Molecular breeding and marker assisted selection
Molecular Breeding or Marker assisted breeding (MAB) is the process of using the results of DNA tests to assist in the selection of individuals to become the parents in the next generation of a genetic improvement program. The choice among various methods of MAB depends on the complexity of the trait and a prior knowledge on the gene (s) or segments of chromosomes (known as quantitative trait loci (QTL). Molecular markers facilitate conventional breeding, improve selection efficiency, reduce cost for developing new varieties, and/or quality control (ensuring line purity and genetic identity).
Aspects of Molecular Breeding
Marker assisted breeding
Genotyping and creating molecular maps- genomics The commonly used markers include Simple sequence repeats (or microsatellites), single nucleotide polymorphisms (SNP). The process of identification of plant genotypes is known as genotyping. Development of SNPs has revolutionized the molecular breeding process as it helps to create dense markers. Another area that is developing is genotyping by sequencing.
Phenotyping – phenomics
To identify genes associated with traits, it is important to measure the trait value – known as phenotype. “omics” for measurement of phenotypes is called phenomics. The phenotype can be indicative of the measurement of the trait itself or an indirectly related or correlated trait.
QTL mapping or association mapping
Genes (Quantitative trait loci (abbreviated as QTL) or quantitative trait genes or minor genes or major genes) involved in controlling trait of interest is identified. The process is known as mapping. Mapping of such genes can be done using molecular markers. QTL mapping can involve single large family, unrelated individuals or multiple families (see: Family based QTL mapping). The basic idea is to identify genes or markers associated with genes that correlate to a phenotypic measurement and that can be used in marker assisted breeding / selection.
Marker assisted selection or genetic selection
Once genes or markers are identified, they can be used for genotyping and selection decisions can be made.
Marker-assisted backcrossing (MABC)
Backcross is crossing F1 with its parents to transfer a limited number of loci (e.g. transgene, disease resistance loci, etc.) from one genetic background to another. Usually the recipient of such genes is good adapted cultivars otherwise except the gene that is to be transferred. So we want to keep genetic background of the recipient genotypes, which is done by 4-6 rounds of repeated backcrosses while selecting for the gene of interest. We can use markers from the whole genome to recover the genome quickly in 2-3 rounds of backcrossing might be good enough in such situation.
Marker-assisted recurrent selection (MARS)
MARS include identification and selection of several genomic regions (up to 20 or even more) for complex traits within a single population.
Genomic selection is novel approach to traditional marker-assisted selection where selection are made based on few markers. Rather than seeking to identify individual loci significantly associated with a trait, genomics uses all marker data as predictors of performance and consequently delivers more accurate predictions. Selection can be based on genomic selection predictions, potentially leading to more rapid and lower cost gains from breeding. Genomic prediction combines marker data with phenotypic and pedigree data (when available) in an attempt to increase the accuracy of the prediction of breeding and genotypic values.
Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (morphological, biochemical or DNA/RNA variation) linked to a trait of interest (e.g. productivity, disease resistance, abiotic stress tolerance, and quality), rather than on the trait itself.This process has been extensively researched and proposed for plant and animal breeding, nevertheless, as of 2013 “breeding programs based on DNA markers for improving quantitative traits in plants are rare”.
For example, using MAS to select individuals with disease resistance involves identifying a marker allele that is linked with disease resistance rather than the level of disease resistance. The assumption is that the marker associates at high frequency with the gene or quantitative trait locus (QTL) of interest, due to genetic linkage (close proximity, on the chromosome, of the marker locus and the disease resistance-determining locus). MAS can be useful to select for traits that are difficult or expensive to measure, exhibit low heritability and/or are expressed late in development. At certain points in the breeding process the specimens are examined to ensure that they express the desired trait.
Positive and negative selectable markers
The following terms are generally less relevant to discussions of MAS in plant and animal breeding, but are highly relevant in molecular biology research:
Positive selectable markers are selectable markers that confer selective advantage to the host organism. An example would be antibiotic resistance, which allows the host organism to survive antibiotic selection.
Negative selectable markers are selectable markers that eliminate or inhibit growth of the host organism upon selection. An example would be thymidine kinase, which makes the host sensitive to ganciclovir selection.
Gene vs marker
The gene of interest directly causes production of protein(s) or RNA that produce a desired trait or phenotype, whereas markers (a DNA sequence or the morphological or biochemical markers produced due to that DNA) are genetically linked to the gene of interest. The gene of interest and the marker tend to move together during segregation of gametes due to their proximity on the same chromosome and concomitant reduction in recombination (chromosome crossover events) between the marker and gene of interest. For some traits, the gene of interest has been discovered and the presence of desirable alleles can be directly assayed with a high level of confidence. However, if the gene of interest is not known, markers linked to the gene of interest can still be used to select for individuals with desirable alleles of the gene of interest. When markers are used there may be some inaccurate results due to inaccurate tests for the marker. There also can be false positive results when markers are used, due to recombination between the marker of interest and gene (or QTL). A perfect marker would elicit no false positive results. The term ‘perfect marker’ is sometimes used when tests are performed to detect a SNP or other DNA polymorphism in the gene of interest, if that SNP or other polymorphism is the direct cause of the trait of interest. The term ‘marker’ is still appropriate to use when directly assaying the gene of interest, because the test of genotype is an indirect test of the trait or phenotype of interest.
Selection for major genes linked to markers
‘Major genes’ that are responsible for economically important characteristics are frequent in the plant kingdom. Such characteristics include disease resistance, male sterility, self-incompatibility, and others related to shape, color, and architecture of whole plants and are often of mono- or oligogenic in nature. The marker loci that are tightly linked to major genes can be used for selection and are sometimes more efficient than direct selection for the target gene. Such advantages in efficiency may be due for example, to higher expression of the marker mRNA in such cases that the marker is itself a gene. Alternatively, in such cases that the target gene of interest differs between two alleles by a difficult-to-detect single nucleotide polymorphism, an external marker (be it another gene or a polymorphism that is easier to detect, such as a short tandem repeat) may present as the most realistic option.