Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping”.
Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.
Natural population surveyed to determine MTA using LD.
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
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
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)
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
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.
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.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
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.
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)
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
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.
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.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
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.
Strategies for mapping of genes for agronomic traits in plantstusharamodugu
The genomic regions associated with the expression of a quantitative trait is referred to as quantitative trait loci (QTL).
A QTL may contain one or more genes affecting the concerned quantitative trait.
Sax(1923) reported linkage between seed coat colour and seed size, which are qualitative and quantitative traits in common bean and the work highlighted the basic principles for mapping of polygenes based on the detection of association between a quantitative trait phenotype and a genetic marker.
Thoday (1961) explored this QTL concept further by combining elaborate cytogenetic techniques with genetic analysis to map QTLs for several quantitative traits in Drosophila
Association mapping approaches for tagging quality traits in maizeSenthil Natesan
Association mapping has been widely used to study the genetic basis of complex traits in human and animal systems and is a very efficient and effective method for confirming candidate genes or for identifying new genes (Altshuler et al., 2008). Association mapping is now being increasingly used in a wide range of plants (Rafalski, 2010), where it appears to be more powerful than in humans or animals (Zhu et al., 2008). Unlike linkage mapping, association mapping can explore all the recombination events and mutations in a given population and with a higher resolution (Yu and Buckler, 2006). However, association mapping has a lower power to detect rare alleles in a population, even those with large effects, than linkage mapping (Hill et al., 2008). Yan et al., (2010) demonstrated that the gene encoding β-carotene hydroxylase 1 (crtRB1) underlies a principal quantitative trait locus associated with β-carotene concentration and conversion in maize kernels has been identified through candidate gene strategy of association mapping.
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.
Status and prospects of association mapping in crop plantsJyoti Prakash Sahoo
Polygenic inheritance of agronomic traits - controlled by multiple genes whose expression is affected by many factors. Hence phenotypic selection becomes tedious job.
Family mapping (Limitations- Biparental population, Low resolution, Analysis of only 2 alleles, time consuming).
Population or Association mapping (I) increased mapping resolution, (ii) reduced research time, and (iii) greater allele number (Yu and Buckler, 2006).
Potential for genomic selection in indigenous cattle breeds and results of GWAS in Gir dairy cattle of Gujrat by Dr.Pravin Kandhani and Dr. Vijay Trivedi KAMDHENU UNIVERSITY GANDHINAGAR
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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 .
(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.
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.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
2. 4 Cycles of intermating and selection – 15 years
Extensive phenotyping and value judgement
3. Association Mapping &
Advantages
‟Association genetics‟ or
‟association studies,” or
‟linkage disequilibrium
mapping”
Tool to resolve complex
trait variation down to the
sequence level by exploiting
historical and evolutionary
recombination events at the
population level.
Natural population surveyed
to determine MTA using LD.
4. Approaches
• On the basis of distance between two loci
• By analyzing linkage disequilibrium between marker and target gene in natural
population.
LD refers to nonrandom association of alleles at different loci.
LD can occur between more distant sites or sites located in different chromosomes
LD is difference between the observed gametic frequencies of haplotypes and the
expected gametic haplotype frequencies under linkage equilibrium .
D = PAB − PAPB = (PAB.Pab − PAb.PaB)
6. Estimation of LD
AB - 4/8 = 0.5
ab - 3/8 = 0.375
aB - 1/8 = 0.125
Frequencies
Lewontin, 1964
D = PAB-PA.PB
= 0.5-0.5*0.625 = 0.1875
Again if we calculate for “Ab”
D = PAb -PA.Pb
= 0.0-0.5*0.375 = -0.1875
D = PAB.Pab - PAb.PaB
= 0.5*0.375 – 0*0.125
= 0.1875
Standardised estimates
D’ and r2
7. • LD mapping detects and locates quantitative trait loci (QTL) by the strength of the
correlation between a trait and a marker.
• Offers greater precision in QTL location than family-based linkage analysis
• More efficient marker-assisted selection, facilitate gene discovery.
• Does not require family or pedigree information , can be applied to a range of
experimental and non experimental populations.
• Care must be taken during analysis to control for the increased rate of false
positive results arising.
(Mackay and Powell, 2007)
9. Advantages of Natural population
Any panmictic population.
Samples from natural
/breeding and synthetic
population
Random sample or core set
of germplasm .
Superior QTL from elite
germplasm directly used for
MAS.
10. NAM First developed in Maize, Common
founder – B73.
Higher power than AM panel, the
controlled crosses for NAM
minimize population structure and
familial relatedness.
Frequency of rare alleles increases.
Uses both historical LD and
recombinant LD.
BC NAM & DH NAM – also
developed.
11. MAGIC
Population development includes
many rounds of recombination .
- QTL precision & Resolution
Can be used directly or indirectly for
varietal development.
Common Wheat and Rice.
13. Population Structure
Relatedness
IBS (Identical By State)-Two
individual carrying the same
allele but not from common
ancestry.
IBD (Identical By Descend)-
Two individual carrying the
same allele and they have a
common ancestry
