1. Genetic diversity and its assessment
Genetic diversity is the raw material that helps plant species face a wide range of daily global changes [1, 2]. It also represents the number of alternations in the genetic makeup of populations and species, which take place under various evolutionary mechanisms such as genetic drift that involves random matings of individuals within the same population, changing their allele frequencies, and founder effect that causes individuals with new genetic information leading to a new population developed from a larger one [1, 2, 3]. Genetic composition of individuals varies from one population to another due to systematic differences that emerge among individuals from different places promoting their survival and reproduction. Genetic diversity becomes more potent and quick when gene flow among populations is little such as restricted dispersal of seeds or pollens [2, 3]. Plant breeders are able to develop large amount of new productive crops that are of improved tolerance to a variety of diseases and pests as well as its enhanced ability to stand against a changing world. This depends on the volume and range of genetic variation among individuals within the same species, which allows for designing sampling programs [2, 4, 5, 6]. Accordingly, geneticists have focused on evaluating genetic differences within populations using morphological, cytological, biochemical, and molecular markers to identify the characteristics of domestication, propagation, and breeding techniques as well as conservation of plant genetic materials . This work addresses various approaches related to genetic diversity in plants.
2. Biochemical markers
2.1. Storage proteins
One important output of post-transcription and translation processes is the protein, which represents the genetic DNA as well as the structural and enzymatic material of an organism’s cells . Genetic divergence is found to have impacts on proteins. For example, seed proteins that are of essential roles in species are tolerant to environmental occurrences. Recent approaches have employed several technologies to identify the characteristics of various plant cultivars and genotypes . One quickly and precisely technology utilized for such purpose is electrophoresis. The genetic divergence was assessed within Lathyrus sativus through accurate electrophoretic analysis of its seed storage proteins [2, 7], suggesting its fundamental role in evaluating the relationship between taxonomy and genetics at and below the species level .
2.2. Isozyme markers
Isozymes, also called isoenzymes, are proteins exhibiting same catalytic and quantitative function as the enzyme but, meanwhile, they differ in their molecular forms . Various alleles within a single locus are encoded by structural genes to give the allozyme, an allelic variant of the enzyme. Biological analysis of isozymes reveals significant importance, including the assessment of genetic divergence as well as phylogenetic and taxonomic relationships . It also helps to investigate population genetics and developmental biology as well as to conserve the genetic resources of plants [8, 9].
3. Molecular markers
Molecular markers such as restricted fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites (SSRs), and single-nucleotide polymorphisms (SNPs) are considered as effective and efficient tools for evaluating the genetic divergence within and among plant species .
3.1. Restriction fragment length polymorphism (RFLP)
RFLP is a dominant marker that involves breakages of DNA bonds at specific nucleotides by the action of enzymes called restriction endonucleases [8, 10], followed by size fractionation of digested fragments by electrophoresis technique, suggesting for these markers a key role in setting up genetic mapping as well as evaluating genetic diversity and phylogenetic relationships. RFLP markers could be a possible option to identify the characteristics of individuals, to estimate segregational analysis of progenitors as well as to evaluate genetic variation and phylogenetic relationships in the germplasms of lettuce plants, but these techniques proven to be expensive, technically complicated, and away from optimal performance . Therefore, research is needed to develop low cost and more efficient molecular genetic technologies to inhibit or even limit the technical obstacles related to RFLP technique and to study the properties of genetic difference within plants .
3.2. Random amplified polymorphic DNA (RAPD)
RAPD, a PCR-based technique or (AP-PCR), involves the use of arbitrary short primers [8, 10] in a PCR reaction to amplify random sequences from DNA template. RAPD has proven to be a multipurpose technique utilized for constructing genetic map [11, 12], utilization in breeding approaches , identification of resistant genes and hybrid origin , and for assessing plant genetic variance by characterizing differences between populations of the similar germplasm resources [11, 12].
3.3. Amplified fragment length polymorphism (AFLP)
AFLP is a highly reproducible marker that utilizes PCR technique to amplify DNA fragments [8, 10]. It is a DNA fingerprinting-based technique that includes digestion of DNA into small fragments with the help of restriction enzymes. These fragments are ligated by adaptors complementary to their restriction sites followed by selective amplification of the newly formed subset by PCR technique . Autoradiographic and fluorescence technologies are then utilized to visualize the amplified fragments on polyacrylamide gels. AFLP is proven its successful participation in identifying the characteristics of genetic diversity and relationships of plant species [8, 10, 15, 16, 17, 18, 19, 20].
3.4. Microsatellites (SSRs)
Microsatellites are repetitive sequences of nitrogen bases within DNA. These repeats may be mono-, di-, tri-, tetra-, or penta-nucleotides found in eukaryotic nuclear genome [8, 10]. Microsatellites are genetically different. Therefore, they are employed in estimating genetic divergence and recognizing the relationships between plant genotypes [10, 21].