Linkage and QTL mapping Populations and Association mapping population.
F2, Immortalized F2, Backcross (BC), Near isogenic lines (NIL), RIL, Double haploids(DH), Nested Association mapping (NAM), MAGIC and Interconnected populations.
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)
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.
Linkage and QTL mapping Populations and Association mapping population.
F2, Immortalized F2, Backcross (BC), Near isogenic lines (NIL), RIL, Double haploids(DH), Nested Association mapping (NAM), MAGIC and Interconnected populations.
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)
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.
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.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
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.
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
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
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
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.
Morphological, Cytological and Biochemical MarkersJay Khaniya
I've put a lot of effort for create this presentation. This'll help to lot of biotechnology and agricultural students for there assignments and exam study.
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.
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
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
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
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.
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.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
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Salas, V. (2024) "John of St. Thomas (Poinsot) on the Science of Sacred Theol...Studia Poinsotiana
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All the contents are fully attributable to the author, Doctor Victor Salas. Should you wish to get this text republished, get in touch with the author or the editorial committee of the Studia Poinsotiana. Insofar as possible, we will be happy to broker your contact.
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Phenomics assisted breeding in crop improvementIshaGoswami9
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change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
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ISI 2024: Application Form (Extended), Exam Date (Out), Eligibility
MAS ( Marker Assisted Selection)
1. Marker Assisted Selection
By
Kartikey Sootrakar
Ph.D. IIIrd semester
Enroll. 170234001
College of Agriculture, Rewa
J.N.K.V.V., Jabalpur (M.P.)
Doctoral Seminar
on
2. Marker-Assisted Selection
A method of selecting desirable individuals
in a breeding scheme
patterns
based
instead
on
of,
DNA
molecular marker or in
addition to, their trait values.
A tool that can help plant breeders select
more efficiently for desirable crop traits.
MAS is not always advantageous, so careful
relativeanalysis of the costs and benefits
to conventional breeding methods is
necessary.
3. CONVENTIONAL PLANT BREEDING
P1 P2x
DonorRecipient
F1
large populations consisting of
thousands of plantsF2
PHENOTYPIC SELECTION
Bacterial blight screening Phosphorus deficiency plotSalinity screening in phytotron
Field trialsGlasshouse trials
4. MARKER-ASSISTED BREEDING
P1 x P2
Susceptible Resistant
F1
large populations consisting of
F2
thousands of plants
MARKER-ASSISTED SELECTION (MAS)
Method whereby phenotypic selection is based on DNA markers
5. Prerequisites for an efficient marker-assisted
selection program
High throughput DNA
extraction
6. Markers
Markers (morphological, protein, cytological)
also be used in MAS programs.
can
RFLP, SSR, RAPD, AFLP,and SNP
For efficient
Ease of use
Small amount
Low cost
Repeatability
MAS:
of DNA required
of results
High rate of polymorphism
Occurrence throughout the genome
Codominance
7. gene.
Genetic maps
Linkage maps provide a framework for detecting
marker-trait associations and for choosing markers
to employ in MAS.
Once a marker is found to be associated with a trait
in a given population, a dense molecular marker map
in a standard reference population will help identify
markers that are closer to, or that flank, the target.
8. Data managementsystem
Large numbers of samples are handled
sample
multiple
in a MAS program, with each
potentially
markers.
evaluated for
This situation requires an efficient
retrieving,system for labeling, storing,
and analyzing large data
useful
sets,
to
and
theproducing
breeder.
reports
9. Potential advantages of MAS
It can be performed on seedling material
Thus reducing the time required before a plant’s
genotype is known.
In contrast, many important plant traits are
observable only when the plant has reached
flowering or harvest maturity.
Knowing a plant’s genotype before
order
flowering can
thebe particularly useful in to plan
appropriate crosses between selected individuals.
10. MAS is not affected by environmental
conditions
Some crop production constraints (such as
disease, insect pests, temperature and moisture
stress) occur sporadically or non-uniformly.
Therefore, evaluating resistance to those
constraints may not be possible in a given year or
location.
MAS offers the chance to determine a plant’s
resistance level independent of environment.
11. When recessive alleles determine traits of
interest
They cannot be detected through phenotypic
evaluation of heterozygous plants, because their
presence is masked by the dominant allele.
In a traditional backcross program, plants with
recessive alleles are identified by progeny
evaluation after self-pollination or testcrossing
recessive tester.
to a
This time-consuming step can be eliminated in a
MAS program, because recessive alleles are
identified by linked markers.
12. When multiple resistance genes are
pyramided together
line,
in the same variety
or breeding
The presence of each individual gene is
difficult to verify phenotypically.
The presence of one resistance gene may
conceal the effect of additional genes.
This problem can
for
be overcome if markers
are available each of the resistance
genes.
13. A consideration that
MAS
may
is
affect cost
effectiveness of
be
that multiple
markers can evaluated using the same
DNA sample.
Once DNA is extracted and purified, it may
same
be
orused for multiple
traits,
markers, for the
different thus reducing the time and
cost per marker.
MAS may be cheaper and faster than
conventional phenotypic assays, depending on
the trait.
14. MAS maybe more expensive than conventional
techniques,
labor costs.
especially for startup expenses and
Recombination between the marker
leading
and the
gene of interest may occur, to false
positives.
Linkage maps of two chromosomes showing
positions of two resistance genes and nearby
markers.
Drawbacks of MAS
15. Conducting a MAS
(1) TISSUE
SAMPLINGprogram
(2) DNA
EXTRACTION
(3) PCR
(4) GEL
ELECTROPHORESIS
(5) MARKER
ANALYSIS
16. A variety of approaches
MAS: MARKER-ASSISTED SELECTION
- Plants are selected for one or more (up to 8-10) alleles
MABC:
One
to
MARKER-ASSISTED BACKCROSSING
or more (up to 6-8) donor alleles are transferred
an elite line
MARS: MARKER-ASSISTED RECURRENT SELECTION
Selection for several (up to 20-30) mapped QTLs relies
on index (genetic) values computed for each individual
based on its haplotype at target QTLs
17. Conclusion
MAS is a methodology that has already
proved its value.
It is likely to become more valuable as a
larger number of genes are identified and
their functions and interactions elucidated.
Reduced costs and optimized strategies for
integrating MAS with phenotypic selection
are needed before the technology can reach
its full potential.