Molecular Mapping and Mapping Populations

Authors: Anju Nehra*1 and Dr. Rajesh C. Jeeterwal2
1Ph. D. Scholar, SKN Agriculture College, (SKN Agriculture University, Jobner), Jaipur 303329 (Rajasthan)
2Young Professsional- II, ICAR-AICRP on Pearl Millet, Mandor, Jodhpur 342304 (Rajasthan)
*Corresponding author email:

F2, backcross and recombinant inbreds are the three primary kinds of mapping populations mostly used populations for molecular mapping. An F2 population is developed by autogamy (or intermating for cross pollinated species) among F1 individuals. These F 1 individuals are developed by crossing two parents that show important polymorphism for which ever form of loci you're reaching to score. Backcross populations are developed by crossing the F1 with one among the two parents used in the initial cross. The most important disadvantage to exploitation F2 or backcross populations is that the populations aren't eternal. Therefore, your source of tissue to isolate desoxyribonucleic acid or macromolecule are exhausted at some purpose in time. You then would have to be compelled to begin mapping again in another population. Populations of recombinant inbred lines is a robust solution to this drawback. Recombinant inbred lines are developed by single-seed alternatives from individual plants of an F 2 population. (Because of this procedure, these lines also are referred to as F2-derived lines.) Single-seed descent is repeated for many generations. At now, all of the seed from an individual plant is bulked. As an example, a F3:4 RI population underwent single-seed descent through the F3generation, and was bulked to develop the F4. This population of seed can then be grown to get a large amount of seed of each individual line. Significantly, each of the lines is fixed for several recombination events.

RI population level of inbreeding % within-line homozygosity at each locus
F3:4 75.0
F4:5 87.5
F5:6 92.25
F6:7 96.88
F7:8 98.44
F8:9 99.22
These lines have several uses. First, they'll be used be used to derive a map as a result of it primarily is a continuous F2population with unlimited mapping possibilities. in addition, these lines is scored for morphological traits (such as disease resistance or flower color) or quantitative traits (such as yield or maturity). This morphological trait data will then be compiled and those traits is placed on the developing molecular map. These lines are especially powerful for analyzing quantitative traits as a result of replicated trials is analyzed using identical genetic material. The quantitative trait data will then be used to verify if any molecular markers are closely related to those traits.

Genetics of Mapping Molecular Loci

Each of the mapping populations can provides a specific segregation ratio at every locus. The information of those ratios is very important to work out if the population is expressing a skewed segregation ratio at any locus. The proportions for every locus are following for co-dominant and dominant markers segregating in the three types of populations.

Population Codominant loci Dominant loci
F2 population 1:2:1 3:1
Backcross population 1:1 1:1*
RI population 1:1 1:1

*To score a dominant maker during a backcross population, you need to cross the recessive parent with the F1 plant, thus to score RAPD loci you'd have to be compelled to produce two populations, each developed by backcrossing to at least one of the two parents. For this reason, backcross populations haven't been used for mapping RAPD loci.
When we have been analyzing segregating populations by RFLP, RAPD or isozyme markers and have determined that the segregation ratio of every locus doesn't deviate from the expected ratio, that’s able to begin developing the map. (It should be noted here that scientists that develop molecular maps common include those loci with skewed segregation ratios in their mapping analysis.) All of the segregation data is then compiled and wont to derive the linkage relationship among the markers. This analysis is performed using computers and one program wide used is named MAPMAKER. This procedure is predicated on the maximum probability method. The output from this program could be a linear relationship among the markers and therefore the distance between the markers is measured in centimorgans.

Specialized Mapping Populatios and Bulk Segregant Analysis

Often a geneticist isn't interested in developing a molecular map, however would rather notice many markers that are closely connected to a selected trait. The identification of those markers is usually achieved by a procedure referred to as bulk segregant analysis. The essence of this procedure is that the creation of a bulk sample of desoxyribonucleic acid for analysis by pooling desoxyribonucleic acid from individuals with similar phenotypes. As an example, you'll have an interest to find a molecular locus coupled to a disease resistance locus. you'd create two bulk desoxyribonucleic acid samples, one containing desoxyribonucleic acid from plants or lines that are immune to the disease and a second bulk containing desoxyribonucleic acid from plants or lines that are prone to the disease. every of those bulk desoxyribonucleic acid samples can contain a random sample of all the loci within the ordination, aside from those who are in the region of the gene upon that the bulking occurred. Therefore, any distinction in RFLP or RAPD pattern between these two bulks should be connected to the locus upon that the bulk was developed. This is often a strong technique that has gained wide acceptance within the few years since it had been initial described.

Sequence labelled Sites
For many analysis labs, RFLPs aren't an attractive molecular marker system as a result of the labor concerned and therefore the demand of radioisotopes. Sequence labelled sites (or STS) could become a preferred alternative to RFLP markers as a result of they're PCR-based and don't need radioactive probing. STSs are developed by 1st sequencing the ends of a RAPD product or a clone used as the RFLP probe. From the sequence analysis, oligonucleotide primers 18-20 nucleotides long are synthesized that are complementary to every end of the RAPD product or the clone. These new primers are then used to amplify desoxyribonucleic acid by PCR. Two results may occur. 1st the size of multiplying product among completely different DNAs (for example, two parents differing for a disease resistance locus) may well be polymorphic. As an alternative, the amplification product may well be monomorphic (of a similar size). If this can be the case, then it'll be necessary to cut the product with numerous restriction enzymes to identify polymorphisms. Because the primers are longer than those used for RAPD mapping, the PCR reaction is run at a high annealing temperature. This easy modification in reaction temperature ends up in specific and easy amplification pattern that's very reproducible from laboratory to laboratory. (This is often not the case with RAPD technology.) as a result of they're portable from research laboratory research to lab, it's then doable to develop STS markers which will enable the quick location of any gene on a molecular map. First, it’s necessary to define from two to three evenly dispersed STS sites for every chromosome of the species with that you're operating. Then whenever a new gene of interested is identified, the linkage relationship between that gene and every of the STS loci is established. The new gene should map inside twenty five cM of one of the STS loci. Once the new gene is located in relationship to an STS, then you'll go to a RFLP or RAPD map and choose probes or primers which will allow you to identify markers more closely linked to the new gene.


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