustrated, unless specifically identified as an order of performance. It is also to be understood that additional or alternative steps may be employed. As used herein, the term �and/or� includes any and all combinations of one or more of the associated listed items.
The present disclosure provides for novel methods to facilitate germplasm improvement activities through the use of high throughput, nondestructive sampling of seeds. The methods are useful in analyzing seeds in order to identify and select seeds comprising one or more desired traits, markers, and/or genotypes. In one aspect of the disclosure, the analytical methods allow individual seeds that are present in a batch or a bulk population of seeds to be analyzed such that the chemical and/or genetic characteristics of the individual seeds can be determined.
Samples prepared by the present disclosure can be used for determining a wide variety of physical, morphological, chemical and/or genetic traits. Generally, such traits are determined by analyzing the samples for one or more characteristics indicative of at least one genetic or chemical trait. Non-limiting examples of characteristics indicative of chemical traits include, for example, proteins, oils, carbohydrates, fatty acids, amino acids, biopolymers, pharmaceuticals, starch, fermentable starch, secondary compounds, metabolites, etc. Accordingly, non-limiting examples of chemical traits include, for example, amino acid content, protein content, starch content, fermentation yield, fermentation efficiency, energy yield, oil content, determination of protein profiles determination of fatty acid profiles, determination of metabolite profiles, etc.
Non-limiting examples of characteristics indicative of genetic traits may include, for example, genetic markers, single nucleotide polymorphisms, simple sequence repeats, restriction fragment length polymorphisms, haplotypes, tag SNPs, alleles of genetic markers, genes, DNA-derived sequences, RNA-derived sequences, promoters, 5′ untranslated regions of genes, 3′ untranslated regions of genes, microRNA, siRNA, quantitative trait loci (QTL), satellite markers, transgenes, mRNA, ds mRNA, transcriptional profiles, methylation patterns, etc.
In another embodiment, the methods of the present disclosure use high throughput, nondestructive seed sampling with doubled haploid technologies to contribute to germplasm improvement activities including, for example, economization of doubled haploid programs by selecting only preferred seed for doubling, high throughput analysis of haploid and doubled haploid material for both genotypic and chemical characteristics, trait integration and evaluation, marker-assisted breeding, etc.
The methods and devices of the present disclosure can be used in a breeding program to select plants or seeds having a desired genetic and/or chemical trait, wherein a desired genetic trait comprises, for example, at least one or more of a genotype, a haplotype, an allele, a sequence, a transgene, a transcript profile, a methylation pattern, etc. The methods of the present disclosure can be used in combination with any breeding methodology and can be used to select a single generation or to select multiple generations. The choice of breeding method depends on the mode of plant reproduction, the heritability of the trait(s) being improved, and/or the type of cultivar used commercially (e.g., F1 hybrid cultivar, pureline cultivar, etc). Selected, non-limiting approaches for breeding the plants of the present disclosure are set forth below. It is further understood that any commercial and non-commercial cultivars can be utilized in a breeding program. Factors including, for example, without limitation, emergence vigor, vegetative vigor, stress tolerance, disease resistance, branching, flowering, seed set, seed size, seed density, standability, threshability, etc. will generally dictate the choice.
In a particular embodiment, the methods of the present disclosure are used to determine the genetic characteristics of seeds in a marker-assisted breeding program. Such methods allow for improved marker-assisted breeding programs wherein nondestructive direct seed sampling can be conducted while maintaining the identity of individual seeds from the seed sampler to the field. As a result, the marker-assisted breeding program results in a �high-throughput� and more efficient platform wherein a population of seeds having a desired trait, marker or genotype can be more effectively bulked in a shorter period of time, with less field and labor resources required. Such advantages will be more fully described below.
In one embodiment, the present disclosure provides a method for analyzing individual seeds within a population of seeds having genetic differences. The method comprises removing a sample comprising cells with nucleic acids from seeds in the population without affecting the germination viability of the seeds; analyzing the nucleic acids extracted from the sample for the presence or absence of at least one genetic marker; selecting seeds from the population based upon the results of the nucleic acid analysis; and cultivating plants from the selected seed.
As described above, the sampling systems and methods of this disclosure protect germination viability of the seeds so as to be non-destructive. Germination viability means that a predominant number of sampled seeds, (i.e., greater than about 50% of all sampled seeds) remain viable after sampling. In a particular embodiment, at least about 75% of sampled seeds, and in some embodiments at least about 85% of sampled seeds remain viable. It should be noted that lower rates of germination viability may be tolerable under certain circumstances or for certain applications, for example, as genotyping costs decrease with time because a greater number of seeds could be sampled for the same genotype cost. It should also be noted that sampling does not need to have any effect on viability at all.
In another embodiment, germination viability is maintained for at least about six months after sampling to ensure that the sampled seed will be viable until it reaches the field for planting. In a particular embodiment, the methods of the present disclosure further comprise treating the sampled seeds to maintain germination viability. Such treatment may generally include any means known in the art for protecting a seed from environmental conditions while in storage or transport. For example, in one embodiment, the sampled seeds may be treated with a polymer and/or a fungicide to protect the sampled seed while in storage or in transport to the field before planting.
In one embodiment, the samples of the present disclosure are used in a high-throughput, non-destructive method for analyzing individual seeds in a population of seeds. For example, the method comprises removing a sample from a seed while preserving the germination viability of the seed; and analyzing the sample for the presence or absence of one or more characteristics indicative of a genetic or chemical trait. The method may further comprise selecting seeds from the population based on the results of the analysis; and cultivating plants or plant tissue from the selected seed.
DNA may be extracted from the sample using any DNA extraction methods known to those of skill in the art which will provide sufficient DNA yield, DNA quality, PCR response, sequencing methods response, etc. A non-limiting example of suitable DNA-extraction methods is SDS-based extraction with centrifugation. In addition, the extracted DNA may be amplified after extraction using any amplification method known to those skilled in the art. For example, one suitable amplification method is the GenomiPhi� DNA amplification prep from Amersham Biosciences.
Further, RNA may be extracted from the sample using any RNA extraction methods known to those of skill in the art which will provide sufficient RNA yield, RNA quality, PCR response, sequencing methods response, etc. A non-limiting example of suitable RNA-extraction methods is SDS-based extraction with centrifugation with consideration for RNase-free reagents and supplies. In addition, the extracted RNA may be amplified after extraction using any amplification method known to those skilled in the art. For example, one suitable amplification method is the Full Spectrum� RNA Amplification from System Biosciences.
The extracted nucleic acids are analyzed for the presence or absence of a suitable genetic polymorphism. A wide variety of genetic markers for the analysis of genetic polymorphisms are available and known to those of skill in the art. As used herein, genetic markers include, but are not limited to, simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), insertions or deletions (Indels), single feature polymorphisms (SFPs, for example, as described in Borevitz et al. 2003 Gen. Res. 13:513-523) or transcriptional profiles, nucleic acid sequences, etc. A nucleic acid analysis for the presence or absence of the genetic marker can be used for the selection of seeds in a breeding population. The analysis may be used to select for genes, QTL, alleles, genomic regions (haplotypes) that comprise or are linked to a genetic marker, etc. Herein, analysis methods are known in the art and include, but are not limited to, PCR-based detection methods (for example, TaqMan assays), microarray methods, nucleic acid sequencing methods, etc. The genes, alleles, QTL, and/or haplotypes to be selected for can be identified using newer techniques of molecular biology with modifications of classical breeding strategies.
In one embodiment, the method of the present disclosure generally comprises sampling transgenic seeds to test for the presence or absence of a transgene or the zygosity of a transgene (number of transgenes) in a population of seeds in a high throughput manner. The method generally comprises automatically removing a tissue sample from at least one or more seeds in a population of seeds using an automated seed sampler system, for example, such as described in U.S. patent application Ser. No. 11/213,435 (Publication No. US2006/004624), which is incorporated by reference herein in its entirety. The tissue sample can be removed from the at least one or more seeds such that germination viability of the at least one or more seeds is generally preserved. The automated sampler system places each tissue sample from the at least one or more seeds into individual compartments of a multi-compartment sample tray, for example, such as a 384-well microplate known to those of skill in the art, etc. Once each tissue sample has been taken from the at least one or more individual seeds, at least one or more of DNA, RNA, carbohydrate, oil, and protein can be extracted (e.g., using extraction buffers, etc.) from the sample in the sample tray using standard methods known to those skilled in the art. For example, when testing for the presence or absence of a transgene of interest, DNA is extracted from each tissue sample.
In a preferred embodiment, the automated seed sampler system is operable to deposit removed tissue samples into individual compartments of the sample tray wherein extraction buffer is already present within the sample tray compartments. Thus, the deposited tissue sample is deposited directly into the extraction buffer within the sample compartment. Depositing the tissue samples directly into the extraction buffer may be advantageous wherein the samples are stored before being assayed such that upon testing, the samples are already in extraction buffer solution. Further, depositing the tissue samples directly into the extraction buffer may allow for more complete capture of the tissue sample, etc.
The handling of sample trays and extraction of DNA from samples may further be accomplished in a high throughput manner by utilizing robotic arms on a freely configurable work table including incubators, shakers, centrifuges, etc. in addition to standard lab equipment. Various liquid handling tools equipped with one or more pipetting tips are used for liquid transfer. The automated components of the work table, robotic arms, the liquid handling tools, etc. are controlled by software via a computer. The automation provides cost savings on material, labor, and time and improved consistency of DNA yield and accuracy of the assay. The seeds can be tested for a gene of interest, e.g., a transgene for a trait and selected for further product development quickly. The method also eliminates the need to grow out plants from seeds in green houses and/or field plots for testing thereby further reducing the cost of product development.
The high throughput manner of the example methods of the present disclosure allows for multiple seeds to be analyzed in relatively short periods of time.
Any seed can be utilized in a method or device of the present disclosure. In a particular embodiment, the seed is selected from the group consisting of alfalfa seed, apple seed, banana seed, barley seed, bean seed, broccoli seed, cabbage seed, carrot seed, cauliflower seed, celery seed, castor bean seed, citrus seed, clover seed, coconut seed, coffee seed, maize seed, cotton seed, cucumber seed, Douglas fir seed, eggplant seed, Eucalyptus seed, Loblolly pine seed, linseed seed, lettuce seed, melon seed, millet seed, oat seed, olive seed, palm seed, pea seed, peanut seed, pepper seed, poplar seed, pumpkin seed, Radiata pine seed, radish seed, rapeseed seed, rice seed, rye seed, spinach seed, sorghum seed, Southern pine seed, soybean seed, squash seed, strawberry seed, sugarbeet seed, sugarcane seed, sunflower seed, sweetgum seed, switchgrass seed, tea seed, tobacco seed, tomato seed, triticale seed, turf seed, watermelon seed, wheat seed, and Arabidopsis thaliana seed. In a more particular embodiment, the seed is selected from the group consisting of cotton seed, cucumber seed, maize seed, melon seed, soybean seed, rapeseed seed, rice seed and wheat seed. In an even more particular embodiment, the seed is a maize seed or a soybean seed.
In another embodiment, crops analyzed by the methods described herein include forage crops, oilseed crops, grain crops, fruit crops, ornamental plants, vegetable crops, fiber crops, spice crops, nut crops, turf crops, sugar crops, beverage crops, tuber crops, root crops, forest crops, etc.
In one embodiment, the seed is selected based on the presence or absence of one or more characteristics that are genetically linked with a trait or QTL. Examples of traits or QTLs which are often of interest include but are not limited to herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, increased nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal, or a combination of traits as a multiple trait index. Alternatively, the seed can be selected based on the presence or absence of one or more characteristics that are genetically linked with a haplotype associated with a trait or QTL. Examples of such trait or QTL may again include without limitation herbicide tolerance, disease resistance, insect or pest resistance, altered fatty acid, protein or carbohydrate metabolism, increased grain yield, increased oil, increased nutritional content, increased growth rates, enhanced stress tolerance, preferred maturity, enhanced organoleptic properties, altered morphological characteristics, other agronomic traits, traits for industrial uses, or traits for improved consumer appeal, or a combination of traits as a multiple trait index, etc.
Selection of a breeding population could be initiated as early as the F2 breeding level, if homozygous inbred parents are used in the initial breeding cross. An F1 generation could also be sampled and advanced if one or more of the parents of the cross are heterozygous for the alleles or markers of interest. The breeder may analyze an F2 population to retrieve the marker genotype of every individual in the population. Initial population sizes, limited only by the number of available seeds for analysis, can be adjusted to meet the desired probability of successfully identifying the desired number of individuals. See Sedcole, J. R. (incorporated by reference herein in its entirety). �Number of plants necessary to recover a trait.� Crop Sci. 17:667-68 (1977) (incorporated by reference herein in its entirety). Accordingly, the probability of finding the desired genotype, the initial population size, and the targeted resulting population size can be modified for various breeding methodologies and inbreeding level of the sampled population.
Advantages of using the methods of this disclosure include, without limitation, reduction of labor and field resources required per population or breeding line, increased capacity to evaluate a larger number of breeding populations per field unit, and increased capacity to analyze breeding populations for desired traits prior to planting. Field resources per population are reduced by limiting the field space required to advance the desired genotypes. For example, a population of 1,000 individuals may be planted at 25 seeds per row consuming a total of 40 rows in the field. Using conventional tissue sampling, all 1,000 plants would be tagged and manually sampled by scoring leaf tissue. Molecular marker results would be needed prior to pollination and only those plants containing the desired genetic composition would be pollinated. Thus, if it was determined that 50 seeds contained the desired genetic composition, conventional breeding methodology would have required the planting of 1000 plants to retain the desired 50 seeds. By contrast, the methods of this disclosure allow the breeder to analyze the 1,000 seeds in the lab and select the 50 desired seeds prior to planting. The 50 individuals can then be planted in the field, consuming only two 25 seed rows. Additionally, the methods of this disclosure do not require tagging or sampling in the field, thereby significantly reducing the required manual labor resources.
In addition to reducing the number of field rows per population, the methods of this disclosure may further increase the number of populations the breeder can evaluate in a given breeding nursery. Using the above example wherein 50 seeds out of each population of 1000 seeds contained the desired genetic composition, a breeder applying the methods of this disclosure could evaluate 20 populations of 50 seeds each using the same field area consumed by a single population using conventional field tissue sampling techniques. Even if the populations are selected for a single allele, using a 1:2:1 expected segregation ratio for an F2 population, the breeder could evaluate 4 populations in the same field area as a single field tissue sampled population.
A potential further advantage to the methods of the present disclosure is the mitigation of risks associated with growing plants in certain geographies where plants may grow poorly or experience poor environmental conditions, or may even be destroyed during storms. For example, seeds with the �best� genotype or marker composition could be planted in geography 1 and seeds with the �next best� genotype could be planted in geography 2. In this case geography 2 would be a backup in case any problem befell the plants grown in geography 1. This is very difficult to do with the traditional method of taking tissue samples from germinated plants for genotyping, because these plants would then need to be uprooted and transplanted to the second geography. Using the methods of this disclosure avoids the problem of transplantation and also simplifies the logistics of the breeding program.
The methods of the disclosure may further be used in a breeding program for introgressing a trait into a plant. Such methods comprise removing a sample comprising cells with nucleic acids from seeds in a population, analyzing the nucleic acids extracted from each seed for the presence or absence of at least one genetic marker, selecting seeds from the population based upon the results of the nucleic acids analysis; cultivating a fertile plant from the seed; and utilizing the fertile plant as either a female parent or male parent in a cross with another plant.
The identification of high recurrent pair allele frequencies via the methods of the present disclosure again allows for a reduced number of rows per population and an increased number of populations, or inbred lines, to be planted in a given field unit. Thus, the methods of the present disclosure may also effectively reduce the resources required to complete the conversion of inbred lines.
The methods of the present disclosure further provide quality assurance (QA) and quality control (QC) by assuring that regulated or unwanted transgenes, undesirable genetic traits, or undesirable inherited phenotypes are identified and discarded prior to planting. This application in a QA capacity could effectively eliminate unintentional release infractions. A further extension of the method is to screen for the presence of infectious agents and remove contaminated seed prior to shipping.
The methods of the present disclosure may be further applied to identify hybrid seed for transgene testing. For example, in a conversion of an inbred line at the BCnF1 stage, a breeder could effectively create a hybrid seed lot (barring gamete selection) that was 50% hemizygous for the trait of interest and 50% homozygous for the lack of the trait in order to generate hybrid seed for testing. The breeder could then analyze all F1 seeds produced in the test cross and identify and select those seeds that were hemizygous. Such method is advantageous in that inferences from the hybrid trials would represent commercial hybrid genetics with regard to trait zygosity.
Other applications of the methods of this disclosure for identifying, tracking, and stacking traits of interest carry the same advantages identified above with respect to required field and labor resources. Generally, transgenic conversion programs are executed in multi-season locations which carry a much higher land and management cost structure. As such, the impact of either reducing the row needs per population or increasing the number of populations within a given field unit are significantly more dramatic on a cost basis versus temperate applications.
The methods of this disclosure may be used for seeds from plants with two or more transgenes, wherein accumulating or stacking of transgenic regions into plants or lines is achieved by addition of transgenes by transformation, or by crossing parent plants or lines containing different transgenic regions, or any combination of these. Analyses can be conducted to select individual seeds on the basis of the presence of one or more characteristics associated with at least one transgene. Such characteristics include, but are not limited to, a transgene per se, a genetic marker linked to a transgene, mRNA expressed from a transgene, and a protein product of a transgene.
Still further, the methods of this disclosure may be used to improve the efficiency of the doubled haploid program through selection of desired genotypes at the haploid stage and identification of ploidy level to eliminate non-haploid seeds from being processed and advancing to the field. Both applications again result in the reduction of field resources per population and the capability to evaluate a larger number of populations within a given field unit.
However, processes for producing DH seed generally suffer from low efficacy even though methods have been developed in an attempt to increase DH production frequency, including treatment with colchicine. Outstanding issues include low production of haploid seed, reduced gamete viability resulting in diminished self-pollination for DH plant generation, and inadequate DH seed yield for breeding applications.
The methods of the present disclosure represent an advance in breeding applications by facilitating the potential for selection at the haploid as well as the diploid seed stage. For example, in one embodiment, the disclosure provides for the high-throughput analysis of a population of haploid seed. The method generally comprises non-destructively removing a sample from a plurality of seeds in the population and analyzing the sample for the presence of one or more characteristics indicative of at least one genetic or chemical trait as described herein.
In another embodiment, the disclosure provides for the high-throughput bulking of a population of doubled haploid seeds. The method comprises selecting one or more individual seeds exhibiting at least one preferred characteristic from a population of haploid seeds and producing a population of doubled haploid seeds from the selected seeds. Each doubled haploid seed is then non-destructively sampled and the samples are analyzed for the presence or absence of one or more characteristics indicative of at least one genetic or chemical trait. Based on the results of the analysis, one or more individual doubled haploid seeds are selected and plants or plant tissue is cultivated from the selected doubled haploid seeds.
In various embodiments, the methods of the disclosure include analyzing seed for one or more characteristics, such as genetic markers, to determine whether the seed is in a haploid or diploid state. The present disclosure also provides a methods for analyzing haploid and doubled haploid seed for one or more characteristics, such as transgenes or markers linked to or diagnostic of transgenes, for characteristics related to event performance, event evaluation, and trait integration. Further, the present disclosure provides a method to assay haploid seed in order to select preferred genotypic and phenotypic classes to undergo doubling.
In another embodiment, the present disclosure provides a basis for determination of linkage phase. By using seed endosperm tissue derived from a diploid plant, the parental marker haplotypes can be determined using a genotyping system that enables detection of different allele frequencies in DNA samples. Since endosperm tissue is triploid, with two copies derived from the female gamete, the linkage phase of the parental line can be derived by dissecting heterozygous progeny genotypes (see FIG. 1). The DNA sample from endosperm tissue allows for a determination of the ploidy level of the genetic marker. A diploid ploidy level in the genetic marker indicates maternal inheritance and a haploid ploidy level in the genetic marker indicates paternal inheritance.
Further, differential allele frequency data can be used to infer the genetic linkage map but, unlike methods requiring haploid material (Gasbarra et al. 2006 Genetics 172:1325-1335 (incorporated by reference herein in its entirety)), using the above-described allele frequency calling. Determination of the genetic linkage map has tremendous utility in the context of haplotype characterization, mapping of marker (or haplotype)�trait associations. This method is particularly robust on a single, vs. bulked, seed basis and is thus well-suited to the present disclosure.
In a particular embodiment, the disclosure further provides an assay for predicting embryo zygosity for a particular gene of interest (GOI). The assay predicts embryo zygosity based on the ratio of the relative copy numbers of a GOI and of an internal control (IC) gene per cell or per genome. Generally, this assay uses an IC gene that is of known zygosity, e.g., homozygous at the locus (two IC copies per diploid cell), for normalizing measurement of the GOI. The ratio of the relative copy numbers of the IC to the GOI predicts the GOI copy number in the cell. In a homozygous cell, for any given gene (or unique genetic sequence), the gene copy number is equal to the cell's ploidy level since the sequence is present at the same locus in all homologous chromosomes. When a cell is heterozygous for a particular gene (or hemizygous in the case of a transgene), the gene copy number will be lower than the cell's ploidy level. If the GOI is not detected, the cell is null for the locus, as can happen for a negative segregant of a transgenic event or in a mutagenized population. The zygosity of a cell at any locus can thus be determined by the gene copy number in the cell.
In another particular embodiment, the disclosure provides an assay for predicting corn embryo zygosity. In corn seed, the endosperm tissue is triploid, whereas the embryo tissue is diploid. Endosperm copy number is reflective of the zygosity of the embryo: a homozygous (positive or negative) endosperm accompanies a homozygous embryo, heterozygous endosperm (whether a GOI copy number of 1 or 2) reflects a heterozygous (GOI copy number of 1) embryo. Endosperm that is homozygous for the IC will contain three IC copies. Endosperm GOI copy number can range from 0 (homozygous negative embryo) to 3 (homozygous positive embryo); and endosperm GOI copy number of 1 or 2 is found in seed where the embryo is heterozygous for the GOI (or hemizygous for the GOI if the GOI is a transgene). The endosperm GOI copy number (which can range from 0 to 3 copies) can be determined from the ratio of endosperm IC copy number to endosperm GOI copy number (which can range from 0/3 to 3/3, that is, from 0 to 1), which can then be used to predict zygosity of the embryo.
In another embodiment, the present disclosure provides a basis for improving the ability to monitor one or more germplasm pools for shifts in the frequencies of one or more genetic characteristics, wherein said genetic characteristics include markers, alleles, and haplotypes. Methodology is known in the art to compare genetic marker frequency between recently derived populations and their ancestral lines in order to identify those genetic loci that are increasing in frequency over time (U.S. Pat. Nos. 5,437,697 and 5,746,023 (both incorporated by reference herein in their entirety)). Those loci with frequencies that exceed the expected allele frequency are inferred to have been subject to selection. Further, given that the predominant selection criterion in breeding programs is yield, it is expected that those increasingly frequent alleles may be linked to yield.
In a particular embodiment, the present disclosure provides a method to enable haplotype-assisted breeding. By comparing the frequency of haplotypes in emerging elite lines with the haplotype frequency in the ancestral elite lines (as determined via pedigree analysis), identification of haplotypes that are deviating from the expected haplotype frequency is possible. Further, by evaluation of haplotype effect estimates for said haplotypes, it is also possible to link said haplotypes of increasing frequency with phenotypic outcomes for a suite of agronomic traits. The haplotype composition of individual seeds sampled from a plurality of seeds can be determined using genetic markers and the seeds with preferred haplotypes are selected and advanced. Thus, more informed breeding decisions and establishment of superior line development programs is enabled by this technology.
In this example, tubulin was used as the IC gene, and the GOI was a transgene encoding neomycin phosphotransferase II (NPT II), which is used for kanamycin resistance selection. Endosperm (triploid) tissue was taken from seed (either by hand sampling or by scraping a seed with an automated sampler of the present disclosure). The endosperm-sampled seed was germinated, and leaf tissue (diploid) from successfully germinated plants was also sampled for genetic analysis. The leaf tissue correlates directly with embryo zygosity and was thus used to demonstrate that endosperm zygosity generally predicted zygosity of the embryo and to confirm homozygosity calls from the endosperm. Total genomic DNA was extracted from endosperm tissue and from leaf tissue, and quantitatively analyzed using an Invader� assay with oligonucleotide probes specific for the gene of interest, NPT II, or for the internal control gene, tubulin. The ratio of the GOI to IC was measured using conventional molecular biology techniques. See Table 1. A summary of results of multiple experiments are shown in Table 2.
Results indicated that endosperm zygosity generally predicted zygosity of the embryo (as indicated by the leaf zygosity) and was reliable in predicting homozygosity for all seeds that germinated. Furthermore, endosperm zygosity analysis gave few false-negative homozygous predictions (especially when the endosperm tissue was obtained with the automated sampler). These results demonstrate that for a cell of a known ploidy level, the ratio of copy number of a GOI to that of an IC indicates the zygosity of that cell. Furthermore, the zygosity assay of the present disclosure can predict zygosity of one tissue based on the zygosity of another, that is, the assay can predict the embryo zygosity based on the endosperm zygosity.
Example 2 This example demonstrates the use of the methods of the present disclosure in a program for marker-assisted selection of soybeans for Low Linolenic Acid.
An example of the application of the methods of the present disclosure is selection of soybean plants with both high yield and decreased linolenic acid content. Soybean progeny performance as it relates to low linolenic acid relies mainly on two major quantitative trait locus (QTL) at Fad3-1b and Fad3-1c. Analysis of segregating plants demonstrated that Fad3-1b and Fad3-1c additively control linolenic content in soybean. Therefore, by using a combination of markers for Fad3-1b and Fad3-1c, a breeder using the disclosure can accurately predict linolenic acid content in soybean plants. The markers can be used to infer the genotypic state of a seed at any stage in the breeding process, for example, at the finished inbred line stage, or the F1, F2, F3, etc.
Example 3 This example demonstrates the use of the methods of the present disclosure in a program for selection of recurrent parent alleles in a backcross breeding program.
The methods of the present disclosure can be used for selection of transgenes as well as identification of recurrent parent alleles. The identification of genotypes with desired recurrent parent allele frequencies before planting allows the number of rows per population to be reduced throughout the entire breeding program along with an increase in the number of populations included in the conversion program within a given field unit. This results in improved land usage, reduced land and labor costs, etc.
Example 4 This example demonstrates the use of the methods of the present disclosure for use in DNA line fingerprinting and linkage phase determination.
Example 5 This example demonstrates the methods of the present disclosure for evaluating transgenic seed for segregation distortion. Seeds of an F1 cross between Line A (Homozygous Event 1 and Event 2) and Line B (Homozygous Event 1) were induced in a maternal haploid induction isolation. The resulting kernels were selected using plumule color to obtain a population of putative haploid seed.
Individual putative haploid kernels from the population of putative haploid seed were selected and non-destructively sampled using an automated seed sampler system as generally described in U.S. patent application Ser. No. 11/213,435 (Publication No. US 2006/004624 (incorporated by reference herein in its entirety)), which is hereby incorporated by reference in its entirety. Markers were applied to the samples to determine the presence of the Event 2 gene and the Event 1 gene. The sampling process clips off some pericarp and endosperm tissue and uses this as the base for analysis. It is important to note that endosperm tissue is triploid and contains genetic contribution from both parents. If the gene of interest is detected using this method, it accurately predicts the presence of the desired gene in the haploid embryo. For the purposes of this study, samples from 180 kernels were analyzed and data were obtained on 175 due to sampling issues.
Example 6 This example demonstrates the utility of automated, high-throughput sampling in the preselection of haploid seed from a population of seeds.
The experiment comprised sampling 20 F2 populations using a nondestructive, high throughput seed sampling system and analyzing the samples to verify the pre-selection of haploid seed. Each population of F2 seed was nondestructively sampled or the F2 plants were tissue sampled for DNA analysis. The nondestructive seed samples were collected from individual seeds in the population of seeds using an automated seed sampler system as generally described in U.S. patent application Ser. No. 11/213,435 (Publication No. US 2006/004624 (incorporated by reference herein in its entirety)), which is hereby incorporated by reference in its entirety. Selection of desirable genotypes was based on selecting materials with the greatest allelic frequencies of the desired haplotypes based on modeling parameters. The selected F2 plants were pollinated with haploid inducing male pollinators and the resulting seed is harvested. Following harvest, haploid kernels were sorted out from the non-haploid seed and the haploids were sampled on a kernel basis using nondestructive, high throughput sampling and subsequent genotyping. The preferred haploid seed was selected and subjected to a chromosome doubling procedure to produce doubled haploids. This approach allows non-preferred genotypes to be culled before doubling and increases the frequency of preferred material that is processed through the resource intensive doubling process.
Example 7 This example illustrates sampling of transgenic seeds by the apparatus and method of the present disclosure and further testing of the sample for the presence or absence of a transgene or testing of zygosity (number of transgene) in the seed in a high throughput manner utilizing a 384-well plate and robotics. Not only did the automation provide cost savings on material, labor, and time, but it also improved consistency of DNA yield and accuracy of the assay. The seeds were tested for a gene of interest, e.g., a transgene for a trait and selected for further product development quickly. This also eliminated the need to grow out plants from seeds in green houses and/or field plots for testing, thereby further reducing the cost of product development.
Transgenic soybean seeds were produced by methods disclosed, for example, in U.S. Pat. Nos. 5,416,011, 5,569,834, 5,824,877, 5,914,451, 6,384,301, 7,002,058, and/or US 2005/0005321 (each of which is incorporated by reference herein in its entirety). Soybean embryos were transformed with pMON 70900 comprising a CP4 gene under the control of an FMV.35S promoter. The CP4 gene confers tolerance to the herbicide glyphosate.
Seeds were humidified for at least four days at about 20-24� C. and about 65% relative humidity. The seeds were then transferred to an automated sampling system, for example as described in US 2006/004624 or US 2007/0207485 (both of which are incorporated by reference herein in their entirety), wherein the sample trays consisted of a 384-well microtiter plates. Prior to sampling the seeds, about 20 μl of about 20% SDS was added to each well of the 384-well sample tray using a WellMate liquid dispenser system (Thermo Fisher Scientific, NH, USA). As the seeds were sampled by the automated sampling system, removed tissue samples from each of the seeds was deposited in individual wells of the 384-well sample tray. Two beads (Precision Ball Bearing) were added to each well and the sample trays were capped with a mat using the Matrix Super Sealer. The sealed trays were shaken and then placed in a freezer at about −80� C. until used for DNA extraction.
DNA was extracted by the reagents described in the method of DellaPorta et al. (Plant Mol. Biology Reporter, 1:19-21, 1983). About 380 μl of warm SDS-extraction buffer was added to each well of the seed plate and the plate was incubated at about 65�5� C. for about 45-60 minutes. About 135 μl of 5M Potassium Acetate was added to each well using the WellMate. Addition of solutions and incubation were done by an automated integrated system including BenchCel (Velocity 11, CA, USA), FlexDrop (PerkinElmer, Mass., USA), and an incubator (Liconic, Mass., USA).
The plates were sealed with the mats and solutions were mixed with the tissue in a shaker for about 1 minute. The plates were centrifuged at about 3848 ref for about 15 minutes. About 100 μl of the supernatant was transferred to a corresponding well in a quadrant of a 384-Filter Plate on a 384-collection extraction box (Corning, Mass., USA) with isopropanol with PlateMate Plus (Thermo Fisher Scientific, NH, USA). Each plate was centrifuged at about 5026.5 ref for about 20 minutes. Isopropanol supernatant mixture from each well was removed, about 65 μl of ethanol added, and each plate was centrifuged for about 3 min at about 1000 g. Leftover ethanol was aspirated and then the DNA pellet was dried for about 3 min. Finally the pellet was resuspended in about 85 μl of water. Addition and removal of reagents, centrifugation, and drying of the pellet were done in an automated integrated system including BenchCel, Bravo, and V-spin (all by Velocity 11, CA, USA). The plates were sealed with PlateLoc (Velocity 11, CA, USA) and stored from about 2� C. to about −20� C. until further analysis.
About 3 μL of DNA was added to each well of a 384-well plate for determining zygosity of the seed for CP4 (homozygote, heterozygote, and null) using the Invader kit (ThirdWave Technologies, Madison, Wis.). The population of seeds showed a segregation of about 1:2:1 in a cross of two heterozygote soybean plants.
Patent CitationsCited PatentFiling datePublication dateApplicantTitleUS2756903Jun 3, 1952Jul 31, 1956Alfred KreidlerDevice for extracting articles from a containerUS3350372Jan 6, 1964Oct 31, 1967Gulf Oil CorpEthylene/acrylate ester copolymersUS3530372Mar 1, 1968Sep 22, 1970Laukien GuentherMethod and apparatus for selecting plant seeds for sowingUS3642128Jun 5, 1970Feb 15, 1972Golden Wonder LtdApparatus using air jets for sorting by weightUS3852914Sep 1, 1972Dec 10, 1974Sensors IncMethod for determining the viability of seeds prior to germinationUS3861788Dec 3, 1973Jan 21, 1975Neotec CorpOptical analyzer for agricultural productsUS4037970Jan 30, 1976Jul 26, 1977Neotec CorporationOptical analyzer for agricultural productsUS4040747Aug 15, 1974Aug 9, 1977Neotec CorporationOptical analyzer for agricultural productsUS4260262Nov 28, 1978Apr 7, 1981Neotec CorporationGrain quality analyzerUS4278183Apr 18, 1979Jul 14, 1981National Research Development CorporationDispensing apparatus and methodUS4375854Mar 31, 1981Mar 8, 1983Rca CorporationStone sorting apparatus and methodUS4480765Dec 13, 1982Nov 6, 1984Tonus Egidio LNeedle seederUS4654592Jan 14, 1985Mar 31, 1987Varian Associates, Inc.Concurrent NMR analysis of multiple samplesUS4696308Apr 9, 1986Sep 29, 1987The Cleveland Clinic FoundationCore sampling apparatusUS4734584Sep 16, 1986Mar 29, 1988Trebor Industries, Inc.Quantitative near-infrared measurement instrument for multiple measurements in both reflectance and transmission modesUS4752689Mar 10, 1987Jun 21, 1988Satake Engineering Co., Ltd.Apparatus for evaluating the quality of rice grainsUS4818380Apr 19, 1988Apr 4, 1989Ishida Scales Mfg. Co., Ltd.Method and apparatus for sorting articlesUS4827776Aug 8, 1986May 9, 1989Gale Jody AHay sampling deviceUS4884696Mar 21, 1988Dec 5, 1989Kaman PelegMethod and apparatus for automatically inspecting and classifying different objectsUS4931061Mar 28, 1989Jun 5, 1990Union Oil Company Of CaliforniaPlant seed compositionsUS4946046Jan 25, 1990Aug 7, 1990Sheldon AffleckApparatus for sorting seeds according to colorUS5051699Aug 29, 1989Sep 24, 1991Kabushiki Kaisha ToshibaMagnetic resonance imaging systemUS5132538May 24, 1991Jul 21, 1992Nirsystems IncorporatedMeasuring percentage of protein in whole grain samplesUS5221518Aug 13, 1991Jun 22, 1993Mills Randell LDNA sequencing apparatusUS5245188May 7, 1992Sep 14, 1993Satake Engineering Co., Ltd.Apparatus for evaluating the grade of rice grainsUS5253302Dec 30, 1992Oct 12, 1993Robert MassenMethod and arrangement for automatic optical classification of plantsUS5412220Mar 5, 1993May 2, 1995United Industrial Products, Ltd.Optical scanning device for lumberUS5416011Nov 23, 1993May 16, 1995Monsanto CompanyMethod for soybean transformation and regenerationUS5475221May 11, 1994Dec 12, 1995Brimrose Corporation Of AmericaOptical spectrometer using light emitting diode arrayUS5533145Oct 26, 1994Jul 2, 1996Zellweger Uster, Inc.Continuous two dimensional monitoring of thin webs of textile materialsUS5569834Feb 14, 1995Oct 29, 1996Monsanto CompanyKanamycin resistantUS5590791Feb 1, 1995Jan 7, 1997Binder & Co. AktiengesellschaftMethod and apparatus for sorting wasteUS5668374May 7, 1996Sep 16, 1997Core Laboratories N.V.Method for stabilizing near-infrared models and determining their applicabilityUS5669511Sep 14, 1995Sep 23, 1997Satake CorporationGrain sorting apparatusUS5677474Jun 7, 1995Oct 14, 1997Washington UniversityProducing commercially valuable polypeptides with genetically transformed endosperm tissueUS5733592May 24, 1996Mar 31, 1998Buhler AgMethod for cleaning and sorting bulk materialUS5751421Feb 27, 1997May 12, 1998Pioneer Hi-Bred International, Inc.Near infrared spectrometer used in combination with a combine for real time grain analysisUS5764819Dec 7, 1993Jun 9, 1998Dekalb Genetics CorporationMethods for classifying plants for evaluation and breeding programs by use of remote sensing and image analysis technologyUS5824877Oct 25, 1996Oct 20, 1998Monsanto CompanyMethod for soybean transformation and regenerationUS5833947Feb 23, 1996Nov 10, 1998The Regents Of The University Of CaliforniaMonitoring the vasodilatory or vasoconstrictive effects of a physiologically active substanceUS5836438May 17, 1996Nov 17, 1998Daewoo Electronics, Co., Ltd.Device for automatically turning over work piecesUS5837458May 20, 1996Nov 17, 1998Maxygen, Inc.Methods and compositions for cellular and metabolic engineeringUS5864984Jun 19, 1995Feb 2, 1999Paradigm Research CorporationSystem and method for measuring seedlot vigorUS5914451Apr 6, 1998Jun 22, 1999Monsanto CompanyEfficiency soybean transformation protocolUS5918977Feb 9, 1996Jul 6, 1999Wolfking Danmark A/SMethod and plant for mixing and analyzing unhomogeneous flowable foodstuff, fodder or pharmaceutical materialUS5991025May 11, 1998Nov 23, 1999Pioneer Hi-Bred International, Inc.Near infrared spectrometer used in combination with an agricultural implement for real time grain and forage analysisUS6100526Feb 6, 1998Aug 8, 2000Dsquared Development, Inc.Grain quality monitorUS6150158Oct 15, 1998Nov 21, 2000E. I. Du Pont De Nemours And CompanyAutomatically depositing one seed into a small target container by controlling air pressure in a vertical hollow transport tube, detecting whether only one seed has been positioned, recording which containers are defectiveUS6237286Sep 11, 1997May 29, 2001Williames Hi-Tech International Pty Ltd.Nursery trays and handling mechanisms thereforUS6266864Aug 26, 1999Jul 31, 2001Ethicon, Inc.Method for fabricating a needle assemblyUS6384301Jan 14, 2000May 7, 2002Monsanto Technology LlcRapid and efficient process which does not involve a callus-phase tissue cultureUS6397678May 4, 2001Jun 4, 2002Shay PopperMethod and apparatus for measuring objects, particularly useful for measuring diamondsUS6537826Sep 6, 2000Mar 25, 2003Akira HoriganeFixing; freezing; cutting; use in preparation of biological or chemical samples subject to deformation, destruction, and denaturingUS6646264 *Oct 30, 2000Nov 11, 2003Monsanto Technology LlcMethods and devices for analyzing agricultural productsUS6705827Aug 24, 2001Mar 16, 2004Aagrinomics, LlcRobotic seed-handling apparatus and methodsUS6706989Feb 2, 2001Mar 16, 2004Pioneer Hi-Bred International, Inc.Automated high-throughput seed sample processing system and methodUS6782991Mar 14, 2003Aug 31, 2004Renholmens Mekaniska Verkstad AbBoard turnerUS6809819Sep 26, 2000Oct 26, 2004Monsanto Technology LlcMethods for determining oil in seedsUS6879389Jun 3, 2002Apr 12, 2005Innoventor Engineering, Inc.Methods and systems for small parts inspectionUS6947144Apr 4, 2001Sep 20, 2005Dongbu Hannong Chemical Co., Ltd.vivo monitoring method of transgenic plants and system using the sameUS6959617May 21, 2003Nov 1, 2005Monsanto Technology LlcSeed coring system and method for arranging seed cores for analysisUS7002058Dec 20, 2001Feb 21, 2006Monsanto Technology LlcTransforming soybean (Glycine max) using Agrobacterium mediated transformation of a plant tissue explant and subsequent regeneration of the transformed cells into a whole plantUS7044306Apr 2, 2003May 16, 2006Monsanto Technology LlcAutomated picking, weighing and sorting system for particulate matterUS7123750Jan 29, 2002Oct 17, 2006Pioneer Hi-Bred International, Inc.Automated plant analysis method, apparatus, and system using imaging technologiesUS7367155 *Dec 20, 2000May 6, 2008Monsanto Technology LlcApparatus and methods for analyzing and improving agricultural productsUS7403855Dec 19, 2002Jul 22, 2008Pioneer Hi-Bred International, Inc.Method and apparatus for tracking individual plants while growing and/or after harvestUS7502113Aug 26, 2005Mar 10, 2009Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS7591101Aug 26, 2005Sep 22, 2009Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS7611842Aug 26, 2005Nov 3, 2009Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS20010013486Oct 20, 1998Aug 16, 2001Masakazu YamakawaElectronic parts conveying apparatus and methodUS20010014750Apr 23, 2001Aug 16, 2001Cargill, Incorporated A Delaware CorporationCorn processingUS20010024796Dec 15, 2000Sep 27, 2001Selifonov Sergey A.Performing high throughput magnetic resonance imaging spectroscopy to screen libraries of chemical or biological compositions; identifying metabolic disorder genes, modulators and catalysts; optimizing reaction conditionsUS20020144458Feb 2, 2001Oct 10, 2002Hunter James L.Automated high-throughput seed sample processing system and methodUS20030142852Jan 29, 2002Jul 31, 2003Hugh LuAutomated plant analysis method, apparatus, and system using imaging technologiesUS20030148258Apr 4, 2001Aug 7, 2003Joo-Kon KimIn vivo monitoring method of transgenic plants and system using the sameUS20040091888 *Mar 20, 2003May 13, 2004Takeshi NishioDNA fragment which consists of a nucleotide sequence contained in a cysteine-rich protein, receptor kinase or glycoprotein gene; determining haplotypes by immobilizing probes onto support and hybridizingUS20040141641Jan 21, 2003Jul 22, 2004Mcdonald Miller BairdSeed image analyzerUS20040160607Feb 12, 2004Aug 19, 2004Chia-Po LinApparatus and method for accessing and processing reflection image from microwell-plate-based biochipUS20050005321Jun 16, 2004Jan 6, 2005Monsanto Technology LlcMethod and apparatus for preparation of genetically transformable plant tissueUS20050082207Sep 21, 2004Apr 21, 2005Deppermann Kevin L.High throughput automated seed analysis systemUS20050154221Apr 17, 2003Jul 14, 2005Zenon LysenkoHaving an unsaturated fatty acid or fatty ester; metathesis of the feedstock with a lower olefin; the resulting vinyl ester monomer may be epoxidized, hydroformylated or reductively aminated before oligomerization or polymerization to produce omega-epoxy, hydroxy, or amino vinyl estersUS20060004624Sep 21, 2004Jan 5, 2006Melara German OForecast and replenishment analyticsUS20060042527Aug 26, 2005Mar 2, 2006Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS20060042528Aug 26, 2005Mar 2, 2006Monsanto Technology LlcAutomated testing of seedsUS20060046244Aug 26, 2005Mar 2, 2006Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS20060046264Aug 26, 2005Mar 2, 2006Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS20060048247Aug 26, 2005Mar 2, 2006Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS20060112628Dec 20, 2000Jun 1, 2006Kotyk John JApparatus and methods for analyzing and improving agricultural productsUS20070048872Aug 25, 2006Mar 1, 2007Deppermann Kevin LHigh throughput screening of fatty acid compositionUS20070204366Feb 28, 2007Aug 30, 2007Monsanto Technology LlcMethods of seed breeding using high throughput nondestructive seed samplingUS20070207485Feb 28, 2007Sep 6, 2007Kevin DeppermannAutomated contamination-free seed sampler and methods of sampling, testing and bulking seedsUS20070240241Apr 6, 2007Oct 11, 2007Monsanto Technology LlcMethod of predicting a trait of interestUS20070240242Apr 6, 2007Oct 11, 2007Monsanto Technology LlcMethod for multivariate analysis in predicting a trait of interestUS20080000815Jun 27, 2007Jan 3, 2008Deppermann Kevin LSmall object sorting system and methodUS20080113367Nov 13, 2007May 15, 2008Pioneer Hi-Bred International, Inc.Clip based sampling of seed for the removal of specific seed tissue or structures for seed analysisUS20080131254Nov 13, 2007Jun 5, 2008Pioneer Hi-Bred International, Inc.Apparatus, method and system for handling, positioning, and/or automatically orienting objectsUS20080131924Nov 13, 2007Jun 5, 2008Pioneer Hi-Bred International, Inc.Methodologies, processes and automated devices for orientation, sampling and collections of seed tissues from individual seedsUS20080203201Feb 15, 2008Aug 28, 2008Deppermann Kevin LAgricultural sample grinderUS20080243392Jun 10, 2008Oct 2, 2008Pioneer Hi-Bred International, Inc.Method and apparatus for tracking individual plants while growing and/or after harvestUS20080310674May 29, 2008Dec 18, 2008Monsanto Technology LlcSeed sorterUS20080317279May 28, 2008Dec 25, 2008Monsanto Technology LlcAutomated high-throughput seed sampler and methods of sampling, testing and bulking seedsUS20090032441Apr 23, 2008Feb 5, 2009Pioneer Hi-Bred International, Inc.Method and computer program product for distinguishing and sorting seeds containing a genetic element of interestUS20100044356 *Aug 21, 2009Feb 25, 2010Pioneer Hi-Bred International, Inc.Apparatus for removal of specific seed tissue or structure for seed analysis* Cited by examinerNon-Patent CitationsReference1Archibald et al., "Development of Short-Wavelength Near-Infrared Spectral Imaging for Grain Color Classification," SPIE vol. 3543, 1998, pp. 189-198.2Bauman et al., Inheritance of Variations in Oil Content of Individual Corn (Zea mays L.) Kernels, Crop Science, 5:137-138 (1965).3Brumback, Jr., et al., "Automating fatty acid analyses from seeds: from field samples to data bases," Lab. Inf. Manage., 21 (1993) pp. 215-222.4Cabrera et al., Open Storage of Soybean Seed in Mississippi, Mississippi Agricultural and Forestry Experiment Station, Sep. 2002. .5Cabrera et al., Open Storage of Soybean Seed in Mississippi, Mississippi Agricultural and Forestry Experiment Station, Sep. 2002. <http://msucares.com/pubs/techbulletins/tb204.htm>.6Callaway A. S. et al., "High-Throughput Transgene Copy Number Estimation by Competitive PCR", Plant Molecular Biology Reporter, vol. 20, Sep. 2002, pp. 265-277.7Chunwongse J. et al., "Pre-germination genotyping screening using PCR amplification of half-seeds" Theoretical and Applied Genetics, Springer, Berlin, DE, vol. 86, No. 6, Jan. 1993, pp. 694-698.8Dahmer et al., "A Rapid Screening Technique for Determining the Lipid Composition of Soybean Seeds", Journal of the American Oil Chemists' Society, Springer, Berlin, DE, vol. 66, Jan. 1989, pp. 543-549.9Daun et al., "Comparison of Three Whole Seed Near-Infrared Analyzers for Measuring Quality Components of Canola Seed", vol. 71, No. 10, 1994, pp. 1063-1068.10Dellaporta et al., A Plant DNA Minipreparation: Version II, Plant Molecular Biology Reporter, vol. 1, No. 4, pp. 19-21 (1983).11Delwiche, "Single Wheat Kernel Analysis by Near-Infrared Transmittance: Protein Content," Analytical Techniques and Instrumentation, vol. 72, No. 1, 1995, pp. 11-16.12Demidov Dimitri et al., "Additive effects of the feed-back insensitive bacterial aspartate kinase and the Brazil nut 2S albumin on the methionine content of transgenic narbon bean (Vicia narbonensis L.).", Molecular Breeding, vol. 11, No. 3, Apr. 2003, pp. 187-201.13Dowell et al., "Automated Single Wheat Kernel Quality Measurement Using Near-Infrared Reflectance," ASAE Annual International Meeting, 1997, paper No. 973022.14Dowell, "An Intelligent Automated System for Determining Peanut Quality," IEEE International Workshop on Intelligent Robots and Sytems, IROS, pp. 237-241 (1990).15Dowell, "Automated Color Classification of Single Wheat Kernels Using Visible and Near-Infrared Reflectance," Cereal Chemistry, vol. 75(1), 1998, pp. 142-144.16Dr. Jolanta Soos, "Industrial Process Monitoring Requires Rugged AOTF Tools", Laser Focus World, Aug. 1994.17Gambhir et al. "Simultaneous Determination of Moisture and Oil Content in Oilseeds by Pulsed Nuclear Magnetic Resonance," JAOCS, 62(1):103-108 (1985).18Gasbarra et al. "Constructing the Parental Linkage Phase and the Genetic Map Over Distances <1 cM Using Pooled Haploid DNA", Genetics 172:1325-1335 (2006).19Gillaspie, Jr., Sensitive Method for Testing Peanut Seed Lots for Peanut Stripe and Peanut Viruses by Immunocapture-Reverse Transcription-Polymerase Chain Reaction, Plant Disease, May 2000, pp. 559-561.20Guidetti Geri, Viability Myths, , 4 pages.21Guidetti Geri, Viability Myths, <http://waltonfeed.com/self/upack/ag506a1.html>, 4 pages.22Halloin et al. "Proton Magnetic Resonance Imaging of Lipid in Pecan Embryos," JAOCS, 70(12):1259-1262 (1993).23Heil et al. "Magnetic Resonance Imaging and Modeling of Water Up-take into Dry Beans," Lebensm-Wiss u-Technol, 25:280-285 (1992).24Higley P M et al., "Evaluation of Seed Biopsy Methods for Nondestructive Seed Health Testing", Phytopathology, St. Paul, MN, US, vol. 79, No. 10, Jan. 1989, p. 1140.25J.P. Hazebroek, "Analysis of genetically modified oils" Progress in Lipid Research 39 (2000) pp. 477-506.26Jones D A L M Barber et al., "An analysis of seed development in Pisum sativum L. XVI. Assessing variation for fatty acid content by use of a non-destructive technique for single-seed analysis", Plant Breeding, vol. 114, No. 1, 1995, pp. 81-83.27Karcz Jagna et al., "Structural and embryological studies of diploid and tetraploid Arabidopsis thaliana (L.) Heynah", Acta Biologica Cracoviensia Series Botanica, vol. 42, No. 2, 2000, pp. 113-124.28Kotyk et al., High-Throughput Determination of Oil Content in Corn Kernels Using Nuclear Magnetic Resonance Imaging, JAOCS, vol. 82, No. 12, 2005, pp. 855-862.29Kramer et al., Transgenic Avidin Maize is Resistant to Storage Insect Pests, Nature Biotechnology, vol. 18, Jun. 2000, pp. 670-674.30Krisnangkura K. et al., "Continuous transmethylation of palm oil in an organic solvent", Jaoch, vol. 69, 1992.31Krysan, Breakthrough Technologies, Ice-Cap. A High-Throughput Method for Capturing Plant Tissue Samples for Genotype Analysis, Plant Physiology, Jul. 2004 vol. 135, pp. 1162-1169.32Lakshminarayana et al. "Spatial distribution of oil in groundnut and sunflower seeds by nuclear magnetic resonance imaging," J. Biosci 17(1):87-93 (1992).33MacNamara et al., "Multiplex sample NMR: an approach to high-throughput NMR using a parallel coil probe," Analytica Chimica Acta, 397:9-16 (1999).34Massie and Norris, "Spectral Reflectance and Transmittance Properties of Grain in the Visible and Near Infrared", Transactions of the ASAE, Winter Meeting of the American Society of Agricultural Engineers, 1965, pp. 598-600.35McCarthy Paul L. et al., "Rapid identification of transformed wheat using a half-seed PCR assay," Biotechniques, vol. 32, No. 3, Mar. 2002, pp. 560-564.36McEntyre et al., "Comparison of Water Absorption Patterns in Two Barley Cultivars, Using Magnetic Resonance Imaging," Cereal Chem., 75(6):792-795 (1998).37McGinty et al. "A System for Automatic Weight Determination of Individual Grain Kernels: Principles and Evaluation," Cereal Chem. 19(5)196-199 (1974).38Morrison, Sampling in Seed Health Testing, The American Phytopathology, 1999, 89: 1084-1087.39Orman and Schumann, "Comparison of Near-Infrared Spectroscopy Calibration Methods for the Prediction of Protein, Oil, and Starch in Maize Grain," J. Agric. Food Chem. vol. 39, 1991, pp. 883-886.40P.A. Hailey-Pfizer Central Research, "The Role of NIR Spectroscopy in the Measurement of Pharmaceutical Manufacture", .41P.A. Hailey�Pfizer Central Research, "The Role of NIR Spectroscopy in the Measurement of Pharmaceutical Manufacture", <http://www.brimrose.com/hailey.html>.42Paige et al. "Apparatus for Automatic Measurement of Kernel Weight, Length, and Thickness," Crop Sci. 31:1314-1318 (1991).43Pioneer Hi-Bred International, Inc., Downloadable Photos-Laser-Assisted Seed Selection, , printed as of Nov. 25, 2008, 4 pages.44Pioneer Hi-Bred International, Inc., Downloadable Photos�Laser-Assisted Seed Selection, <http://www.pioneer.com/web/site/portal/menuiteam.b9e99dcb8e2cfd8ecfe6d10093a0/>, printed as of Nov. 25, 2008, 4 pages.45PR Newswire, Monsanto Collaborates with Foss to Develop Analytical Tools for Soybeans, Installs Improved Low-Linolenic Calibration System for 2007 Fall Harvest, Sep. 20, 2007, 3 pages.46Rapid Identification of Organic Contaminants in Retreated Waste Water Using AOTF near-IR Spectrometry, ISA 1995 Meeting Proceedings, pp. 87-95, 1995.47Robutti, "Maize Kernel Hardness Estimation in Breeding by Near-Infrared Transmission Analysis," Analytical Techniques and Instrumentation vol. 72, No. 6, 1995, pp. 632-636.48Rubel et al. "Simultaneous Determination of Oil and Water Contents in Different Oilseeds by Pulsed Nuclear Magnetic Resonance," JAOCS 71(10):1057-1062 (1994).49Saito et al. "Application of Magnetic Resonance Imaging to Non-Destructive Void Detection in Watermelon," Cryogenics 36(12):1027-1031 (1996).50Sander et al., "System for Automatic Weight Determination of Individual Grain Kernels," Transactions of the ASAE, pp. 1146-1147 (1973).51Schuster Ivan et all, "Correlation between high molecular weight gluten subunits composition and bread-making quality in Brazilian wheat," Brazilian Journal of Genetics, vol. 20, No. 4, Dec. 1997, pp. 667-671.52Sedcole, J.R. "Number of plants necessary to recover a trait," Crop Sci. 17:667 (1977).53Seed Meister Luminar 3076, Brimrose Corporation of America, Baltimore, MD, .54Seed Meister Luminar 3076, Brimrose Corporation of America, Baltimore, MD, <http://www.brimrose.com/seed�meister.html>.55Serial Extraction of Endosperm Drillings (SEED)-A Method for Detecting Transgenes and Proteins in Single Viable Maize Kernels, Varaporn Sangton, et al., Plant Molecular Biology Reporter 19: 151-158, Jun. 2001, International Society for Plant Molecular Biology.56Serial Extraction of Endosperm Drillings (SEED)�A Method for Detecting Transgenes and Proteins in Single Viable Maize Kernels, Varaporn Sangton, et al., Plant Molecular Biology Reporter 19: 151-158, Jun. 2001, International Society for Plant Molecular Biology.57Siebenmorgen et al. "A Data Acquisition/Control System for Individual Kernel and Thin-Layer Grain Drying Research" Am. Soc. of Agri. Engrs., Univ. of Ark., 1991 Int'l Summer Meeting, Paper 91-3042, pp. 1-16 (1991).58Smith et al., Genetic Purity and Testing Technologies for Seed Quality: A Company Perspective, Seed Science Research, 1998, vol. 8, pp. 285-293.59Song et al., "Non-invasive Measurement of Moisture Distribution in Individual Wheat Kernels by Magnetic Resonance Imaging," SPIE, 2345:414-422 (1994).60Soybean Cyst Nematode, Plant Pathology, Iowa State University, University Extension, Ames, Iowa, Pm-879, Revised Oct. 1995, 6 pages.61Van Der Mey J A M et al., "Mass Screening for Alkaloid Content in Lupinus-Albus", Applied Plant Science, vol. 1, No. 2, 1987, pp. 80-82.62Von Post et al., A High-Throughput DNA Extraction Method for Barley Seed, Euphytica 130: 255-260, 2003.63Yoshida et al., "An automatic sequential single-seed weighing system: variation in soybean seed weight," J. Fac. Agr. Hokkido Univ. 61(2):225-232 (1982).Referenced byCiting PatentFiling datePublication dateApplicantTitleUS8071845Aug 2, 2010Dec 6, 2011Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS8245439Oct 3, 2011Aug 21, 2012Monsanto Technology LlcAutomated high-throughput seed sampler and methods of sampling, testing and bulking seedsUS8312672May 16, 2011Nov 20, 2012Monsanto Technology LlcMethods of seed breeding using high throughput nondestructive seed samplingUS8434259Dec 13, 2010May 7, 2013Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS8436225Nov 22, 2011May 7, 2013Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS8443545Jul 24, 2012May 21, 2013Monsanto Technology LlcAutomated high-throughput seed sampler and methods of sampling, testing and bulking seedsUS8519297Aug 21, 2009Aug 27, 2013Pioneer Hi-Bred International, Inc.Apparatus for removal of specific seed tissue or structure for seed analysisUS8523092Sep 13, 2010Sep 3, 2013Pioneer Hi-Bred International, Inc.System and method for creating a test sample from individual seeds or tissue structuresUS8535877May 20, 2011Sep 17, 2013Pioneer Hi-Bred International, Inc.Methods for removal of specific seed tissue or structure for seed analysisUS8539713Aug 15, 2011Sep 24, 2013Monsanto Technology LlcAutomated contamination-free seed sampler and methods of sampling, testing and bulking seedsUS8561346Jan 28, 2011Oct 22, 2013Monsanto Technology LlcAutomated seed sampler and methods of sampling, testing and bulking seedsUS8568821Apr 7, 2009Oct 29, 2013Pioneer Hi Bred International IncApparatus and method for coating ears of cornUS8579118Aug 21, 2009Nov 12, 2013Pioneer Hi-Bred International, Inc.Method for preparing ears of corn for automated handling, positioning and orientingUS8609179Aug 21, 2009Dec 17, 2013Pioneer Hi-Bred International, Inc.High throughput automated apparatus, method and system for coating ears of cornUS8662425Oct 16, 2012Mar 4, 2014Pioneer Hi Bred International IncHigh-throughput, seed sampling and collection system and methodClassifications U.S. Classification47/58.10RInternational ClassificationA01G1/00, A01H3/00, A01C1/00, A01B79/02, A01B79/00Cooperative ClassificationA01H5/10, A01H1/04, A01H1/02, C12Q1/6895, C12N15/8241European ClassificationA01H5/10, C12N15/82C, A01H1/04, C12Q1/68M10F, A01H1/02Legal EventsDateCodeEventDescriptionMay 16, 2014FPAYFee paymentYear of fee payment: 4Mar 4, 2014IPRAia trial proceeding filed before the patent and appeal board: inter partes reviewEffective date: 20140108Free format text: TRIAL NO: IPR2014-00333Opponent name: E.I. 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