Mapping population by Sanjay H B

1. A note on mapping population
Mapping population
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. They also help in the identification of molecular markers that are
linked to genes/loci of interest; such markers can be used for marker assisted selection (MAS)
for the genes of interest. Thus, mapping populations serve as the basic tools needed for the
identification of genomic regions harboring genes/QTLs and for estimating the effects of QTLs.
The primary mapping populations are of the following different types:
(1) F2, (2) F2-derived F3 (F2:3), (3) backcross (BC), (4) backcross inbred lines (BILs), (5) doubled
haploids (DHs), (6) recombinant inbred lines (RILs), (7) near-isogenic lines (NILs), (8)
chromosomal segment substitution lines (CSSLs), (9) immortalized F2, (10) advanced
intercross lines, (11) recurrent selection backcross (RSB) populations, and (12) interconnected
populations.
F2 Population
A F2 mapping population comprises the progeny produced by selfing or sib-mating of the F1
individuals from a cross between the selected parents. The F1 individuals would be
heterozygous for all the loci for which their parents differ from each other. Each F2 individual
is expected to have a unique combination of linkage blocks from the two parents, and this
difference is the basis for detection of linkage between pairs of loci. Since F2 generation is the
product of a single meiotic cycle, only one round of recombination can occur between any two
loci. Therefore, the estimates of recombination frequencies between pairs of loci obtained from
F2 populations serve as a reference point. In a F2 population, the ratios expected for dominant
and codominant markers are 3:1 and 1:2:1, respectively statistical analysis. F2 populations are
the best suited for preliminary mapping of markers and oligogenes. Creation of F2 populations
requires only two generations, which is the minimum for developing a biparental mapping
population. Further, their development requires the minimum effort as compared to the other
mapping populations. The F2 populations provide estimates of additive, dominance, and

2. epistatic components of the genetic variance. These populations capture the recombination
events from both male and female parents (actually, gametes in self-pollinated crops) of the F2
plants. They are ideal for identifying heterosis QTLs, except for the limitation of replications.
Since F2 populations are produced after one round of recombination, the markers identified to
be linked with the target genes are likely to be located at a greater distance than those
detected using recombinant inbred line (RIL) populations.
F2-Derived F3 Population
A F2-derived F3 or F2:3 population is obtained by selfing the F2 individuals for a single
generation and harvesting the seeds from each F2 plant separately so that each F2 plant is
represented as an individual plant progeny. The DNA for genotyping is obtained from individual
F2 plants or it can be reconstructed from a bulk of at least 20 plants from each F3 family (Yu et
al. 1997) since this bulked DNA may be expected to represent the genotype of the parental F2
plant. Similar to F2 populations, F2:3 populations are not perpetual. F2:3 populations are
suitable for mapping of oligogenic traits controlled by recessive genes and of QTLs since data
can be recorded on multiple plants in each F2:3 family to compensate for sampling error. The
mean phenotypic value from multiple plants in a F2:3 family can be considered to represent the
phenotype of its parent F2 plant.
Backcross Population
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, i.e., the parent having the recessive form of the target trait.
Such a backcross is called testcross, 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, i.e., no
segregation, for dominant markers present in repulsion phase in relation to the target trait. In
contrast, progeny from backcross with the dominant parent (generally designated as B1) would
display 1:0 ratio for the trait phenotype and dominant markers present in coupling phase with

3. respect to the target trait. However, a 1:1 ratio would be obtained in B1 for codominant
markers and dominant markers present in repulsion phase. Thus, in the case of codominant
markers, the order of backcross as well as the phase of linkage is not important when only
markers are to be scored. The backcross populations offer one specific advantage as they can
be further utilized for marker-assisted backcrossing (MABC) for introgression of the target traits
as proposed in the advanced backcross QTL method, But the construction of backcross
populations, like that of F2:3 populations, requires one more generation than that of F2
populations. Further, it requires crossing of the F1 plants with the selected parent, which
imposes additional work and may limit the population size in many crop species. The BC
populations are similar to F2 populations as they are not perpetual and cannot be evaluated in
replicated trials, which makes them unsuitable for QTL mapping. In addition, they capture the
recombination events of only one parent.
DoubledHaploids
Doubled haploid(DH) plantsare obtained bychromosomedoublingof haploidplantsusually
derived by culture of anthers/pollen grains produced by F1 plants. In some crop species, haploids can
also be produced from certain interspecific crosses.The DH lines are completely homozygous at all the
loci in the genome, and unlike RILs, they do not have any residual heterozygosity. The expected ratio for
the genes as well as markers in a DH population is 1:1 irrespective of the marker being dominant or
codominant. DHs are similar to F2 in that they both are products of one meiotic cycle occurring in F1.
But the frequency of recombinants would be higher in a DH population than in the corresponding F2
population. DH populations, like RILs, are perpetual as they can be multiplied and maintained
indefinitely and can be shared among researchers/ laboratories. They can be evaluated in replicated
trials and are suitable for mapping both qualitative and quantitative characters. In addition, only
additive and additive × additive interaction genetic variances can be estimated from DH populations as
they consist of only homozygous plants. Therefore, DH populations are not suitable for mapping
heterosis QTLs.
RecombinantInbred Lines
Recombinantinbredlines(RILs) are asetof homozygous linesproduced bycontinuous
inbreeding/selfingof individual F2plants. RILsare alsocalledF2-derivedinbredlinesorsingle seed
descent(SSD) linesbecause they are derivedfromF2populations usually bythe SSDprocedure. Each
generation of selfingreduces heterozygosity toone-half of thatinthe previous generation, andthere is
a correspondingincrease inhomozygosity. Asaresult, ina F4:5 RIL population, 87.5% of the RILswill be

4. homozygous fora givenlocus, while92.25 % of the plantsinthe RIL population willhave become
homozygous forthislocus. Itmay be pointedoutthat the above will alsobe the levelof homozygosity.
The RIL population consists, almostexclusively, of the twohomozygotes (e.g., AA andaa) for a locusand
a rather small proportion of the heterozygote (e.g., Aa), dependingonthe numberof generations, upto
whichSSD procedure wasfollowed. RILpopulations canonly be usedfordetectingadditive andadditive
× additive components of the geneticvariance.
Near-IsogenicLines
Near-isogeniclines(NILs) are pairsof homozygous linesthatare identical ingenotype, except
for a single gene/locus. Butinpractice, NILsdifferforthe single gene andavariable length
of the genomicregions flankingthislocus;inaddition, they mayalsodifferforsome random
genomicsegmentslocatedelsewhereinthe genome. Thus, apairof NILs will mostlikely
differforallelesatfew toseveral loci, whichjustifies the use of the term“nearisogenic”for
such lines. NILs are generally produced by backcross procedure , in which a donor parent (DP, a
homozygous line havingthe trait/allele of interest) iscrossed witharecurrent
parent (RP, a homozygous line lacking this trait/allele), and the F1 plants are backcrossed to the RP. The
backcross (BC) generation so obtained and the subsequent BC progeny are backcrossed to the RP. In
each BC generation, astrictselection isdone forthe trait/allele being
introgressed fromthe DP because eachbackcrossingreduces the proportionof DP genome inthe
progeny to50 % of that presentinthe previous generation.
Backcross InbredLines
Backcross inbredlines (BILs) are developed bybackcrossingthe F1from a cross between two
homozygous lines toone of the parentsandcontinued selfingof the BC1F1progeny to obtain
homozygous lines. Satoetal. (2003) produced a setof 98 BILs inrice by backcrossingthe F1
fromthe crossNipponbare ( japonica) _Kasalath(indica) toNipponbare andcontinued selfingof the
BC1F1 progeny toobtainBC1F5 lines. The datafromBIL population were analyzedusingthe methodfor
backcross F2 population andtreatingthe heterozygotes asmissingdatasince amethod foranalysis of
BIL population wasnotavailable. A possibleadvantage of BILsmaybe the increasedfrequency of the
allelescontributed bythe parentusedforbackcrossing. Therefore, itwouldbe desirable touse the
parentwiththe highervalue of the targettrait for backcrossingwiththe F1hybrid.
Advanced IntercrossLines
An advanced intercross line (AIL) population is developed by intermating the individuals of F2 and
subsequent generations from a suitable cross. Intermating in the segregating generations maintains
heterozygosity in the population and allows recombination between the QTLs and the markers linked to
them in every generation leading to a more precise location of the QTLs. It was estimated that the

5. confidence interval of QTLs would be reduced by up to five-fold in AILs as compared to that in an F2
population.
MultiparentAdvanced GenerationIntercrossPopulations
The multiparentadvancedgeneration intercross (MAGIC) populations are acollection of RILs
produced froma complex cross/outbred population involvingseveral parental lines.The parental lines
may be inbred lines, clones,orindividuals selectedonthe basisof theiroriginoruse. MAGIC
populations are anextension of the advanced intercross line,butdifferfromthemwithrespecttothe
involvementof multiple parentsintheirconstruction. A simpleapproachtogenerate aMAGIC
population istoproduce a complex cross involvingmultiple, typically eight, parental linesandtoisolate
RILs fromthiscross. The eightparental linesare crossed inpairstoproduce four differentsingle crosses,
and these single crosses are crossed inpairstogenerate twodouble crosses. Finally, the twodouble
crossesare matedtogethertoproduce an eight-parentcomplexcross. Thiscomplex crossishandled as
perthe SSD procedure todevelop the required numberof RILs, whichtogetherconstitutethe MAGIC
population.
NestedAssociationMappingPopulation
In order to combine the advantages of both linkage mapping and association mapping strategies, a
structured population generated by crossing a set of diverse founder parents to one or two common
parents has been suggested. Each selected founder is crossed to one or few common parents (nested
parents) and a set of 250 RILs from each of these crosses is generated using the SSD method. For
example, a population of 5,000 RILs was generated using 26 founder parents and one nested parent B73
in maize. The nested association mapping strategy enables efficient utilization of genetic and genomic
resources forgeneticdissection of complextraits.