I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
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.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
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.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
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
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Biotechnology for Crop Improvement.
Molecular Plant Breeding-Marker Assisted Breeding/Selection.
Comparison between three main and commonly discussed marker systems- RFLP, RAPD and AFLP.
Basic Understanding for Simple Sequence Repeats, SCAR and CAPS.
Strategies to overcome food shortages using molecular plant breeding approaches, Application of various molecular marker systems and examples.
Reference List.
Presenter: Brenda Chong
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.
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
Targeted Induced Local Lesions IN Genome. Mutations (Single base pair substitution) are created by traditionally used chemical mutagens. Identify SNPs and / or INDELS in a gene / genes of interest from a mutagenized population.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Biotechnology for Crop Improvement.
Molecular Plant Breeding-Marker Assisted Breeding/Selection.
Comparison between three main and commonly discussed marker systems- RFLP, RAPD and AFLP.
Basic Understanding for Simple Sequence Repeats, SCAR and CAPS.
Strategies to overcome food shortages using molecular plant breeding approaches, Application of various molecular marker systems and examples.
Reference List.
Presenter: Brenda Chong
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.
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
Targeted Induced Local Lesions IN Genome. Mutations (Single base pair substitution) are created by traditionally used chemical mutagens. Identify SNPs and / or INDELS in a gene / genes of interest from a mutagenized population.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
Presentation by Jacob van Etten.
CCAFS workshop titled "Using Climate Scenarios and Analogues for Designing Adaptation Strategies in Agriculture," 19-23 September in Kathmandu, Nepal.
this presentation is about the molecular markers as we all know the molecular markers are the DNA sequences it can be easily detected and its inheritance is easily monitored.so the main basics of the molecular markers is the polymorphic nature so it can used as molecular markers.and this will gives you the idea about AFLP, RFLP, RAPD, SNPS,ETC.
Marker assisted selection is the breeding strategy in which selection for a gene is based on molecular markers closely linked to the gene of interest rather than the gene itself, and the markers are used to monitor the incorporation of the desirable allele from the donor source. Selection of a genotype carrying desirable gene via linked marker (s) is called Marker Assisted Selection. MAS can be applied to possible to use this kind of information.
The prerequisites for the classical procedure of MAS are the tight linkage between molecular marker and gene of interest and high heritability of the gene of interest. It is noteworthy that the “quality” and the number of markers have a major impact on the success of MAS. The quality of markers relates to their characteristics and to the cost and the efficiency of the genotyping process. The number of markers affects the reliability of the linkage between them and the gene(s). In other words, screening a large number of markers has the potential to identify close and reliable linkage between the marker and the gene of interest. MAS has greater potential for efficient gene pyramiding combining several important genes in one cultivar. MAS is gaining considerable importance as it can improve the efficiency of plant breeding through precise transfer of genomic regions of interest and acceleration of the recovery of the recurrent parent genome. Marker-assisted selection is gaining considerable importance as it would improve the efficiency of plant breeding through precise transfer of genomic regions of interest (foreground selection) and accelerating the recovery of the recurrent parent genome (background selection). The use of MAS in crop improvement will not only reduce the cost of developing new varieties but will also increase the precision and efficiency of selection in the breeding program as well as lessen the number of years required to come up with a new crop variety.
Role of Marker Assisted Selection in Plant Resistance RandeepChoudhary2
Topic Role of Marker Assisted Selection in Plant Resistance is described in detail including some case studies.
Types of markers used in genetic engineering and biotechnology are described in detail.
Marker assisted selection is a process whereby a marker (morphological, biochemical or one
based on DNA/RNA variation) is used for indirect selection of a genetic determinant of a trait
of interest. Since the first reported linkage of an agronomically important trait (a quantitative
trait locus affecting seed weight) to a simply controlled gene (seed colour) in common bean by
Sax (1923), it has taken more than 60 years for genetic markers to become a qualified tool for
plant breeding programs. In rice, the Xieyou 218 hybrid was the first to be developed through
MAS to select individuals carrying a bacterial blight-resistant gene. Marker-assisted selection
(MAS) can be applied at the seedling stage, with high precision and reductions in cost. Genetic
mapping of major genes and quantitative traits loci (QTLs) for agricultural traits is increasing
the integration of biotechnology with the conventional breeding process. Traits related to
disease resistance to pathogens and to the quality of some crop products are offering some
important examples of a possible routinary application of MAS. For more complex traits, like
yield and abiotic stress tolerance, a number of constraints have severe limitations on an efficient
utilization of MAS in plant breeding. However, the economic and biological constraints such
as a low return of investment in small-grain cereal breeding, lack of diagnostic markers, and
the prevalence of QTL-background effects hinder the broad implementation of MAS but over
the past 2 decades, a number of R-genes conferring resistance to a diverse range of pathogens
have been mapped in many crops using molecular markers.
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.
Marker assisted selection or marker aided selection is an indirect selection process where a trait of interest is selected based on a marker linked to a trait of interest, rather than on the trait itself. This process has been extensively researched and proposed for plant and animal breeding.Marker-assisted breeding uses DNA markers associated with desirable traits to select a plant or animal for inclusion in a breeding program early in its development. ... This genetic test is helping breeders to select for hornless cattle, which makes it safer for the animals themselves and the people handling them.
Molecular Markers: Indispensable Tools for Genetic Diversity Analysis and Cro...Premier Publishers
Recent progress in molecular biology has led to the development of new molecular tools that offer the promise of making plant breeding faster. Molecular markers are segments of DNA associated with agronomically important traits and can be used by plant breeders as selection tools. Breeders can use marker-assisted selection (MAS) to bypass the traditional phenotype-based selection methods in order to improve crop varieties with pyramiding the desirable traits within short time. Various molecular markers such as RAPD, SSR, ISSR, RFLP, AFLP, SNP, SCAR, CAPS, etc. are extensively used for plant genetic diversity studies and crop improvement biotechnology. These markers are different in characteristic properties, applicability to various plants, unique in the resolving power and also have own advantages and disadvantages. This review article provides a valuable insight into different molecular marker techniques, classification, their advantages, disadvantages, ways of actions, uses of molecular markers in plant genetic diversity analysis and quantitative trait loci (QTL) mapping. It could be helpful for plant scientists and breeders in MAS breeding and crop improvement biotechnology in the post-genomic era.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
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.
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 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.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
3. The differences that distinguish one plant from another are encoded in the
plant’s genetic material, the DNA. DNA is packaged in chromosome pairs,
one coming from each parent. The genes, which control a plant’s
characteristics, are located on specific segments of each chromosome.
Introduction
Genetic diversity
The differences that distinguish one plant from another are encoded in the
plant’s genetic material, the DNA. DNA is packaged in chromosome pairs,
one coming from each parent. The genes, which control a plant’s
characteristics, are located on specific segments of each chromosome.
http://www.isaaa.org/resources/publications/pocketk/19/default.asp
4. DNA Fingerprinting
DNA fingerprinting, also called DNA typing, DNA profiling, genetic
fingerprinting, genotyping, or identity testing, is genetics method
used for isolating and identification the base-pair pattern in
individual’s DNA
• Paternity and Maternity test
• Plant Variety Protection
• Genetic purity test
• Studying biodiversity
• Tracking genetically modified crops
DNA fingerprinting is used in several ways.
DNA fingerprinting, also called DNA typing, DNA profiling, genetic
fingerprinting, genotyping, or identity testing, is genetics method
used for isolating and identification the base-pair pattern in
individual’s DNA
• Paternity and Maternity test
• Plant Variety Protection
• Genetic purity test
• Studying biodiversity
• Tracking genetically modified crops
5. DNA Fingerprinting
An Example: Using DNA in Paternity and Maternity test / Plant variety
protection and genetic purity test
marker
F1F M
1
2
3
4
5
6
S1 S2
F = female parent, M = male parent
F1 = Hybrid
S1 = Sample#1
: Same female / different male
S2 = Sample#2
:Different female / Same male
Testing can be done on seed or leaf
marker
5
6
7
8
9
10
DNA profile using 10 different marker (dominant
marker)
F = female parent, M = male parent
F1 = Hybrid
S1 = Sample#1
: Same female / different male
S2 = Sample#2
:Different female / Same male
7. DNA Fingerprinting
• Genetic distance
• Cluster analysis
Useful information for
Breeder to arrange
heterotic group
Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties.
Molecular Breeding 10: 181–191, 2002
8. Molecular Breeding
Molecular breeding (MB) may be defined in a broad-sense as the use of
genetic manipulation performed at DNA molecular levels to improve characters of
interest in plants and animals (MAB+GMO)
Marker-assisted breeding (MAB) and is defined as the application of
molecular biotechnologies, specifically molecular markers, in combination with
linkage maps and genomics, to improve plant or animal traits on the basis of
genotypic assays this term is covered several modern breeding strategies,
including marker-assisted selection (MAS), marker-assisted backcrossing (MABC),
marker-assisted recurrent selection (MARS), and genome-wide selection (GWS) or
genomic selection (GS) (Ribaut et al., 2010)
Molecular breeding (MB) may be defined in a broad-sense as the use of
genetic manipulation performed at DNA molecular levels to improve characters of
interest in plants and animals (MAB+GMO)
Marker-assisted breeding (MAB) and is defined as the application of
molecular biotechnologies, specifically molecular markers, in combination with
linkage maps and genomics, to improve plant or animal traits on the basis of
genotypic assays this term is covered several modern breeding strategies,
including marker-assisted selection (MAS), marker-assisted backcrossing (MABC),
marker-assisted recurrent selection (MARS), and genome-wide selection (GWS) or
genomic selection (GS) (Ribaut et al., 2010)
Molecular breeding (MB) may be defined in a broad-sense as the use of
genetic manipulation performed at DNA molecular levels to improve characters of
interest in plants and animals (MAB+GMO)
Marker-assisted breeding (MAB) and is defined as the application of
molecular biotechnologies, specifically molecular markers, in combination with
linkage maps and genomics, to improve plant or animal traits on the basis of
genotypic assays this term is covered several modern breeding strategies,
including marker-assisted selection (MAS), marker-assisted backcrossing (MABC),
marker-assisted recurrent selection (MARS), and genome-wide selection (GWS) or
genomic selection (GS) (Ribaut et al., 2010)
Guo-Liang Jiang: Molecular Markers and Marker-Assisted Breeding in Plants
9. Some traits, like flower color, may be controlled by only
one gene. Other more complex characteristics like crop
yield or starch content, may be influenced by many genes.
Traditionally, plant breeders have selected plants based on
their visible or measurable traits, called the phenotype.
This process can be difficult, slow and influenced by the
environment.
Molecular Breeding
Some traits, like flower color, may be controlled by only
one gene. Other more complex characteristics like crop
yield or starch content, may be influenced by many genes.
Traditionally, plant breeders have selected plants based on
their visible or measurable traits, called the phenotype.
This process can be difficult, slow and influenced by the
environment. http://www.isaaa.org/resources/publications/pocketk/19/default.asp
10. USING MOLECULAR MARKERS
Some of the advantages of using molecular markers instead of
phenotypes to select are:
o Early selection (at seedling, or even for seeds)
o Reduced cost (fewer plants, shorter time)
o Reduced cycle time (if gene is recessive or measured after
flowering)
o Screening more efficient (if it is a complex trait)
Moreaux, 2011
Molecular Breeding
USING MOLECULAR MARKERS
Some of the advantages of using molecular markers instead of
phenotypes to select are:
o Early selection (at seedling, or even for seeds)
o Reduced cost (fewer plants, shorter time)
o Reduced cycle time (if gene is recessive or measured after
flowering)
o Screening more efficient (if it is a complex trait)
Moreaux, 2011
Chance to select the
right plant before
flowering
Chance to select heterozygous plant
USING MOLECULAR MARKERS
Some of the advantages of using molecular markers instead of
phenotypes to select are:
o Early selection (at seedling, or even for seeds)
o Reduced cost (fewer plants, shorter time)
o Reduced cycle time (if gene is recessive or measured after
flowering)
o Screening more efficient (if it is a complex trait)
Moreaux, 2011
12. Marker Assisted Selection (MAS)
The use of DNA markers that are tightly-linked to
target loci as a substitute for or to assist phenotypic
screening or selection.
Molecular Breeding Method
Marker Assisted Selection (MAS)
The use of DNA markers that are tightly-linked to
target loci as a substitute for or to assist phenotypic
screening or selection.
13. Marker Assisted Selection
Early generation selection
The main advantage is to discard
many plant with unwanted gene
combinations, especially those
that lack essential disease
resistance traits .
This has important in the later
stages of the breeding program
because the evaluation for other
traits can be more efficiently and
cheaply designed for fewer
breeding lines .
Early generation selection
The main advantage is to discard
many plant with unwanted gene
combinations, especially those
that lack essential disease
resistance traits .
This has important in the later
stages of the breeding program
because the evaluation for other
traits can be more efficiently and
cheaply designed for fewer
breeding lines .
http://www.knowledgebank.irri.org/ricebreedingcourse/Marker_assisted_breeding.htm
Early generation selection
The main advantage is to discard
many plant with unwanted gene
combinations, especially those
that lack essential disease
resistance traits .
This has important in the later
stages of the breeding program
because the evaluation for other
traits can be more efficiently and
cheaply designed for fewer
breeding lines .
15. Marker Assisted Selection
Category Gene Sweetness Texture Flavor Germination
/Vigor
Shelf life
Important gene controlling endosperm in sweet corn
Germination
/Vigor
Standard sweet su1 10%
sucrose
creamy good good short
Sugar-enhanced se 2X sucrose creamy good good longer
Super sweet sh2,bt1,
bt2
3X-8X
sucrose
Less
creamy
poor poor Longsh2,bt1,
bt2
3X-8X
sucrose
Less
creamy
Kamol Lertrat / Taweesak Pulam: Breeding for incresing sweetness in corn
16. Marker Assisted Selection
In recent years new varieties have been developed that have
different combinations of the three major genes (su, se and
sh2 ) ‘stacked’ together.
In recent years new varieties have been developed that have
different combinations of the three major genes (su, se and
sh2 ) ‘stacked’ together.
Category Kernels type Advantage Variety name
High sugar sweet
corn
• 25% sh2 kernels
• 25% se kernels
• 50% su kernels
• su vigor
• higher sugar
• Sweet Chorus
• Sweet Rhythm
High sugar sweet
corn
• 100% sh2 kernel
• se trait in all kernels
• high sugar
• long shelf life
• tender
• Gourmet Sweet™
• Multisweet™
• Xtra-Tender Brand™
http://www.uvm.edu/vtvegandberry/factsheets/corngenotypes.html
17. Marker Assisted Backcross (MABC)
MABC aims to transfer one or a few genes/QTLs of
Interest from one genetic source into a superior
cultivar or elite breeding line to improve the
targeted trait.
Molecular Breeding Method
Marker Assisted Backcross (MABC)
MABC aims to transfer one or a few genes/QTLs of
Interest from one genetic source into a superior
cultivar or elite breeding line to improve the
targeted trait.
18. Two levels of selection in which markers may be applied in
backcross breeding.
• Select backcross progeny carrying the target gene which
tightly-linked to flanking markers (foreground selection).
• Select backcross progeny with background markers
(background selection) to accelerate the recovery of the
recurrent parent genome.
Marker Assisted Backcross
Two levels of selection in which markers may be applied in
backcross breeding.
• Select backcross progeny carrying the target gene which
tightly-linked to flanking markers (foreground selection).
• Select backcross progeny with background markers
(background selection) to accelerate the recovery of the
recurrent parent genome.
Two levels of selection in which markers may be applied in
backcross breeding.
• Select backcross progeny carrying the target gene which
tightly-linked to flanking markers (foreground selection).
• Select backcross progeny with background markers
(background selection) to accelerate the recovery of the
recurrent parent genome.
19. Marker Assisted Backcross (MABC)
FOREGROUND SELECTION
Use markers to transfer genes or QTL of
major effects. One or multiple genes
may be transferred. Markers should be
closely linked to the gene of interest to
avoid loosing them by recombination
BACKGROUND SELECTION
Use markers to control for genetic
background in a BC cycle. To speed the
process of recovery of the elite
germplasm, markers may be used along
the genome.
FOREGROUND SELECTION
Use markers to transfer genes or QTL of
major effects. One or multiple genes
may be transferred. Markers should be
closely linked to the gene of interest to
avoid loosing them by recombination
BACKGROUND SELECTION
Use markers to control for genetic
background in a BC cycle. To speed the
process of recovery of the elite
germplasm, markers may be used along
the genome.
Marker
FG+BG
Highest RPG
Carrying target gene
http://passel.unl.edu/pages/informationmodule.php?idinformationmodule=1087488148&topicorder=7&maxto=10
FOREGROUND SELECTION
Use markers to transfer genes or QTL of
major effects. One or multiple genes
may be transferred. Markers should be
closely linked to the gene of interest to
avoid loosing them by recombination
BACKGROUND SELECTION
Use markers to control for genetic
background in a BC cycle. To speed the
process of recovery of the elite
germplasm, markers may be used along
the genome.
Marker
FG
Conversion
completed
20. resistance donor P1 X P2 F1 BC1F1 BC2F1 BC3F1
Marker Assisted Backcross (MABC)
Background selection:
Increase the level of recovering recurrent parent genome in BC generation
Faster recovering
RP genome
DNA marker chrom 1
Target gene chrom 2
chrom 3
# plants
number plants to consider
Faster recovering
RP genome
number plants to consider
without and marker data
# plants
50 % 100 %% recurrent parent
genome in BC1F1
50 % 100 %% recurrent paren
genome in BC1F1
with
Decrease number of
Plant to consider
21. Marker Assisted Pyramiding
Pyramiding is the process of combining multiple genes/QTLs together
into a single genotype. This is possible through conventional breeding
but extremely difficult or impossible at early generations. DNA markers
may facilitate selection because :
• DNA marker assays are non-destructive
• Markers for multiple specific genes/QTLs can be tested without
phenotyping.
• The most widespread application for pyramiding has been for
combining multiple disease resistance genes in order to develop durable
disease resistance.
Molecular Breeding Method
Pyramiding is the process of combining multiple genes/QTLs together
into a single genotype. This is possible through conventional breeding
but extremely difficult or impossible at early generations. DNA markers
may facilitate selection because :
• DNA marker assays are non-destructive
• Markers for multiple specific genes/QTLs can be tested without
phenotyping.
• The most widespread application for pyramiding has been for
combining multiple disease resistance genes in order to develop durable
disease resistance.
Pyramiding is the process of combining multiple genes/QTLs together
into a single genotype. This is possible through conventional breeding
but extremely difficult or impossible at early generations. DNA markers
may facilitate selection because :
• DNA marker assays are non-destructive
• Markers for multiple specific genes/QTLs can be tested without
phenotyping.
• The most widespread application for pyramiding has been for
combining multiple disease resistance genes in order to develop durable
disease resistance.
http://www.knowledgebank.irri.org/ricebreedingcourse/Marker_assisted_breeding.htm
22. Marker Assisted Pyramiding
Segregating population
Marker tightly link
to the gene
Marker tightly link
to the gene
Select by marker
Instead of phenotyping
In early generation
Fixed 2 resistant gene
26. Quantitative Trait Loci (QTL)
Quantitative trait
• Trait that show continuous variation in population
• combined effect of several genes
• bell curve distribution of phenotypic values, produces a range of phenotypes
Quantitative trait
• Trait that show continuous variation in population
• combined effect of several genes
• bell curve distribution of phenotypic values, produces a range of phenotypes
Variety A Variety B Quantitative trait
- Plant height
- Grain yield
- Some disease resistant
frequency
Trait value
Purpose of QTL study using in plant breeding is
1.To localize chromosomal region that significantly effect
the variation of quantitative trait in the population
2. Introgression of favorable QTLs region in to elite variety
QTL mapping
27. Quantitative Trait Loci (QTL)
A quantitative trait locus/loci (QTL) is the location or
region of individual locus or multiple loci in the genome that
affects a trait that is measured on a quantitative .
• Develop mapping population (F2, DH, NIL, BC, RIL)
• Genotyping (Polymorphic marker)
• Constructing of linkage maps (linkage between marker)
• Phenotyping (screen in field)
• QTLs analysis
- Test association between phenotypic trait and marker
- Identify major /minor QTL
QTLs mapping process
A quantitative trait locus/loci (QTL) is the location or
region of individual locus or multiple loci in the genome that
affects a trait that is measured on a quantitative .
• Develop mapping population (F2, DH, NIL, BC, RIL)
• Genotyping (Polymorphic marker)
• Constructing of linkage maps (linkage between marker)
• Phenotyping (screen in field)
• QTLs analysis
- Test association between phenotypic trait and marker
- Identify major /minor QTL
28. Quantitative Trait Loci (QTL): An example with rice
Linkage maps
Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Mada:baru:Theor Appl Genet (2012) 124:867–874 DOI 10.1007/s00122-
29. Quantitative Trait Loci (QTL): An example with rice
QTL analysis
Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Mada:baru:Theor Appl Genet (2012) 124:867–874 DOI 10.1007/s00122-
LOD explain linkage between marker and QTLs
R2 explain phenotypic variance by QTLs (PVE)
Transfer QTL to elite germplasm
Validate QTLs
30. Marker Assisted Recurrent Selection (MARS)
When much of the variation is controlled by many
minor QTLs ( 20-30 QTLs), MABC has limited applicability
because estimates of QTL effects are inconsistent and
gene pyramiding becomes increasingly difficult as the
number of QTLs increases.
A more effective strategy is to deploy MARS to
increase the frequency of favorable marker alleles in
the population.
When much of the variation is controlled by many
minor QTLs ( 20-30 QTLs), MABC has limited applicability
because estimates of QTL effects are inconsistent and
gene pyramiding becomes increasingly difficult as the
number of QTLs increases.
A more effective strategy is to deploy MARS to
increase the frequency of favorable marker alleles in
the population.
Roberto Tuberosa: Dept. of Agroenvironmental Sciences and Technology , University of Bologna, Italy
When much of the variation is controlled by many
minor QTLs ( 20-30 QTLs), MABC has limited applicability
because estimates of QTL effects are inconsistent and
gene pyramiding becomes increasingly difficult as the
number of QTLs increases.
A more effective strategy is to deploy MARS to
increase the frequency of favorable marker alleles in
the population.
31. Marker Assisted Recurrent Selection (MARS)
MARS involves:
• Defining a selection index for F2 or F2-derived
progenies, use index to weight significant marker for
target QTLs (20-30 QTLs)
• Recombining selfed progenies of the selected
individuals
• Repeat the procedure for a number of cycles
MARS involves:
• Defining a selection index for F2 or F2-derived
progenies, use index to weight significant marker for
target QTLs (20-30 QTLs)
• Recombining selfed progenies of the selected
individuals
• Repeat the procedure for a number of cycles
Roberto Tuberosa: Dept. of Agroenvironmental Sciences and Technology , University of Bologna, Italy
32. Marker Assisted Recurrent Selection (MARS)
Steps in a MARS in Maize:
1. MAS in Cycle 0
• Create an F2 (Cycle 0)
• Test-cross the F2
• Evaluate progeny in multiple environments
• Identify markers associated with trait of interest
• Create an index weighting significant markers
by their effect using multiple linear regression
(Lande and Thompson 1990).
• Recombine best progeny (best individuals from Cycle 0)
2. Select in greenhouse or off-season nursery (up to 3
cycles in low h2 environment).
1. MAS in Cycle 0
• Create an F2 (Cycle 0)
• Test-cross the F2
• Evaluate progeny in multiple environments
• Identify markers associated with trait of interest
• Create an index weighting significant markers
by their effect using multiple linear regression
(Lande and Thompson 1990).
• Recombine best progeny (best individuals from Cycle 0)
2. Select in greenhouse or off-season nursery (up to 3
cycles in low h2 environment).
Patricio J. Mayor and Rex Bernardo:
Genomewide Selection and Marker-Assisted Recurrent Selection in Doubled Haploid
versus F2 Populations
1. MAS in Cycle 0
• Create an F2 (Cycle 0)
• Test-cross the F2
• Evaluate progeny in multiple environments
• Identify markers associated with trait of interest
• Create an index weighting significant markers
by their effect using multiple linear regression
(Lande and Thompson 1990).
• Recombine best progeny (best individuals from Cycle 0)
2. Select in greenhouse or off-season nursery (up to 3
cycles in low h2 environment).
33. Genomic Selection
Genomic selection (GS) is a new approach for
improving quantitative traits in large plant
breeding populations that uses whole genome
molecular markers and combines marker data
with phenotypic data in an attempt to increase
the accuracy of the prediction of breeding and
genotypic values.
Genomic selection (GS) is a new approach for
improving quantitative traits in large plant
breeding populations that uses whole genome
molecular markers and combines marker data
with phenotypic data in an attempt to increase
the accuracy of the prediction of breeding and
genotypic values.
Genomic selection (GS) is a new approach for
improving quantitative traits in large plant
breeding populations that uses whole genome
molecular markers and combines marker data
with phenotypic data in an attempt to increase
the accuracy of the prediction of breeding and
genotypic values.
http://genomics.cimmyt.org/
34. Genomic Selection
Objective of GS is to predict the breeding value of each
individual instead of identifying QTL for use in a traditional
marker-assisted selection (MAS) program
• Requires high-density molecular markers (LD level)
• GS considers the effects of all markers together and captures most of
the additive variation
• Marker effects are first estimated based on a so-called
“training population” that needs to be sufficiently large (> 300)
• Breeding value is then predicted for each genotype in the
“testing population” using the estimated marker effects
Objective of GS is to predict the breeding value of each
individual instead of identifying QTL for use in a traditional
marker-assisted selection (MAS) program
• Requires high-density molecular markers (LD level)
• GS considers the effects of all markers together and captures most of
the additive variation
• Marker effects are first estimated based on a so-called
“training population” that needs to be sufficiently large (> 300)
• Breeding value is then predicted for each genotype in the
“testing population” using the estimated marker effects
Roberto Tuberosa: Dept. of Agroenvironmental Sciences and Technology , University of Bologna, Italy
35. Genomic Selection Scheme
Statistic model
Genomic Selection Scheme
Predict trait value
base on genotype
result
Selection or intermate for
Next cycle
Predict trait value
base on genotype
result