Germplasm is living tissue from which new plants can be grown. It can be a seed or another plant part – a leaf, a piece of stem, pollen or even just a few cells that can be turned into a whole plant. Germplasm contains the information for a species’ genetic makeup, a valuable natural resource of plant diversity.

Agriculture benefits from uniformity among crop plants within a variety, which ensures consistent yields and make management easier. However, genetic uniformity leaves crops especially vulnerable to new pests and stresses. Genetic diversity of germplasm gives plant breeders the sustained ability to develop new high yielding, high quality varieties that can resist constantly evolving pests, diseases and environmental stresses. Sexually compatible wild species and landraces – ancestral varieties of crop species- are the key to genetic diversity, but the amount of land where plants grow wild continues to shrink and many plant species and varieties are disappearing. This is why the plant science community has developed conservation programs to gather, preserve, evaluate, catalogue and distribute germplasm for people all over the world to use.

Farming could be considered the original biological technology (biotechnology) when, some 10,000 years ago, humans began to cultivate and harvest specific plants to produce food. With increasing knowledge of genetics, plant breeders have accelerated the selection process, steadily increasing crop yields and enhancing quality. Some of the new technologies include:

• genomics, the study of the genome* of organisms;
• genotyping, the process of determining the genotype*;
• induced mutation, an externally generated change in the structure of DNA* or chromosomes often resulting in a visible or detectable trait alteration;
• phenomics, a field of study concerned with the characterization of phenotypes*; and 
• proteomics, the large-scale study of proteins, particularly their structures and functions. 

Definition

• Wikipedia

Resources

• Bioinformatics Info

• Bioinformatics Information Portal

• Bioinformatics Organization

• European Bioinformatics Institute

Primers

• Bioinformatics
  National Center for Biotechnology Information

• How are massive plant genomics data organized and interpreted?
  Boyce Thompson Institute for Plant Research

Publications

• Bioinformatics
  Oxford University Press

• Bioinformatics - Sequence and Genome Analysis
  David W. Mount - Cold Spring Harbor Laboratory Press 2004

• Bioinformatics: a practical guide to the analysis of genes and proteins
  Andreas D. Baxevanis, B. F. Francis Ouellette - John Wiley & Sons 2001

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An organism’s specific genomic complement, or the DNA sequences of all of its genes and intervening DNA regions, constitutes its genotype.

Most genes are present in a species in a number of different variants, or alleles, which may or may not affect the function of the gene.

By scoring genetic locations within an individual’s genome to know which alleles it has inherited from its parents, the specific genotype can be identified.

For example, if a particular gene confers resistance to a disease, seedling plants can be screened for the presence of this gene and only those with the resistant allele of the gene can be grown for further testing and propagation.

Such early genotyping and selection can result in large savings in labor, land and materials when screening large populations, particularly when alternative phenotypic screens, such as infecting all of the plants with the disease organism, are labor-intensive and expensive.

High-throughput methods enable the simultaneous testing of thousands of genes in hundreds of individuals, making it feasible to select for multiple traits in large plant populations. 

A mutation is any change in DNA sequence that can be passed from parent to offspring. Mutations occur naturally at a low rate in all living organisms.

In fact, mutation is one of the sources of genetic diversity.

By inducing mutations, scientists have been able to increase genetic variation in crop species.

Breeders depend on genetic variation to produce varieties with desirable traits, such as resistance to diseases and insects.

Unlike recombinant DNA methods, induced mutation does not add any genetic material into the species, although it can remove it by making deletions of DNA.

To induce mutations, chemicals or irradiation interact with internal enzymes that replicate or repair DNA in living organisms. 

Essentially, induced  mutation produces results that could have occurred naturally over much longer times than it takes to induce such results.

Since the 1940s, over 2,200 crop varieties have been developed by inducing mutations to alter genetic traits and then selecting among the progeny for improved types. For example, semi-dwarf rice, low saturated fat sunflower seeds, redder grapefruit and many flowers are derived from induced mutations.

While the term genomics refers to the characterization of the DNA constitution of an organism, the term phenomics refers to the characterization of the phenotypic, or observable, traits of the organism.

Since genes can be recessive or dominant, whether an organism visibly exhibits a trait depends upon which types of genes it inherited from its parents.

When an organism has one gene (allele) that is recessive and one that is dominant for the same trait, only the dominate trait will be visible in the final form, or phenotype.

While genotyping can be performed at early stages of plant growth using only DNA, phenotypes generally require observation of the actual plant growth stage of interest.

With recent advances in genotyping technology, it has become much easier to determine a plant’s genotype than its phenotype.

Thus, there is intense interest in phenomics, which refers to the development of efficient, high-throughput methods to determine phenotypes of many individuals for multiple traits.

This extends not only to visible traits such as leaf shape or fruit color, but also to biochemical or metabolic traits that may be of interest. 

In general, the DNA in genes codes for the manufacture of proteins by the cellular protein synthesizing machinery.

Genes encoded by the DNA are converted into proteins selectively during development, such that only a subset of genes is being actively transcribed (read into messenger RNA molecules) and translated (converted into proteins) at any given time.

Thus, while an individual organism’s genotype is more or less fixed and constant in all of its cells, the proteome, or sum of all the proteins currently present, varies by cell type, developmental stage, and environmental conditions.

Proteomics is the study of the proteins that are produced by an organism or cell under various conditions.

Since tens of thousands of different proteins can be produced by an organism, proteomics employs techniques to first separate and then identify each of these proteins in an extracted sample.

Information about the proteins that are present can be linked with metabolic pathways to shed light on the types of processes that are occurring in the cells and to regulation of the genes that encode the proteins.       

The practical importance of inter-species hybridization* lies in recombining properties of different species that drifted apart in the process of evolution. Wild relatives of crop species are dispersed far and wide and grow under diverse environments, which is why wild species offer so many diverse characteristics.

In general, most cultivated species have lost many traits initially inherent in their wild ancestors, such as resistance to unfavorable environmental factors, adaptation to different soil and climate conditions and resistance to pathogens, due to natural or directed selection.

Hybridization between a crop plant and a related wild species enables valuable genes from the wild species to be used for genetic improvement of the crop plant.

Many modern crop varieties incorporate resistance to fungal, bacterial and viral diseases that have been introduced through wide crosses between domesticated varieties and related wild species.

In plant breeding this practice is limited to introducing traits that are not available in the cultivated species as crossing to wild species also brings many unfavorable traits that have been selected against in modern varieties.

* Hybridization: Sexual cross between genetically different parents