2. A population that is suitable for linkage mapping of genetic markers is known as
mapping population.
Mapping populations are generated by crossing two or more genetically diverse
lines and handling the progeny in a definite fashion.
Mapping populations are used for determining genetic distances between pairs of
loci/genes and to map them to specific locations in the genome.
There are basically two types of mapping populations, viz., primary and secondary
mapping populations.
Primary mapping populations are created by hybridization between two
homozygous lines usually having contrasting forms for the traits of interest.
Secondary mapping populations are developed by crossing two lines/individuals
selected from a mapping population, they are developed mainly for fine mapping
of the genomic region of interest.
Mapping Population
3. Types of Mapping population
F2
F2 : F3
Back cross (BC)
Backcross inbred lines (BILs)
Doubled haploids (DHs)
Recombinant inbred lines (RILs)
Near isogenic lines (NILs)
Advanced intercross lines
Immortalized F2
CSSLs
RSB
4. Developed with minimum efforts
Best for preliminary mapping
Require less time for development
The simplest form of a mapping population is F2 population. Parent 1 (P1) and parent 2
(P2) are two parents contrasting for trait of interest crossed to get F1 population.
Individual F1 plant is then selfed to produce an F2 population. F2 populations are
outcome of single meiotic cycle. The segregation ratio for codominant marker is 1:2:1
(homozygous like P1:heterozygous:homozygous like P2) while segregation ratio for each
dominant marker is 3:1.
F2 populations
Outcome of only one meiotic cycle
Limited use for fine mapping
Not immortal population
Difficult to map quantitative trait
Merits
Demerits
5. Selfing of F2 individuals for single generation results in F2:3 populations.
Such populations suitable for specific situations like, mapping of quantitative
trait, mapping of recessive genes.
Demerit of F2:3 population is, like f2 population it is also not immortal.
F2:F3 populations are suitable for mapping of oligogenic traits controlled by
recessive genes.
F2:F3
6. Markers are used in MABC
Less time to develop
Cannot used for quantitative trait
Not immortal
Backcross populations are generated by crossing F₁ plants with either of the two
parents of the concerned F₁. Genetic analysis can be performed only when there is
detectable phenotypic segregation for the target trait in the backcross generation.
Therefore, the F₁ is, as a rule, backcrossed to the recessive parent, ie., the parent
having the recessive form of the target trait. Such a backcross is called testeross, is
usually denoted by B2. and exhibits 1:1 ratio for the trait phenotype, dominant
molecular markers present in coupling phase with respect to the target trait, and
codominant markers in either phase. However, it would show 1:0 ratio, Le., no
segregation, for dominant markers present in repulsion phase in relation to the target
trait. In contrast, progeny from backcross with the dominant parent would display
ratio for the trait phenotype and dominant markers present in coupling phase with
respect to the target trait.
Merit Demerit
Back Cross(BC)
7. Immortal population
Can be replicated over different locations
Important for QTL mapping
Product of many meiotic cycles so useful to identify tightly linked markers
RIL population is developed using continuous selfing or sibmating progeny of
individual member of F2 population until complete homozygosity is achieved.
Single seed descent method is best for development, bulk or pedigree method
without selection can be used. Segregation ratio of RILs is 1:1.
Recombinant inbred lines (RILs)
Merits
Demerits
Require many seasons to develop RILs
RIl development is difficult in crop having high inbreeding depression
8. Immortal/ permanent population
Used in mapping of both qualitative
Fast production of homozygous lines
DH produced from chromosome doubling of pollen/egg derived haploid plants from F1.
Another method of producing the haploids is wide crossing. For example haploids in barley,
can be produced by wide crossing with Hordeum bulbosum. During the early stages of seed
development the H. bulbosum chromosomes are eliminated producing haploid embryo. In
DH all markers segregate in 1:1 ratio.
and quantitative trait.
Double Haploids (DH)
Merit Demerits
High cost involvedin establishing tissue
culture
Somaclonal variation arise during DH
production
9. Near Isogenic lines (NILs)
NILs are lines of genetic codes that are identical except for differences at a few
specific location or genetic loci
NILs can be developed by repeated selfing or backcrossing of f1 with recurrent
parent. Irrespective of dominat or codominant marker NILs segregate in 1:1 ratio.
Merits :
Immortal population
Used for tagging traits
used for fine mapping
Demerits :
Many generation require to develop NILs
Cannot use in linkage mapping
Increase cost time and efforts
Linkage drag
10. The multiparent advanced generation intercross (MAGIC)
populations are a collection of RILs produced from a complex
cross/outbred population involving several parental lines.
The parental lines may be inbred lines, clones, or individuals
selected on the basis of their origin or use.
MAGIC populations are perpetual, lack population structure,
can be used for both linkage and association analyses, and can
be developed at an appropriate stage during the intermating
process to afford the desired mapping resolution.
They are an ideal resource for construction of high-density
maps, and they allow modeling of cytoplasmic effects.
These populations can be used as training populations for
genomic selection
MAGIC
