Molecular Tools for Nursery Plant Production

Most of the traits of interest for plant breeding programs are quantitative traits. These traits are controlled by many genes and environmental factors. Phenotypic selection is the most common used form of selection in traditional genetic improvement programs. However, by using this method, you will not know which genes are actually being selected. With the development of molecular markers, marker assisted selection (MAS) become increasingly important in the coming years. MAS involve the selection of plants carrying genomic regions that are involved in the expression of traits of interest through molecular markers [1].

Molecular markers can be thought as constant landmarks in the plant genome. There are different kinds of molecular markers, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), microsatellites and single nucleotide polymorphisms (SNPs). These molecular markers allow high density DNA marker maps.

There are three types of relationships between the markers and the genes of interest. First, the molecular marker is located within the gene of interest. Second, the marker is in linkage disequilibrium (LD) with gene of interest throughout the whole population. Third, the marker is not in linkage disequilibrium with gene of interest throughout the whole population [2]. This study will give a general review about molecular markers used in nursery plants

Molecular markers

In genetics, a molecular marker is a fragment of DNA that associated with a certain location within the genome. Molecular markers are usually phenotypically neutral and could identify by techniques such as southern hybridization or PCR. Several different kinds of molecular marker could be applied on plant selection: such as restriction fragment length polymorphisms (RFLPs), is detected by southern hybridization. The principle of RFLPs is detecting a site in a genome where the distance between two restriction sites varies among different individuals. These sites are identified by restriction enzyme digests of chromosomal DNA. It requires a radioactive probe when do southern blotting.

Other methods involve using PCR, such as amplified fragment length polymorphisms (AFLPs) uses restriction enzymes to digestc genomic DNA [3]. Usually this technique has three steps: first, digestion of total plant DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. Second, selective amplification of a subset of these fragments with two PCR primers that have corresponding adaptor and restriction site specific sequences. Third, run the amplicons on a gel matrix, followed by visualization of the band pattern. Random amplified polymorphic DNA (RAPDs) markers are about 10 nucleotide length DNA fragments from PCR amplification of random segments of genomic DNA. RAPDs are able to differentiate between genetically distinct individuals. In recent years, RAPD has been used to characterize the phylogeny of diverse plant and animal species [4]. Single nucleotide polymorphisms (SNPs) refer to a single nucleotide difference in the sequence of a gene or segment of the genome [5]. There are a variety of methods for analyzing SNPs; detection of SNPs can be done without gels, such as high resolution melting method. All of the above molecular markers have been applied widely among crops and ornamentals and the advantages and disadvantages have been listed in Table 1 [6]. The best molecular markers are those that distinguish multiple alleles per locus (highly polymorphic) and are co-dominant (each allele can be observed).

Table 1: Advantages and disadvantages of most commonly-used DNA markers.

Sequence-related amplified polymorphism (SRAP) is a simple marker technique aimed for the amplification of open reading frames. Based on two-primer amplification, SRAP combines simplicity, reliability, moderate throughput ratio and facile sequencing of selected bands [7].

Current status of applications of molecular markers in nursery plants production

Molecular marker technologies have been widely used in ornamental plants. Most of the traits of ornamental importance are quantitative traits with complex inheritance and regulated by several genes, the environment and their interactions. Moreover, improving polygenic traits through MAS is a complex process [8]. Because more than one gene is involved in a quantitative trait, these genes have smaller individual effects on the phenotype. So the effect of the individual genes cannot be easily identified. In the following tables, the reader can find a brief summary of the current status regarding application of MAS in the different ornamentals. Gene-markers associated for important traits in ornamentals are listed in Table 2. Furthermore, marker selections in ornamentals by using amplified fragment length polymorphisms (AFLPs) method are showed in Table 3.

Table 2: Selected examples of gene-marker associated for important traits in ornamentals.

Table 3: Selected examples of amplified fragment length polymorphisms (AFLPs) marker assisted selection in ornamentals.

In nursery plants production, the majority of application of molecular marker is used for genetic diversity studies. However, MAS for quantitative traits is a difficult task in ornamentals, as with many other crops. Further advances in molecular technology and genome programs will soon create a wealth of information that can be exploited for the genetic improvement of ornamental crops. High-throughput genotyping, for example, will allow direct selection on marker information based on population-wide LD. Methods to effectively analyze and use this information in selection are still to be developed. The eventual application of these technologies in practical breeding programs will be on the basis of economic grounds, which, along with cost-effective technology, will require further evidence of predictable and sustainable genetic advances using MAS. Until complex traits can be fully dissected, the application of MAS will be limited to genes of moderate-to large effect and to applications that do not endanger the response to conventional selection. Until then, observable phenotype will remain an important component of genetic improvement programs, because it takes account of the collective effect of all genes.