This document discusses molecular markers and their use in plant breeding and genetics. It defines different types of markers, including morphological, biochemical, and molecular markers. Molecular markers are DNA sequences that can be easily detected and whose inheritance can be monitored. The document discusses different classes of molecular markers, including PCR-based techniques like RAPD, SSR, and AFLP, as well as applications like diversity analysis, genotyping, and linkage mapping. It also covers topics like genetic distance, linkage mapping, mapping populations, and scoring mapping populations to construct genetic maps.
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.
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
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
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.
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.
Gene mapping means the mapping of genes to specific locations on chromosomes.
Such maps indicates the positions of genes in the genome and also distance between them.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
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.
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 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
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.
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.
Gene mapping means the mapping of genes to specific locations on chromosomes.
Such maps indicates the positions of genes in the genome and also distance between them.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
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.
Molecular markers for measuring genetic diversity Zohaib HUSSAIN
Molecular markers for measuring genetic diversity
Introduction:
The molecular basis of the essential biological phenomena in plants is crucial for the effective conservation, management, and efficient utilization of plant genetic resources (PGR).
Determining genetic diversity can be based on morphological, biochemical, and molecular types of information. However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity
Comparison of different methods
Morphological characterization does not require expensive technology but large tracts of land are often required for these experiments, making it possibly more expensive than molecular assessment. These traits are often susceptible to phenotypic plasticity; conversely, this allows assessment of diversity in the presence of environmental variation.
Biochemical analysis is based on the separation of proteins into specific banding patterns. It is a fast method which requires only small amounts of biological material. However, only a limited number of enzymes are available and thus, the resolution of diversity is limited.
Molecular analyses comprise a large variety of DNA molecular markers, which can be employed for analysis of variation. Different markers have different genetic qualities (they can be dominant or co-dominant, can amplify anonymous or characterized loci, can contain expressed or non-expressed sequences, etc.).
Genetic marker
The concept of genetic markers is not a new one; in the nineteenth century, Gregor Mendel employed phenotype-based genetic markers in his experiments. Later, phenotype-based genetic markers for Drosophila melanogaster led to the founding of the theory of genetic linkage. A genetic marker is an easily identifiable piece of genetic material, usually DNA that can be used in the laboratory to tell apart cells, individuals, populations, or species. The use of genetic markers begins with extracting proteins or chemicals (for biochemical markers) or DNA (for molecular markers) from tissues of the plant (for example, seeds, foliage, pollen, sometimes woody tissues).
Molecular markers In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or insertion. Markers can exhibit two modes of inheritance, i.e. dominant/recessive or co-dominant. If the genetic pattern of homozygotes can be distinguished from that of heterozygotes, then a marker is said to be co-dominant. Generally co-dominant markers are more informative than the
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.
Genetic markers, Classical markers, DNA markers, MICROSATELLITES, AFLP, SNP: Single Nucleotide Polymorphism, QTL: Quantitative Trait Locus, Activities of marker-assisted breeding, Marker-based breeding and conventional breeding Perspectives,The application of molecular technologies to plant breeding is still facing the following drawbacks and/or challenges
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Banoth Madhu
Banoth Madhu: Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in Crop Plants. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
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.
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.
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.
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)
Crop modeling for stress situations, cropping system , assessing stress through remote sensing, understanding the adaptive features of crops for survival under stress .
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
We all have good and bad thoughts from time to time and situation to situation. We are bombarded daily with spiraling thoughts(both negative and positive) creating all-consuming feel , making us difficult to manage with associated suffering. Good thoughts are like our Mob Signal (Positive thought) amidst noise(negative thought) in the atmosphere. Negative thoughts like noise outweigh positive thoughts. These thoughts often create unwanted confusion, trouble, stress and frustration in our mind as well as chaos in our physical world. Negative thoughts are also known as “distorted thinking”.
Students, digital devices and success - Andreas Schleicher - 27 May 2024..pptxEduSkills OECD
Andreas Schleicher presents at the OECD webinar ‘Digital devices in schools: detrimental distraction or secret to success?’ on 27 May 2024. The presentation was based on findings from PISA 2022 results and the webinar helped launch the PISA in Focus ‘Managing screen time: How to protect and equip students against distraction’ https://www.oecd-ilibrary.org/education/managing-screen-time_7c225af4-en and the OECD Education Policy Perspective ‘Students, digital devices and success’ can be found here - https://oe.cd/il/5yV
The Indian economy is classified into different sectors to simplify the analysis and understanding of economic activities. For Class 10, it's essential to grasp the sectors of the Indian economy, understand their characteristics, and recognize their importance. This guide will provide detailed notes on the Sectors of the Indian Economy Class 10, using specific long-tail keywords to enhance comprehension.
For more information, visit-www.vavaclasses.com
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Ethnobotany and Ethnopharmacology:
Ethnobotany in herbal drug evaluation,
Impact of Ethnobotany in traditional medicine,
New development in herbals,
Bio-prospecting tools for drug discovery,
Role of Ethnopharmacology in drug evaluation,
Reverse Pharmacology.
2. Introduction
Understanding biology and genetics at molecular level has become
important for better understanding and manipulation of genome
architecture.
Identification of markers associated with desirable breeding traits
are useful for marker assisted breeding and genomics and
development of transgenics.
It reduce breeding time and cycles required for crop improvement.
Understanding the inheritance of molecular level of agriculture
traits creates a new opportunity for plant breeding.
3. Markers
These are easily identifying characters of an individual.
These are character whose pattern of inheritance can be
followed at morphological, biochemical and molecular levels.
4. Morphological markers
These are qualitative traits which can be detected visually.
The have been found in nature due to mutagenesis.
Limitation
It cause large effect on phenotype that they are undesirable in
breeding programme.
They mask the effect of linked genes and it makes them difficult to
identify desirable linkage for selection.
They are highly influence by environment and its gene interaction.
5. Biochemical markers
These are the proteins produced by gene expression.
Particularly isozymes are successfully used as biochemical
markers.
They are phenotypic markers which are affected by tissue,
plant growth, etc.
6. Molecular markers
It is a DNA sequence which is readily detected and whose
inheritance can easily monitored.
These are based on naturally occurring DNA polymorphism.
It is the section of nucleotide sequence used for the identification of
desired QTL or gene.
Most widely used due to the abundance.
Selectively neutral as they are non-coding sequence.
Not affected by environmental factors.
7. Characteristics of molecular markers
It must be polymorphic which measure the genetic diversity.
Co-dominant inheritance which can detect different forms of
markers.
It should be evenly and frequently distributed in organism
genome.
9. Co-dominant and Dominant
Co-dominant markers
can clearly discriminate
between homozygotes
and heterozygotes
Whereas dominant
markers do not
10. Classes of molecular markers.
1. Non- PCR Base
Technique
i. RFLP
2. PCR Base
Technique
i. RAPD
ii. SSRP
iii. AFLP
iv. AP-PCR
3. Targeted PCR and
Sequencing
i. STS
ii. SCARS
iii. STM
iv. CAPS
11. Application of molecular markers
Phylogeny and plant evolution
Diversity analysis of germplasm
Genotyping of cultivars
Barcoding sequence information from nuclear and
organellar genome
12. Genetic Distance
Genetic linkage occur when particularly genetic loci for genes are
inherently joined.
Genetic loci on the same chromosome are physically connected and
tend to stay together during meiosis, and are thus genetically linked
called as autosomal linkage.
Greater the distance between markers, the greater the chance of
recombination occurring during meiosis
Distance along a linkage map is measured in terms of the frequency
of recombination between genetic markers
13. Mapping functions are required to convert recombination fractions
into centiMorgans (cM)
When map distances are small (<10 cM), the map distance equals the
recombination frequency
However, this relationship does not apply for map distances that are
greater than 10 cM
14. Linkage Mapping
i. Genetic linkage maps were originally built to map phenotypic mutant.s
ii. Modern linkage maps use molecular markers (predominantly, DNA markers).
iii. Different types of mapping populations are used.
iv. Mapping studies in diploid and allopolyploids use similar tools and techniques.
v. Linkage maps in autopolyploid necessitates different mapping strategies.
vi. Linkage maps are useful for:
- tagging markers along chromosomes
- identifying markers linked to genes and cloning genes
- identifying quantitative trait loci for traits of interest
- marker assisted selection
- comparative mapping and evolutionary studies
15. Mapping Population
Mapping population is the population used for gene mapping.
Commonly used mapping populations are obtained from
controlled crosses.
Selection of mapping population involves choosing of parents
and determining a mating scheme.
16. Steps to construct the mapping population
Select the parent plant
Produce a mapping population
Scoring in mapping population
i. Screening for polymorphism
ii. Scoring
iii. Linkage analysis
17. Select the parent plant
For construction of map, the selected plant are genetically different
or divergent to exhibit different polymorphism but not so much
distant as the causes sterility.
Wild species which shows different polymorphic can also be
selected for cross.
After selecting the surveyed plants, DNA should be isolated and
digested with restriction enzyme and screened for polymorphism.
18. Production of a mapping population
Requires a segregating plant population (i.e. a population derived
from sexual reproduction).
The parents selected will differ for one or more traits of interest.
Population sizes: generally range from 50 to 250 individuals.
For high-resolution mapping larger populations are required.
If map is used for QTL studies then the mapping population must be
phenotypically evaluated (i.e. trait data must be collected) before
subsequent QTL mapping.
19. mapping population
cont……
In self pollinated species, parents that are both highly
homozygous (inbred).
In cross pollinating species, the situation is more complicated
being heterozygous.
20. Types of mapping population
F2 Population
F2 derived F3 population
Backcross Mapping population
Recombinant Inbred Lines (RILs)
Near Isogenic Lines (NILs)
Double haploids (DHs)
21. F2 population
It is developed by selfing among F1 individuals.
Merits:
It requires less time for development and can be developed with
minimum efforts
Demerits:
Quantitative traits cannot be precisely mapped using F2 population.
It is not a long term population.
F2 population
22. F2 derived F3 population
It is obtained by selfing the F2 individuals for a single generation.
Merits:
It is suitable for specific situations like mapping QTLs and recessive
genes
It is used for reconstitution of respective F2 plants.
Demerit:
It is not long term population.
23. Backcross Population.
It is developed by crossing the F1 with one of two parents used in the initial
cross.
Backcross with recessive parent is usually used in genetic analysis.
Merits:
It requires less time to be developed.
It is used for marker assisted backcross breeding.
Demerits:
This population is not eternal.
24. Near Isogenic Lines.
NILs are developed by repeated selfing or backcrossing the F1 individuals
to the recurrent parents.
Merits:
They are immortal mapping population.
They are suitable for tagging the trait and quite useful in functional
genomics.
Demerits:
It requires many generations for development.
It is not useful for linkage mapping.
Linkage drag is a potential problem in constructing NILs.
25. Recombinant Inbred Lines.
They are developed by single seed selections from individual plants of an
F2 population.
They are produced by continuous selfing or sib mating the progeny of
individual members of an F2 population until complete homozygosity is
achieved.
Merits:
RILs can be propagated indefinitely without further segregation.
They are useful in identifying tightly linked markers.
Demerits:
It requires many generation to develop RILs and developing RILs are
relatively difficult in crops with high inbreeding depression.
26. Doubled Haploids
Doubled Haploids are developed by chromosome doubling of anther
culture derived haploid plants from F1.
They are product of one meiotic cycle.
Merits:
They can be replicated and evaluated over locations and years and
maintained without any genotypic change.
They can be useful for both qualitative and quantitative characters.
It can be used for instant production of homozygous lines.
Demerits:
Suitable culturing methods / haploid production methods are not available
for number of crops.
Anther culture induced variability.
27.
28. Scoring in mapping population
Once the mapping population is obtained DNA is isolated from
each individual plant in population.
It is important the chromosome of each plant is mapping.
It should contains a unique array of parental chromosome
segment.
29. Steps for scoring technique
Screening for polymorphism
Probes are selected from library and tested against the parent
to determined which restriction enzyme will detect the
polymorphism between the parents.
It required no. of enzyme depending upon the variation.
30. Scoring
When a suitable enzyme detected it can be scored in mapping
population.
To accomplish this a series of agarose gel must prepared and
filters are prepared from them.
These filter consist of one restriction enzyme and each filter
set contain one digested DNA from each individual
population.
31. Linkage analyses
Data obtained from linkage scoring at mapping population
used to construct linkage map.
It is base on the degree to which probes tend to consegregate.
32. Specialised mapping
Bulk Segregant Analysis (BSA)
Combining markers and population
Characterization of mapping population
Segregation distortion in linkage mapping
33. Bulk Segregant Analysis
Indirect selection by using qualitative traits.
It is useful in analysis of conventional markers.
It is base on the principle of Segregant population.
F2 population is divided in two pools of contrasting individuals.
It helps in selecting the recessive alleles and dominant alleles.
34. Combining markers and population
The segregation ratio is jointly determined by the nature of
marker and types of mapping populations.
Markers such as AFLP, RAPD are often scored as dominant
markers whereas markers like RFLP, Microsatellite shows a
co- dominant
35. Characterization of mapping population
The molecular genotype of any individual is independent of
environment, it is not influenced by GxE interaction
However trait phenotype could be influenced by the
environment, particularly in case of quantitative characters.
Therefore, it is important to precisely estimate the traits value
by evaluating genotypes in multilocation testing
36. Segregation distortion of markers
Significant deviation from expected segregation ratio in a given
marker population combination is referred to as segregation
distortion.
Several reasons for segregation distortion:
i. Gamete/ zygote lethality
ii. Meiotic drive
iii. Sampling and selection during population development
37. Conclusion
It permit direct identification of genotypes or cultivar in any
tissue at any developmental stage in an environmental
independent manner.
Enables to distinguish heterozygous or homozygous due to co-
dominant markers.
It is a novel approach in plants for exploiting the genetic
variation in natural population for resolving traits in crop
plants.
Editor's Notes
Secondary dormancy
i. Thermodormancy
ii. Conditional dormancy
