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.
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
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.
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
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.
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: Genomic Estimated 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)
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.
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: Genomic Estimated 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)
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.
It comprises on mating designs used in plant breeding programs. 6 basic mating designs are briefly explained in it with their requirements as well limiting factors...
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.
Mating design is a schematic cross between the groups or strains of plants are made in a plant breeding that is common in agriculture and biological sciences
Analysis of variance in offspring plants results from a mating design
To evaluate the effects of additive, dominance ,and epistasis and heritability value equal to the value of genetic expectations
Gene mapping | Genetic map | Physical Map | DNA Data Analysis (upgraded)NARC, Islamabad
Genes are useful markers but not ideal.
Mapped feature that are not genes are called DNA markers.
DNA markers must have at least two alleles to be useful.
DNA sequence features that satisfy this requirement are-
– Restriction Fragment Length Polymorphism (RFLP)
Southern hybridization
PCR
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)
Mapping- determining the location of elements with in a genome, with respect to identifiable land marks.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.
In simple mapping of genes to specific locations on chromosomes.
Two types
Genetic map
Physical Map
They are useful in predicting results of dihybrid and trihybrid crosses.
It allows geneticists to understand the overall complexity and genetic organization of a particular species.
Identify genes responsible for diseases.
Identify genes responsible for traits.
genetic maps are useful from an evolutionary point of view.
Introduction
Backcross breeding & its types
Marker assisted breeding
Marker assisted backcross breeding (MABC)
Main strategies
Advantages over conventional breeding
Case studies
Future outlook
Conclusion
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
2. • Population suitable for linkage mapping of genetic markers .
• Population were in both marker and target traits segregate.
• Crossing the genetically diverse lines and handling the progenies in a definite
fashion.
• Determines genetic distance b/w genes or loci and map them to specific location
in genome.
• Identifies the markers linked to genes /loci of interest (used for MAS).
• Choice depends on objective , cost and accessibility and availability of marker
system.
Introduction
3. • Source of parents
• Homozygous (DH to avoid residual heterozygosity)
• Maximum polymorphism at DNA and Phenotypic level – should differ for as
many traits as possible.
• Polymorphic for many molecular markers to construct dense linkage map.
Whether the adapted or exotic germplasm should be used for developing mapping
population?
Selection of Parents
4. Types of Mapping Population
Primary
• Created by hybridization between
homozygous lines.
F2 population
F2 Derived F3 (F2 :F3 )population
Immortalized F2
Backcross population (BC)
Double Haploids(DHs)
Recombinant inbred Lines(RILs)
Near Isogenic Lines(NILs)
Chromosome Segment Substitution Lines(CSSL)
Inter connected populations
MAGIC Populations
Secondary
• Created by crossing two lines
selected from mapping
population.
• Fine mapping
5.
6. • Produced by selfing or sibmating of the F1s between selected parents
• Simplest and rapid method
• Unreplicated block and traits scored in individual plants.
• Maize- most of the traits – dominance & epistatic variance
F2 x Testers --------- Test cross progenies evaluated.
Merits:
• Appropriate populations for preliminary mapping
• Useful in identifying heterotic QTLs
• Estimates additive , dominance , epistatic variance
• Requires less time and efforts for development
Demerits:
• Linkage established using F2 population is
based on one cycle of meiosis
• Ephemeral
• Quantitative traits cannot be precisely mapped
using F2 Population.
• Of limited use for fine mapping and map
saturation
F2 POPULATION
7. • Obtained by selfing F2 individuals for single generation and F2 plants harvested on single
plant basis to maintain individual plant progeny.
• Bulked DNA from F3 family represent the individual F2 plant.
• Mean phenotype of multiple plants in F2 :F 3 relates to the phenotype of its parent F2 plant.
• Suitable for mapping quantitative traits
and mapping recessive genes.
• Useful for reconstitution of individual
F2 genotypes.
Demerits:
• Requires extra season than F2
• Underestimates dominance , epistatic components since increased level of inbreeding.
• Ephemeral.
F2 Derived F3 (F2 :F 3 )population
8. • Gardiner et al- 1993 – first to use Immortalized F2 population in maize.
F3 progeny from F2 were intermated in 2 groups and seeds from 20 such plants
are harvested in bulk and this is followed for each F2 plant.
• Hua et al 2002
9. • 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.
• Provides an opportunity to map heterotic QTLs and interaction effects from
multilocation data.
• IF2 population by itself is not perpetual , but can be reconstructed from
Parents RIL which are perpetual - term Immortalized.
10. To analyse the specific genes or other regulatory DNA elements derived from one
parent (donor)in the background of another parent(recurrent),The hybrid F1 plant
is backcrossed to recurrent parent.
• In genetic analysis,
backcross with recessive parent
(testcross) is used.
Back cross Population
11. MERITS:
• The elite combination is not lost
• Less time require to develop.
• the populations can be further utilized for marker-assisted backcross
breeding.
DEMERITS:
• Cant used for quantitative traits.
• The recombination information in BC is based on only one parent .
• Ephemeral
12. Doubled Haploids
• DH lines - identical set of chromosomes
• Haploid plants – Anther/ ovule culture,
Bulbosum technique, use of haploid
inducer strains (Maize).
• DH obtained artificially by colchicine
treatment of haploid plants.
13. Use of haploid inducer strains – RWS or RWK 76
• Haploid embryo develops by elimination of
inducer strain chromes but with triploid
endosperm.
Haploid seed selection:- based on colour of
embryo and endosperm.
Female – rnj rnj (colurless)
Male inducer - Rnj Rnj (violet color)
The haploid seeds produced will have
coloured endosperm with colourless
embryo.
Diploid seeds – both embryo and
endosperm coloured.
Selfed seeds- both colourless.
14. Merits:
• DHs are permanent mapping population -
replicated and evaluated over locations and
years.
• Used in mapping of both qualitative and
quantitative trait.
• Fast production of homozygous line and
perpetual.
DEMERITS:
• Since it involves in in vitro techniques,
relatively more technical skill are required.
• Not suitable for mapping heterosis QTL and
estimates only additive variance.
• Recombination from the male side alone is
accounted.
15. RILs are the homozygous selfed or sibmated progeny of the individual of an
F2 population .
Single seed descent method is best for development.
Bulk and pedigree method without selection also used.
RILs with more than 98%homozygosity are produced by selfing within 8-9
generations . segregation ratio of RILs is 1:1
Sibmating is used when selfing is not possible – since rate of decrease of
heterozygosity is only one fourth. So it requires twice as many generation as
compared to selfed progeny to attain homozygosity.
Recombinant inbred lines
16. Epigenetic RIL population – Arabidopsis
Two parental lines with little difference in DNA sequence but with contrasting
patterns of DNA methylation was crossed .
Member lines of epiRILs were with same genotype and differ only in epigenetic
modifications.
Merits:
• Perpetual population, they can be replicated over different locations
• RILs can be propagated without seggregation.
• Product of many meiotic cycles so useful to identify tightly linked markers.
• Twice efficient than F2 and suitable for fine mapping and map saturation.
Demerits:
• Require many season to develop RILs.
• RIL development is difficult in crops having high inbreeding depression.
18. NILs developed through backcrossing are similar to recurrent parent but differ for the
gene of interest, while NILs developed though selfing are similar in pair but differ for
the gene of interest (however, differ a lot with respect to the recurrent parent)
19. MERITS:
• Perpetual population
• Used for fine mapping
• useful in functional genomics
DEMERITS:
• Many generations require to develop
NILs
• Increased cost, time and efforts.
• Directly useful only for molecular
tagging of the gene concerned, but not
for linkage mapping
• Linkage drag is a potential problem in
constructing NILs.
20.
21. • CSSL are a series of homozygous lines with single distint chromosome segment
from DP. Produced by crossing and backcrossing the donor and recipient parents
by using marker –assisted selection (MAS) that finally contain the entire genome
information of the donor parent.
• CSSL s are often called introgression line library
• Types- intervarietal substitution line and introgression line/ alien CSSL.
• Sufficiently large number of plants are used for each backcross so that nearly all
the different segments of the donor parent genome are included in the back
cross.
Chromosomal Segment substitution lines
24. Merits:
• Perpetual
• Detects QTL with small effects.
• They can be evaluated in replicated yield trials, and are suitable for
mapping of both oligogenes as well as QTLS.
• Used for linkage as well as fine mapping in the same manner as are NILS
• Very useful for gene introgression.
Demerits:
• CSSL require as much time as that of NILS.
• Undesirable gene may be linked to favorable gene present in the
introgressed genomic segment :this phenomenon is called Linkage drag.
25. • Involves mating among set of homozygous lines in such a way that two or
more crosses have one parent in common.
• The crosses can be made according to suitable mating design , eg: full
diallel ,half diallel , factorial, nested, etc….
• Half diallel mating design excluding selfs has been used for creating inter
connected mapping population.
Interconnected Population
26. NAM –Nested Association mapping population
A, B – Reference inbreds
1,2,3,….n – diverse inbreds representing diversity in concerned crop species.
27. • RILs collection from a complex cross involving number of parental
lines.(usually-8)
• Parental lines _ inbred lines, clones, individual plants complex cross is
subjected to continuous selfing and the progeny plants in the selfing
generation are handled according to SSD.
• In the end suitably large number of RILs are isolated which together
constitute the MAGIC population.
Multi parent advanced generation inter cross
populations:(MAGIC)
28. Merits:
• MAGIC population are homozygous and can be maintained indefinitely
• for mapping both genes and QTLS and suitable for linkage and association
mapping.
• In some cases the parental lines may be elite breeding lines; in such a
situation the MAGIC lines might be used for variety developmentwithout
any further breeding effort, but once created, they can be multiplied,
distributed, and maintained perpetually.
