The document discusses various types of mapping populations that can be used for linkage mapping of genetic markers and quantitative trait loci (QTL) in plants. It describes biparental populations like F2, backcross, recombinant inbred lines (RILs), and doubled haploids. It also discusses multiparental populations like immortalized F2 and MAGIC (Multi-parent Advanced Generation Intercross) populations. The key properties, advantages, and disadvantages of different mapping populations are summarized. Mapping populations are crucial resources that enable the construction of dense genetic linkage maps and identification of genomic regions associated with traits.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Linkage and QTL mapping Populations and Association mapping population.
F2, Immortalized F2, Backcross (BC), Near isogenic lines (NIL), RIL, Double haploids(DH), Nested Association mapping (NAM), MAGIC and Interconnected populations.
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Linkage and QTL mapping Populations and Association mapping population.
F2, Immortalized F2, Backcross (BC), Near isogenic lines (NIL), RIL, Double haploids(DH), Nested Association mapping (NAM), MAGIC and Interconnected populations.
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROG...Rachana Bagudam
1. FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROGRAMMES.
2. CONVERSION OF AGRONOMICALLY IDEAL GENOTYPES INTO MALE STERILES.
3. GENERATING NEW CYTONUCLEAR INTERACTION SYSTEM FOR DIVERSIFICATION OF MALE STERILES.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
Advanced biometrical and quantitative genetics akshayAkshay Deshmukh
Additive and Multiplicative Model
Shifted Multiplicative Model
Analysis and Selection of Genotype
Methods and steps to select the best model
Bioplot and mapping genotype
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROG...Rachana Bagudam
1. FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROGRAMMES.
2. CONVERSION OF AGRONOMICALLY IDEAL GENOTYPES INTO MALE STERILES.
3. GENERATING NEW CYTONUCLEAR INTERACTION SYSTEM FOR DIVERSIFICATION OF MALE STERILES.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
Advanced biometrical and quantitative genetics akshayAkshay Deshmukh
Additive and Multiplicative Model
Shifted Multiplicative Model
Analysis and Selection of Genotype
Methods and steps to select the best model
Bioplot and mapping genotype
In this presentation, we will delve into the principles of QTL mapping and explore various strategies for mapping QTLs in plants. We will also discuss the advantages and limitations, and provide insights into how QTL mapping is advancing our understanding of genetics.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Genetic markers, Classical markers, DNA markers, MICROSATELLITES, AFLP, SNP: Single Nucleotide Polymorphism, QTL: Quantitative Trait Locus, Activities of marker-assisted breeding, Marker-based breeding and conventional breeding Perspectives,The application of molecular technologies to plant breeding is still facing the following drawbacks and/or challenges
MAGIC :Multiparent advanced generation intercross and QTL discovery Senthil Natesan
MAGIC or multiparent advanced generation inter-crosses is an experimental method that increases the precision with which genetic markers are linked to quantitative trait loci (QTL). This method was first introduced by (Mott et al., 2000) in animals as an extension of the advanced intercrossing (AIC) approach suggested by (Darvasi and Soller , 1995)for fine mapping multiple QTLs for multiple traits. Advanced Intercrossed Lines (AILs) are generated by randomly and sequentially intercrossing a population initially originating from a cross between two inbred lines.
MAGIC involves multiple parents, called founder lines, rather than bi-parental control. AILs increase the recombination events in small chromosomal regions for the purpose of fine mapping. These lines are then cycled through multiple generations of outcrossing. Each generation of random mating reduces the extent of linkage disequilibrium (LD), allowing the QTL to be mapped more accurately.
Role of molecular marker play a significant supplementary role in enhancing yield along with conventional plant breeding methods. the result obtain through molecular method are more accurate and at genotypic level. It had wider applications in field of plant breeding, biotechnology, physiology, pathology, entamology, etc. The mapping information obtained from these markers had created a revolution in the sequencing sector and open many pathways for developments, innovations and research.
Process whereby a marker is used for indirect selection of a genetic determinant or determinants of a trait of interest (i.e. productivity, disease resistance, abiotic stress tolerance, and/or quality).
Trait of interest is selected not based on the trait itself but on a marker linked to it.
The assumption is that linked allele associates with the gene and/or quantitative trait locus (QTL) of interest. MAS can be useful for traits that are difficult to measure, exhibit low heritability, and/or are expressed late in development.
Pre-Requisites: Two pre-requisites for marker assisted selection are: (i) a tight linkage between molecular marker and gene of interest, and (ii) high heritability of the gene of interest.
Markers Used: The most commonly used molecular markers include amplified fragment length polymorphisms (AFLP), restriction fragment length polymorphisms (RFLP), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSR) or micro satellites, single nucleotide polymorphisms (SNP), etc. The use of molecular markers differs from species to species also.
A powerful non-transgenic reverse genetics method that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
EcoTILLING is a molecular technique that is similar to TILLING, except that its objective is to uncover natural genetic variation as opposed to induced mutations.
INTRODUCTION
Trichoderma -A Bio-Control Agent
General characteristics, PREPARATION OF MOTHER CULTURE, Materials required, Method of application, Precautions.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
How to Make a Field invisible in Odoo 17Celine George
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The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
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June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
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A Strategic Approach: GenAI in EducationPeter Windle
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MAPPING POPULATIONS
1.
2. INTRODUCTION
The demand being placed on food production globally require greater advances in
genetic improvement of our food crops.
A crucial step towards achieving these advances is the rapid identification of genetic
elements that can be utilized in breeding food crops.
The identification of genes underlying simply inherited traits has been very
successful.
Most traits of biological and economic interest in crop plants are of quantitative
nature, displaying continuous variation and are under polygenic control and
identification of such genes is difficult.
The development of molecular marker technology has renewed interest in genetic
mapping.
RFLP was the first DNA marker to be developed and used in mapping experiment.
The use of DNA markers has allowed construction of dense linkage maps in many
important plant species and has enabled the mapping of the elusive quantitative trait
loci (QTLs).
4. Historical Aspects
• In 1910, Morgan provided the first experimental evidence for the chromosomal
theory: he demonstrated that the inheritance pattern of white-eye gene of
Drosophila indicated it to be located on the X chromosome. One year later, in
1911, Morgan described the essential features of linkage between genes.
• In the year 1913, Sturtevant published the first linkage map of Drosophila.
• Subsequently, morphological markers were used to construct linkage maps in
many species.
• Geneticists mounted search for more abundant markers, and protein
polymorphisms were the first molecular variations used to generate linkage
maps.
• The limited number of protein polymorphisms and the environmental influence
on their expression were the major drawbacks, which favored the development
of DNA markers.
5. LINKAGE MAPPING
Mapping is putting markers (and genes or QTL) in order, indicating
the relative distances among them, and assigning them to their
linkage groups on the basis of their recombination values from all
pair wise combinations.
A linkage map may be thought of as a ‘roadmap’ of the
chromosomes derived from two different parents (Paterson,1996a)
Linkage maps indicate the position and relative genetic distances
between markers along chromosomes.
Construction of linkage maps requires the following:
(1) a suitable marker system,
(2) an appropriate mapping population, and
(3) software for proper analysis of the data.
6. The first step in mapping of markers is to select two genetically divergent parents expected
to differ in lager number of markers and/or trait of interest.
General Procedure for Linkage Mapping Of
Molecular Markers
The selected parents are crossed and a suitable mapping population is developed
The parents are tested with large number of markers to identify polymorphic markers.
All the individuals of the mapping population are screened with the polymorphic marker; this
is called GENOTYPING.
The marker genotype data are analyzed using a suitable software package to estimate
recombination frequencies and genetic distances between marker pairs
7. Group the markers into linkage groups, select the most likely marker order, and prepare
a marker linkage map.
All individuals of the mapping population are evaluated for phenotypic expression of the
trait, this is known as PHENOTYPING.
The trait phenotype and marker genotype data are analyzed using a suitable computer
program to identify the markers governing the target trait.
Estimate the frequency of recombination between the gene and the markers and
ultimately prepare a linkage map.
8. MAPPING POPULATIONS
A POPULATION THAT IS SUITABLE FOR LINKAGE MAPPING OF GENETIC
MARKERS IS KNOWN AS MAPPING POPULATION.
Generated by crossing two or more genetically diverse lines and handling the
progeny in a definite fashion. They are usually produced from controlled
crosses.
Mapping populations serve as basic tools needed for the identification of
genomic regions harbouring genes/ QTLs and for estimating the effects of
QTL.
9. Primary mapping populations are created by hybridization between two homozygous
lines usually having contrasting forms for the traits of interest.
Secondary mapping populations on the other hand, 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.
Mortal mapping populations are short lived populations and each individual of the
populations have their own unique identity.
Immortal mapping populations are the population which can reproduce itself or can be
reproduced without any change in genetic make up of constituent individuals.
Bi-parental mapping populations are obtained by the crosses between two parents.
Multi-parental mapping populations involve more than two parents. E.g. MAGIC.
TYPES OF MAPPING POPULATIONS:
1. PRIMARY AND SECONDARY MAPPING
POPULATIONS.
2. MORTAL AND IMMORTAL MAPPING
POPULATIONS.
3. BIPARENTAL AND MULTIPARENTAL MAPPING
POPULATIONS.
10. Selection of parents for developing mapping
populations
The two lines selected as parents (P1) and (P2), should be
completely homozygous.
They should differ for as many qualitative and metric traits as
possible.
The parents should be polymorphic for as many molecular markers
as possible to afford the construction of dense linkage map.
The parents of mapping populations must have sufficient variation for
the traits of interest at both the DNA sequence and the phenotype
level.
11.
12. F2 POPULATION
It consist of the progeny produced by selfing/ sib
mating of the F1 individuals from a cross between
the selected parents.
Homozygous and heterogeneous population.
Different plants in F2 population differ with each
other.
Product of a single meiotic cycle i.e. one round of
recombination.
The ratios expected for dominant and co
dominant markers are 3:1 and 1:2:1 respectively.
13. Appropriate population for
preliminary mapping of markers
and oligogenes.
Useful in identifying heterotic
QTLs.
Requires less time and efforts for
development.
Linkage established using F2
population is based on one cycle of
meiosis.
Precise evaluation of quantitative
traits and their effects of G*E
cannot be done.
F2 populations are ephemeral and
therefore cannot be maintained
beyond one generation.
Limited use in fine mapping and
QTL mapping
14. F2 derived F3(F2:3) 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.
F2:3 populations are suitable for mapping of oligogenic traits
controlled by recessive genes and of QTLs .
Useful for reconstitution of individual F2 genotypes.
The construction of these populations requires an extra
season than that of F2 populations.
The genotype and, particularly, phenotype of the F3
population do not strictly correspond to that of the F2
generation due to one more round of segregation,
recombination, and inbreeding.
15. Doubled Haploids:
Doubled haploid (DH) plants are obtained
by chromosome doubling of haploid plants
usually derived by culture of anthers/pollen
grains produced by F1 plants.
Seeds from individual DH plants are
harvested separately and maintained as
DH lines in the same way as RILs.
The expected ratio for the genes as well as
markers in a DH population is 1:1
irrespective of the marker being dominant
or co dominant.
DHs are similar to F2 in that they both are
products of one meiotic cycle occurring in
F1. But the differ in the frequency of
recombinants.
16. Double Haploids:-
Completely
homozygous.
Perpetual/ Immortal.
Can be evaluated in
replicated yield trials.
Suitable for mapping of
both qualitative as well
as quantitative traits.
Instant production of
homozygous lines.
Recombination from
male side alone is
accounted
Non-availability of
suitable haploid
production techniques
Anther culture induced
variation.
Differential
regeneration response
of parents.
17. Usually the F1 as a rule is
backcrossed to the
recessive parent i.e., the
parent having the
recessive form of the
target trait. Such a
backcross is called
testcross, and is usually
denoted by B2.
Backcross populations
are generated by
crossing F1 plants with
either of the two
parents of the
concerned F1.
BACKCROSS POPULATION
In the case of co-dominant markers, the order of backcross as well as the phase of
linkage is not important when only markers are to be scored.
But, in the case of dominant markers, the order of backcross is extremely important as
they give difference in segregation ratio with difference in phase of linkage.
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 (Tanksley and Nelson 1996).
18. The construction of backcross populations, like that of F2:3 populations, requires
one more generation than that of F2 populations.
Cannot be evaluated in replicated trials, which makes them unsuitable for QTL
mapping.
They are not perpetual/they are mortal.
They capture the recombination events of only one parent, i.e., the F1.
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.
19. Recombinant Inbred Lines(RILs)
Recombinant inbred lines(RILs) are a set of
homozygous lines produced by sib mating/selfing
of individual F2 plants.
RILs are also called F2-derived inbred lines or
single seed descent (SSD) lines because they
are derived from F2 populations usually by the
SSD procedure.
Wherever possible, F2 plants and their progeny
should be selfed, and sib-mating should be
resorted to only when selfing is not feasible for
some reason.
20. The SSD procedure is followed for
five or more (usually >8) generations,
during which one seed is harvested
from each plant of the F2 and the later
generations and seeds from all the
plants are composited and planted to
raise the next generation.
At the end of SSD procedure, seeds
from each plant are harvested
separately to obtain as many RILs as
there are individual plants in the SSD
population.
Homozygous populations.
21.
22. RILs are immortal.
Most commonly used for QTL
mapping.
Suitable for fine mapping
&map saturation.
RILs are twice as efficient
as an F 2 population.
Multilocation trials can be
conducted as they are
homozygous lines.
Require 6-10 seasons to
develop.
Development difficult in crops
which show non tolerance to
inbreeding depression.
Only used for Additive and AXA
type of interactions.
Genetically variable over time
due to mechanical mixture,
mutations etc..
Smaller confidence interval.
MERITS DEMERITS
23. Immortalized F2 population
Immortalized F2 populations can be developed by paired crossing of the randomly
chosen RILs derived from a cross in all possible combinations excluding reciprocals.
The set of RILs used for crossing along with the F1s produced, provide a true
representation of all possible genotype combinations (including the heterozygotes)
expected in the F2 of the cross from which the RILs are derived.
The RILs can be maintained by selfing and required quantity of F1 seed can be
produced at will by fresh hybridization.
This population therefore provides an opportunity to map heterotic QTLs and
interaction effects from multilocation data.
24. ADVANTAGES
Population identical to the conventional F2 population can be produced and
replicated “n” number of times.
Individual F2 genotypes can be evaluated over the years and locations.
Eliminates the need of genotyping the immortalized F2s. Their genotype can
be deduced based on their parental RILs genotypes. Thus economizing the
cost of mapping.
Can be used for mapping all the traits for which the parents of the RILs and
the RILs show contrasting phenotype.
It is possible to eliminate the additive X dominance(J) and dominance X
dominance (i) effects.
25. Near Isogenic Lines.(NILs)
Near-isogenic lines (NILs) are
pairs of homozygous lines that are
identical in genotype, except for a
single gene/locus.
NILs are generally produced by
backcross procedure. But they
can also be produced by selfing.
The first strategy used for
molecular mapping was based on
NIL itself.
26.
27. Immortal populations
Suitable for gene
tagging
Useful in functional
genomics
Require
many
generations
to develop
Not useful for
linkage mapping.
Linkage drag
MERITS DEMERITS
28.
29. Marker type F2 RILs DHs NILs B1 B2
Codominant 1:2:1 1:1 1:1 1:1 1:1 1:1
Dominant 3:1 1:1 1:1 1:1 1:0 1:1
Segregation ratios at dominant and codominant marker loci in different mapping
populations
Codominant markers: RFLPs, SSRs, CAPSs
Dominant markers: RAPDs, AFLPs, most SCARs, IISRs, SNPs, DArT, SFPs, RAD markers.
31. Multi-parental Population (MAGIC)
Multi-parent Advanced Generation Intercross (MAGIC) populations are a collection of
RILs produced from a complex cross/ outbreed population involving several parental
lines.
The parental lines may be inbred lines, clones, or individuals selected on the basis of
their origin or use.
This concept was first used in mice as “heterogeneous stocks” and later extended to
plants by Mackay and Powell (2007), who also proposed the name MAGIC.
MAGIC populations are perpetual, lack population structure, can be used for both
linkage and association analysis.
They are an ideal resource for construction of high-density maps.
Parents of the MAGIC population may be selected to represent a large part of
variation present in the elite germplasm of a crop species.
33. This complex cross is handled as per the SSD procedure to develop the required number of
RILs, which together constitute the MAGIC population.
A simple approach to generate a MAGIC population is to produce a complex cross involving
multiple, typically eight, parental lines and to isolate RILs from this cross.
The 8 parental lines are crossed in pairs to produce four different single crosses, and these
single crosses are crossed in pairs to generate two double crosses
Finally, the two double crosses are mated together to produce an eight-parent complex cross.
34.
35. APPLICATIONS:
The short term mapping populations like F2, BC, can be a good starting point
in molecular mapping.
Long term mapping populations like RILs, DHs, NILs, CSSLs, Immortalized
F2, MAGIC can be developed for precision phenotyping of the traits of
importance.
RILs, NILs, DHs are homozygous lines and can be used for studying of
additive gene actions or additive QTLs.
Immortalized F2 population, F2 population, BC poulstion can be used for
studying heterotic QTLs.
36. Parent 1 Parent 2
F1
Back crossing Anther Culture
Selfing
F2
Pedigree Method Bulk Method
SSD
RILs
Immortal mapping populations
NILs DHs
Characterization for targettraits Molecular genotyping
Identification of markers linked to target traits MAS
F2 population
Backcross population
X
37. CONCLUSION:-
Development and characterization of mapping populations should become an integral
part of the ongoing breeding programs in important crops.
The role of geneticists and plant breeders become crucial for reaping the full benefits of
molecular plant breeding.
MARKER
MAPPING
POPULATION
SOFTWARE
38. REFERENCES
Marker- assisted plant breeding: Principles and Practices by BD Singh and AK Singh
http://bioinformatics.iasri.res.in
www.ndsu.edu