QTL mapping is a process used to identify genomic regions associated with quantitative traits using DNA markers. It involves selecting parental lines with desirable traits, creating a mapping population such as recombinant inbred lines, phenotyping the population for the target trait, genotyping the population, and constructing a linkage map to detect QTLs. The objectives are to detect QTLs, identify genome regions affecting traits, analyze QTL effects, and determine which alleles are favorable. Different types of mapping populations like backcross, F2, RILs, and near isogenic lines can be used depending on the desired advantages and disadvantages. Methods for QTL detection include analyzing single markers, interval mapping of two flanking markers, and composite interval mapping using

1. QTL Mapping
MSc ag (2) year
Agriculture Genetics and Plant Breeding
Deen Dayal Upadhyaya Gorakhpur University
Gorakhpur
Submitted by.
Shweta Kumari
Submitted to
Department of
Genetics and plant
breeding

2. Introduction
✩ QTL mapping
✩ QTL mapping is the process to identify the genomic region associated
with desirable quantitative trait with the help of DNA marker
✩ In this process DNA markers are tested throughout the genome which
are associated with QTLs.

3. Quantitative Traits Loci
✩ The loci controlling quantitative traits are called quantitative traits Ioci
( QTL)
✩ the term quantitative traits coined by Genderman.
✩ QTL is the region of genome which control quantitative trait
✩ QTL characteristics
✩ The QTLs are controlled by multiple genes ,each segregating according
to Mendel's Law.
✩ These traits also a ected by environment to varying degrees
✩ QTL can show dominant or co-dominant

4. Objective of QTL mapping
✩ The basic objective is to detect QTL
✩ To identify the region of genome that a ects the trait of interest
✩ To analyse the e ect of the QTL on the trait
✩ How much variation for the trait is caused by a specific region
✩ What is the gene action associated with the QTL?
✩ Which allele is associated with the favourable e ect.

5. Procedure for QTL mapping
✩ Selection of diverse parental lines
✩ Creation of mapping population
✩ Phenotyping of the progeny
✩ Genotyping of the progeny
✩ Construction of linkage map.

6. Types of mapping population
✩ Recombinant Inbred line(RIL)
✩ Backcross
✩ F2 population
✩ Double haploid
✩ Near isogenic line(NIL)

7. Backcross mapping population
✩ Advantages: It is easier to
identify QTL as there are less
epistatic and linkage drag
e ects; especially useful for
crosses with wild species.
✩ Disadvantages: Di cult or
impossible in species that are
highly heterozygous and
outcrossing.
✩ Use: best when inbred lines
are available

8. F2 mapping Population
✩ Advantage: Fast and easy to
construct.
✩ Disadvantage: F3 families are
still very heterozygous; so the
precision of the estimates can
be low (because of the high
standard error); can't be
replicated

9. Recombinant Inbred Line
✩ RILs are produced by
continuous selfing progeny of
individual member of an F2
population until complete
homozygous is achieved
✩ Advantages: fixed lines so can
be replicated across many
locations and/or years; can
eliminate problem of
background heterozygosity.
✩ Disadvantages: Can take a
long time to produce. (Some
species are not amenable)

10. Near Isogenic Line
✩ Advantage: Very precise and
statistically strong, as
background is constant;
especially useful for validation
experiments.
✩ Disadvantage: Can take time
to construct; only useful for
specific target QTL

11. Doubled Haploid Line
✩ Advantages: 1)Spontaneous
chromosome doubling of
✩ Haploid microspores in in vitro
culture
✩ 2)Homozygosity achieved in a single
step Plants.
✩ Disadvantages: Less recombination
between linked markers Not all
systems are amenable to in vitro
culture

12. Methods of QTL Detection
✩ Studying single markers one
at a time.
✩ The simplest method for QTL
analysis.
✩ Can be done by t-tests or
ANOVA.
✩ Does not require a complete
linkage map.

13. Simple Interval mapping
✩ Two markers at a time
(flanking markers).
✩ Based on linkage mapping of
markers.
✩ More accurate than
single-marker analysis.

14. Composite interval mapping
✩ For detection of a QTL more than two markers are used
✩ It is based on linkage mapping of the marker.

15. Thank you

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