Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
High throughput phenotyping are fully automated facilities in greenhouses or growth chambers with robotics, precise environmental control, and remote sensing techniques to assess plant growth and performance
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
The use of the term cisgenesis is an attempt to distinguish GM plants or other organisms produced in this way from transgenics that is GM plants that contain DNA from unrelated organisms. Schouten et al. (2006) introduced the term cisgenesis and defined cisgenesis as the modification in the genetic background of a recipient plant by a naturally derived gene from a cross compatible species including its introns and its native promoter and terminator flanked in the normal sense orientation. Since cisgenes shared a common gene pool available for traditional breeding the final cisgenic plant should be devoid of any kind of foreign DNA viz., selection markers and vector- backbone sequences. Sometimes the word cisgenesis is also referred to as Agrobacterium-mediated gene transfer from a sexually compatible plant where only the T-DNA borders may be present in the recipient organism after transformation (EFSA, 2012). The cisgenesis precludes linkage drag, and hence, prevents hazards from unidentified hitch hiking genes (Schouten, and Jacobsen, 2008). Compared to transgenesis, one of the disadvantages shared by cisgenesis is that characters outside the sexually compatible gene pool cannot be introduced. Furthermore, development of cisgenic crops involves extraordinary proficiency and time compared to transgenic crops. Therefore, the required genes or fragments of genes may not be readily accessible but have to be isolated from the sexually compatible gene pool (Holme et al., 2013).
On 16 February 2012, European Food Safety Authority (EFSA, 2012) reported the detail study concerning the safety aspects of cisgenic plants and validated that cisgenic plants are secure to be used in terms of environment, food and feed, similar to the traditionally bred plants. However, the present GMO regulation keeps the cisgenic micro-organisms out from its supervision. The first scientific statement of bringing forth a true plant obtained by cisgenic approach was reported in apple through the insertion of the internal scab resistance gene HcrVf2 influenced by their own regulatory genes into the cultivar Gala, a scab susceptible cultivar (Vanblaere et al., 2011). Barley with improved phytase activity was produced successfully by Holme et al. 2011, through cisgenic approach. Late blight resistant potatoes have developed by cisgene stacking of R- gene (jo et al., 2014).
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
High throughput phenotyping are fully automated facilities in greenhouses or growth chambers with robotics, precise environmental control, and remote sensing techniques to assess plant growth and performance
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
The use of the term cisgenesis is an attempt to distinguish GM plants or other organisms produced in this way from transgenics that is GM plants that contain DNA from unrelated organisms. Schouten et al. (2006) introduced the term cisgenesis and defined cisgenesis as the modification in the genetic background of a recipient plant by a naturally derived gene from a cross compatible species including its introns and its native promoter and terminator flanked in the normal sense orientation. Since cisgenes shared a common gene pool available for traditional breeding the final cisgenic plant should be devoid of any kind of foreign DNA viz., selection markers and vector- backbone sequences. Sometimes the word cisgenesis is also referred to as Agrobacterium-mediated gene transfer from a sexually compatible plant where only the T-DNA borders may be present in the recipient organism after transformation (EFSA, 2012). The cisgenesis precludes linkage drag, and hence, prevents hazards from unidentified hitch hiking genes (Schouten, and Jacobsen, 2008). Compared to transgenesis, one of the disadvantages shared by cisgenesis is that characters outside the sexually compatible gene pool cannot be introduced. Furthermore, development of cisgenic crops involves extraordinary proficiency and time compared to transgenic crops. Therefore, the required genes or fragments of genes may not be readily accessible but have to be isolated from the sexually compatible gene pool (Holme et al., 2013).
On 16 February 2012, European Food Safety Authority (EFSA, 2012) reported the detail study concerning the safety aspects of cisgenic plants and validated that cisgenic plants are secure to be used in terms of environment, food and feed, similar to the traditionally bred plants. However, the present GMO regulation keeps the cisgenic micro-organisms out from its supervision. The first scientific statement of bringing forth a true plant obtained by cisgenic approach was reported in apple through the insertion of the internal scab resistance gene HcrVf2 influenced by their own regulatory genes into the cultivar Gala, a scab susceptible cultivar (Vanblaere et al., 2011). Barley with improved phytase activity was produced successfully by Holme et al. 2011, through cisgenic approach. Late blight resistant potatoes have developed by cisgene stacking of R- gene (jo et al., 2014).
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
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.
Targeting Induced Local Lesions IN Genomes (TILLING) is a combined tool of plant mutagenesis and DNA Biology to investigate useful mutations at Genomic level. First time used for cotton improvement.
Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.
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.
Ang Chong Yi Navigating Singaporean Flavors: A Journey from Cultural Heritage...Ang Chong Yi
In the heart of Singapore, where tradition meets modernity, He embarks on a culinary adventure that transcends borders. His mission? Ang Chong Yi Exploring the Cultural Heritage and Identity in Singaporean Cuisine. To explore the rich tapestry of flavours that define Singaporean cuisine while embracing innovative plant-based approaches. Join us as we follow his footsteps through bustling markets, hidden hawker stalls, and vibrant street corners.
At Taste Of Middle East, we believe that food is not just about satisfying hunger, it's about experiencing different cultures and traditions. Our restaurant concept is based on selecting famous dishes from Iran, Turkey, Afghanistan, and other Arabic countries to give our customers an authentic taste of the Middle East
Roti Bank Hyderabad: A Beacon of Hope and NourishmentRoti Bank
One of the top cities of India, Hyderabad is the capital of Telangana and home to some of the biggest companies. But the other aspect of the city is a huge chunk of population that is even deprived of the food and shelter. There are many people in Hyderabad that are not having access to
Alien introgression in Crop Improvement-New insights
1. Alien Introgression in Crop Improvement –
New Insights
Credit Seminar
Presented by :
Asmat Ara
Ph. D GPB
03/AG(GPB)/2016-D
2. Alien introgression
• Defined as transfer of one or more genes from exotic/un-
adapted/ crop wild relatives (CWR) to adapted breeding
populations.
(Edgar Anderson)
• CWR contain a wealth of genetically important traits due to
their adaptation to a diverse range of habitats and the fact that
they have not passed through the genetic bottlenecks of
domestication.
(Vollbrecht and Sigmon, 2005; FAO, 2008).
3. Why alien introgression ?
Loss in genetic diversity, due to :
Selection for domestication related traits.
Genetic drifts (domestication bottlenecks)
Modern breeding practices.
4. Diagrammatic representation of loss of genetic diversity in crop species
The Symbol ( asterisk )
indicates the novel genetic variation (Mir et al,2014)
7. Historical background
• CWR were used in crop improvement in sugarcane in the
first half of the 20th century.
• Their utility was recognized in breeding programmes of
major crops in the 1940s and 1950s (Plucknett et al. 1987).
• Gene for resistance to leaf rust translocated onto Triticum
aestivum from Aegilopes umbellulata.( Sears, 1950)
• wild gene use in crop improvement gained in prominence by
the 1970s and 1980s with their use being investigated in an
increasing wide range of crops (Hoyt 1988).
8. Use of crop wild relatives in the past 20 years in released cultivars
of 13 crops of international importance
+ indicate number of wild relatives that have contributed beneficial traits to crop varieties
- indicates wild relatives have not contributed beneficial traits in that category
9. Important genes in wheat found in related species
System-wide Genetic Resources Program
(1996)
10. • Stem or black rust (Puccinia graminis f. sp. tritici) and brown or leaf rust
(caused by Puccinia triticina) continue to be a serious threat in many wheat
growing regions of the world.
• Leaf rust res. genes in D genome: Lr21, Lr22a, Lr32, Lr37, Lr39, Lr41, Lr42 &
Lr43
• Lr34 (Ae. tauschii) is a minor/slow rusting gene which provides durable
resistance & presently used extensively in wheat improvement programme in
India and worldwide
• Objective: Evaluation of genetic diversity for stem and leaf rust resistance in D
genome species of wild relatives of wheat
12. Alien gene transfer Non-sexual methods/
Horizontal transfer
Sexual
hybridisation/
Vertical transfer
Interspecific
Intergeneric
Alien gene
detection
Somatic hybridizationGenetic transformation
Genetic
transformation
Direct gene transfer
TransgenesisIntragenesis
& cisgenesis
Interspecific &
intergeneric SH
13. Limitations
Vertical Gene Transfer
(VGT)
Crossability barriers
Chromosome Pairing
Linkage drag
Background effects
Pleiotropic effects
Horizontal Gene
Transfer (HGT)
Regeneration protocol
Isolation of genes from
wild species
Expression of alien genes
Gene flow
Moreover, they provide limited information on genetic basis of complex
traits chromosome locations of QTL.
16. Next Generation Sequencing
Next Generation Sequencing (NGS), also known
as high- throughput sequencing ,allows mass
sequencing of genomes and transcriptomes much
more quickly and cheaply than the previously
used Sanger sequencing.
NGS technologies include :-
• Solexa / Illumina sequencing
• Roche / 454 sequencing
• AB SOLiD sequencing
17. Applications of Gene Sequencing in the context of
gene introgression
• Identification of genes and also in
development of novel molecular markers in
crop species. The markers derived from
sequence information may be used for:
• Characterization of genetic resources and association with
agronomic traits.
• Identification of new sources of biotic and abiotic stress
resistance genes
19. Allele Mining
• Promising approach
to dissect naturally
occuring allelic
variation at
candidate genes
controlling key
agronomic traits.
• Helps in tracing
evolution of alleles,
identification of
new haplotypes and
development of
allele specific
markers.
20. 1. TILLING :
(Targeting Induced Local Lesions IN Genomes)
Reverse genetic strategy that works with a
mismatch- specific endonuclease to detect
induced DNA polymorphisms in genes of
interest.
Developed by Colbert et al. 2001.
(Fred Hutchinson Cancer Research
Center, Seattle , Washington)
American scientists ‘Comai’ &
‘Henikoff’ (2003) have initiated first
TILLING project in Arabidopsis.
21. MERITS of TILLING
It is independent of genome size, reproductive system or generation
time.
High throughput & data analysis can also be automated.
Overcomes disadvantage of knockout gene therapy for a specific gene,
as eliminates the need for removal of gene from gene pool to detect its
function.
TILLING can introduce genetic variation in an elite germplasm without need
to acquire variation & thus avoiding introduction of agriculturally
undesirable traits.
Also overcomes problems of transgenic approach as it is independent of
transgene efficiency and regeneration of plant.
22. EcoTILLING
• It is a method that uses TILLING techniques to look for
natural variations in individuals, usually for population
genetics analysis.
• EcoTILLING can be performed more inexpensively
than full sequencing, the method currently used for most
single nucleotide polymorphism (SNP) discovery.
• But differs from TILLING in that natural polymorphisms
are detected rather than polymorphisms induced through
chemical mutagenesis.
26. Introgression lines (ILs)
• Lines generated by introgression of favourable
gene/QTL/chromosomal segment by developing
isogenic lines using wild species and the
variety/genotype of interest.
Introgression/exotic libraries are constructed using
introgression lines each of which carries a fragment of
defined homozygous chromosomal segment from donor
exotic parent with a homozygous genetic background of
elite parent.
27. Parental survey to detect introgressed segments
from O. australiensis into BPH resistant
introgression line
28. RFLP pattern in F2 population of a cross of BPH resistant
introgression line (IR65482-4-136-2-2) with the recurrent parent
(IR31917-45-3-2).
29. AB-QTL analysis
Approach for simultaneous discovery and transfer of
QTL’s from wild species to crop variety.
Proposed by Tanksley and Nelson
30. Association mapping
Also called as linkage disequilibrium mapping.
A natural population survey to determine marker
trait associations using LINKAGE DISEQUILIBRIUM
The power depends on the strength of this
correlation (i.e., on the degree of LD between the
genotyped marker and the functional variant.
Could be an answer and alternative to family based mapping
To dissect complex traits
31. What is linkage disequilibrium and how ?
Non-random association of alleles at
adjacent loci..
Linkage disequilibrium
around an ancestral
mutation
Ancestral
chromosome
The closer two markers are, the stronger the LD
The resolution with which a QTL can be
mapped is a function of how quickly LD decays
over distance.
32. Linkage vs Association mapping: How it leads to
high resolution..
LINKAGE MAPPING
ASSOCIATION MAPPING
20 generations
6-7 generations
Cardon and John, 2001
33. Approaches for Association mapping
Candidate gene association
mapping
Genome wide association mapping
Relates polymorphism in selected candidate
genes
Genetic variation in whole genome
to find signals
Germplasm
Genotyping
Phenotyping
Population
Structure
LD
Association
mapping
35. 3
3
3
3
3
3
1
2
2
2
2
2
2
= Recurrent
parent allele
= Donor parent
allele
Target
gene
1. Select donor allele at markers linked to target gene.
2. Select recurrent parent allele at other linked markers.
3. Select recurrent parent allele at unlinked markers
throughout genome.
Marker assisted back-crossing
36. A case study:
Development of the
submergence tolerant
Swarna-Sub1 with
details of markers used
for foreground,
recombinant, and
background selection.
The numbers of plants
selected in each
generation are indicated
in parentheses.
Neeraja et al. (2007)
37. Genotype of the Swarna-Sub1 (BC2F2) plant that
is homozygous for the recipient genome except
for the Sub1 region on chromosome 9.
Neeraja et al. (2007
39. Marker- assisted recurrent selection
Used for pyramiding of several genes /QTL’s (of minor effect) in a
single genotype.
Utilised for selection of traits associated with multiple QTL’s
by increasing the frequency of favourable QTL’s or marker alleles.
This approach involves :
1. Identification of F2 progeny which contains favourable alleles for
most, if not all QTL’s.
2. Recombination of the selected progenies to the selfed ones
3. Repetition of these cycles.
40. Genome wide selection
• Approach used to pyramid favourable alleles for minor
effect QTLs at whole genome level.
• Genome selection (GS) considers marker effects across the
whole genome.
• The use of high-density markers is one of the features.
• Based on two distinct and related groups: training and
breeding populations.
• Phenotyping is a key informant in GS to build up accuracy
of statistical models.
• GS may revolutionize plant and tree breeding practices.
Highlights
41. Conclusion
• TILLING and ecoTILLING being swift polymorphism
detection and genotyping methods can be used for
determining the range of variation for genetic mapping
based on linkage analysis.
• Due to reduced costs on sequencing and genotyping
technologies combined with advances in biometrics and
bioinformatics, bright future on application of these novel
approaches is envisaged.
42. Contd…
• AB-QTL approach has to play an increased role in
time to breeding cultivars with wide genetic
background.
• Genomic selection aided by genotyping will help in
identification of more recombination events.
• Utilization of specific populations will help further
mapping of gene/QTL to make selection of desirable
recombinants towards development of superior
genotypes.