Plant and Animal Breeding

In today's competitive marketplace, breeders are always searching for ways to maximize genetic gains. Whether breeding efforts are targeted towards canola for oil production or chickens for table eggs, the importance lies in combining different genetic tools to maximize genetic improvement in multiple traits in an economically feasible way. In order to remain competitive, breeders are challenged to keep up-to-date with the latest methods.

Genetic Foundations can help you identify appropriate technologies to enhance your breeding efforts. More importantly, Genetic Foundations provides technical assistance to help you integrate new tools into your existing breeding program. Take advantage of Genetic Foundations' experience and insights to help accelerate your genetic progress!

The following are examples of how Genetic Foundations can help:

  • Exploit genomic information from diverse databases
  • Develop new genetic markers
  • Locate and interpret genetic maps
  • Marker assisted breeding
  • Evaluate mating designs
  • Trait introgression
  • Organize and arrange genotyping projects
  • Integrate genotypic (marker) and phenotypic (trait) data
  • Evaluate structured breeding populations
  • Estimate levels of inbreeding


Genetic markers and DNA fingerprinting: Pedigrees and parentage tests

Many of today's breeding efforts require accurate tracking of parents and offspring, not to mention ensuring and maintaining mating integrity. Despite the best of intentions, and regardless of built-in systems to minimize problems, mistakes are nearly inevitable. "Things" just seem to happen!

Many such mistakes might go unnoticed, yet they will certainly affect your progress. DNA markers offer the most robust method for tracking parentage. And if a mistake is found, it is often possible to infer how the mistake might have occurred.

The examples below illustrate two different scenarios.

A labeling mix-up was suspected in this example, and a DNA test was conducted to find out. DNA samples from seven individuals were prepared at two different times and tested using several highly variable DNA markers.

Results from three of these markers are shown. Paired samples (adjacent lanes on a DNA gel) from individuals 1-3 and 5-7 appear identical for all three markers, whereas the samples from individual 4 (blue boxes) are clearly different for all three markers, confirming the suspected problem.

Being aware of such a mix-up can be extremely useful for interpreting data from suspect individuals.


In this example, parentage was being tested for 23 offspring from one mating pair to ensure that all individuals had been properly identified. Offspring containing non-parental DNA fragments, such as those found in four individuals (red arrows and ellipses), are indicative of pedigree errors.

Again, the ability to confirm pedigrees can be invaluable for ongoing breeding efforts.

A key point is that similar methods of DNA fingerprinting are used for both matching individuals and for checking parentage.

Genetic Foundations can:

  • help you determine the most appropriate DNA markers for your fingerprinting application
  • help identify and organize the samples you need to collect
  • make arrangements with an outside vendor to process your samples, and
  • interpret the results and plan any further testing as may be indicated

Have a look at this pedigree, representing on investment of five generations to produce an inbred experimental line.

If your R&D program depended on 100% accuracy in such a pedigree, wouldn't it make sense to verify that the matings were executed as planned?

[Note: Lines connect individuals to their parents in previous generations (fathers, 1, as red lines; mothers, 2, as blue lines].


Genomics, bioinformatics, and data mining

Nearly everyone recognizes the tremendous progress recently made in many areas of genomics. How can anyone possibly keep up? It's a real challenge, and frankly, a situation that's not likely to get much easier any time soon. There's simply too much to know. One solution is to become more adept at locating and manipulating information already residing in public and private databases.

Genetic Foundations has broad experience in identifying and extracting data from a variety of databases. If the data are available, we can track them down and make them accessible. How would you like them prepared?

Here are some examples of possible applications:

  • download and compare available sequences corresponding to a gene of interest
  • identify potential microsatellite markers in a region of interest
  • identify putative candidate genes based on functional criteria or positional genomics
  • help train your staff to use existing on-line tools


Data analysis and experimental design

You've finally completed collecting observations for a long-term experiment begun by your predecessor. You've located the original plans, but now your challenge is to analyze all these data.

Genetic Foundations has experience in analyzing both discrete and continuously distributed data. We can help you assess your data and determine the best way to analyze it. If you know what you need, but just need some additional help in getting it, that's OK too. Let us offer some assistance. We use industry-standard analytical tools, (e.g. JMP, SAS) and can help you transform data into more user-friendly formats (e.g. Word, Excel). Contact us to explore how we can help.

Genetic Foundations can also assist with quantitative genetic analyses of various sorts. Whether such datasets represent breeding populations or are instead designed to describe natural populations, we can help you analyze and interpret these statistical results.

The sugar pine seedlings in the picture on the right were part of a larger study examining how variation among seed trees within a population, as well as elevation differences among populations, contribute to seedling growth. Quantitative genetic analyses showed significant variation among parents and among populations.


Family resemblance can even be seen in trees.

Of these four knobcone pine cones, two came from one pair of siblings, and the other two from another pair of siblings.

Can you match up the related pairs?

Answer: The two on the left came from one set of siblings, the two on the right from the other.



Population, ecological, and environmental genetics

Ecological geneticists use genetic tools to describe heritable variation within and among natural populations of plants and animals. Sometimes these genetic tools are based upon protein or DNA markers, and at other times, measurement data are used instead. Whatever the tool, assessing within-species biodiversity is an important step in evaluating population stability and community viability.

Isozymes remain a useful technology for sampling biodiversity within and among populations. This gel depicts genetic variation among incense-cedar trees collected from California's Sierra Nevada mountains.

Genetic Foundations has substantial experience in quantifying genetic variation using various genetic approaches such as markers (e.g. isozymes, organelle and nuclear DNA) and quantitative characters (e.g. statistical analyses, heritability).

In recent years DNA-based methods are increasingly being used to determine what species inhabit a given area or microclimate. This is especially true for microbial communities, cryptic species, and the rhizosphere. Perhaps you have a concern about the potential for microbial contamination in a manufacturing process? Perhaps you wish to design a monitoring system to provide a safeguard against a pathogen outbreak? Genetic Foundations has experience in detecting both eukaryotic and prokaryotic contaminants and pathogens.

In short, Genetic Foundations can help you monitor and assess biodiversity within species, identify cryptic species, or maintain vigilance to avoid unwanted biological agents such as contaminants or pathogens.

Expert witness and intellectual property

Increasingly, DNA evidence is being introduced into criminal and civil litigation. Perhaps you are developing a case in which DNA evidence might be used. Are you prepared? Do you need someone to help assess this potential? How can you assess the strengths or weaknesses of existing DNA evidence? Genetic Foundations can help you determine whether DNA evidence might help your case, or alternatively, assist in defending against potentially flawed evidence.

Are you developing a patent application for a new DNA-based technology? Perhaps you are trying to define how narrow or broad to make your claim. Genetic Foundations can assist you in tracking down background information on related procedures and help to assess the uniqueness and utility of your claim.


Research, lectures, and training

Have you suddenly been asked to research a new topic area, perhaps to prepare a white paper or to satisfy a customer's inquiry? Do you need an independent assessment of a new opportunity? Looking for a quick study to provide additional background on a competitor's new product? Genetic Foundations can help you gain rapid access to this information by capturing and evaluating bibliographic materials from a variety of sources. Our research skills are unsurpassed. Moreover, we can help you draft, edit, or polish technical communications or proposals, recognizing the importance of rapid turnaround to meet impending deadlines.

Genetic Foundations can utilize these same skills to prepare and deliver presentations on a variety of topics related to genetics, genetic applications, or biotechnology. We have considerable experience in speaking to professional and technical audiences, executives, trade organizations, customers, students, and lay audiences.

Genetic Foundations can also help you with your training needs-either for yourself or your staff. "Give a man a fish, and feed him for a day. Teach him how to fish and feed him for a lifetime." Sometimes, it simply makes sense to do something yourself-if you only knew how! Let us give you a hand. Are you trying to learn a new software package? Perhaps you're implementing a new laboratory procedure. We have considerable hands-on experience with a variety of laboratory processes encompassing both protein and DNA manipulations.

Laboratory design and establishment

Building a new laboratory is no small venture. Sure, you can find someone willing to sell you lots of fun stuff, but what do you really need? How do you stretch those capital dollars by minimizing redundancy? Genetic Foundations has designed and established new laboratories in both the public and private sectors-typically on very tight budgets. Let us help you develop the capital budget for your new lab, or instead, let us help you get it set up if your budget is already fixed.

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