QTL mapping and analysis
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QTL mapping is a process used to identify genomic regions associated with quantitative traits using DNA markers. It involves selecting parental lines with desirable traits, creating a mapping population such as recombinant inbred lines, phenotyping the population for the target trait, genotyping the population, and constructing a linkage map to detect QTLs. The objectives are to detect QTLs, identify genome regions affecting traits, analyze QTL effects, and determine which alleles are favorable. Different types of mapping populations like backcross, F2, RILs, and near isogenic lines can be used depending on the desired advantages and disadvantages. Methods for QTL detection include analyzing single markers, interval mapping of two flanking markers, and composite interval mapping using
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Qtl mapping
This document discusses quantitative trait loci (QTL) mapping. It explains that QTL mapping can identify the genomic regions linked to quantitative traits, analyze the effects of QTLs, and provide information on the number, location, effects, and interactions of QTLs. The key aspects of QTL mapping covered are the objectives, principles, analysis methods, required resources like mapping populations, and applications in plant breeding and genetics research.
Mapping and QTL
The document describes the development of a QTL map for Egyptian durum wheat using an F2 mapping population derived from a cross between two parental varieties, Baniswif-1 and Souhag-2. A variety of DNA markers including SSRs, RAPDs, AFLPs, ESTs and SCoTs were used to genotype the mapping population. Traits related to yield and drought tolerance such as root length, plant height, spike characteristics, and biomass were measured. Linkage analysis was performed to construct a genetic linkage map, which was then used to detect QTLs associated with the traits of interest.
Mapping
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.
Mapping population ppt
This document discusses different types of mapping populations used in genetic mapping. It describes F2, backcross, double haploid, recombinant inbred line, and near isogenic line populations. For each type, it provides details on how they are developed and their advantages and disadvantages. It also discusses how marker segregation ratios differ depending on the population type and marker dominance. The document recommends using short-term mapping populations initially for preliminary mapping but developing long-term populations like recombinant inbred lines for global mapping projects.
mapping population
This document discusses different types of mapping populations that can be used for genetic mapping and molecular breeding programs. It describes F2, F2:F3, backcross, doubled haploid (DH), recombinant inbred line (RIL), and near-isogenic line (NIL) populations. For each type, it provides details on how they are developed, their characteristics, and merits and demerits relative to mapping objectives. The document emphasizes that the choice of mapping population depends on the research goals, availability of markers, and existing molecular maps. RILs and DHs allow for replication over environments but require more time and resources to develop.
Molecular markers
Molecular markers are DNA sequences that can be easily detected and whose inheritance can be monitored. They are based on natural polymorphisms and allow studying the inheritance of genes. Common types of molecular markers include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs use restriction enzymes to detect differences in fragment lengths. RAPDs use random primers to detect sequence polymorphisms. AFLPs selectively amplify restriction fragments to detect length differences. SSRs detect variability in simple sequence repeats. Molecular markers are useful for applications like gene mapping, phylogenetic studies, and analyzing genetic diversity.
QTL
This document discusses quantitative trait loci (QTL) mapping. It begins by defining QTLs as genomic regions containing genes associated with quantitative traits. QTL mapping involves correlating genotypic and phenotypic data from a mapping population to identify these regions. Common mapping populations discussed include recombinant inbred lines, double haploids, and backcrosses. Interval mapping and composite interval mapping are presented as methods for QTL analysis. The goals of QTL mapping are to locate genomic regions influencing traits and estimate the effects of QTLs.
Molecular markers
This document provides an overview of different types of molecular markers that can be used in genetics and plant breeding. It discusses morphological markers that are visible traits, as well as several classes of molecular markers including biochemical markers such as allozymes, and DNA-based markers such as RFLPs, microsatellites, AFLPs, STS, and others. The advantages and disadvantages of each type of marker are described. Morphological markers are influenced by the environment while molecular markers directly reflect genotypes. DNA-based markers allow more precise tracking of genetic material and are not affected by the environment.
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Qtl mapping
This document discusses quantitative trait loci (QTL) mapping. It explains that QTL mapping can identify the genomic regions linked to quantitative traits, analyze the effects of QTLs, and provide information on the number, location, effects, and interactions of QTLs. The key aspects of QTL mapping covered are the objectives, principles, analysis methods, required resources like mapping populations, and applications in plant breeding and genetics research.
Mapping and QTL
The document describes the development of a QTL map for Egyptian durum wheat using an F2 mapping population derived from a cross between two parental varieties, Baniswif-1 and Souhag-2. A variety of DNA markers including SSRs, RAPDs, AFLPs, ESTs and SCoTs were used to genotype the mapping population. Traits related to yield and drought tolerance such as root length, plant height, spike characteristics, and biomass were measured. Linkage analysis was performed to construct a genetic linkage map, which was then used to detect QTLs associated with the traits of interest.
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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.
Mapping population ppt
This document discusses different types of mapping populations used in genetic mapping. It describes F2, backcross, double haploid, recombinant inbred line, and near isogenic line populations. For each type, it provides details on how they are developed and their advantages and disadvantages. It also discusses how marker segregation ratios differ depending on the population type and marker dominance. The document recommends using short-term mapping populations initially for preliminary mapping but developing long-term populations like recombinant inbred lines for global mapping projects.
mapping population
This document discusses different types of mapping populations that can be used for genetic mapping and molecular breeding programs. It describes F2, F2:F3, backcross, doubled haploid (DH), recombinant inbred line (RIL), and near-isogenic line (NIL) populations. For each type, it provides details on how they are developed, their characteristics, and merits and demerits relative to mapping objectives. The document emphasizes that the choice of mapping population depends on the research goals, availability of markers, and existing molecular maps. RILs and DHs allow for replication over environments but require more time and resources to develop.
Molecular markers
Molecular markers are DNA sequences that can be easily detected and whose inheritance can be monitored. They are based on natural polymorphisms and allow studying the inheritance of genes. Common types of molecular markers include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs use restriction enzymes to detect differences in fragment lengths. RAPDs use random primers to detect sequence polymorphisms. AFLPs selectively amplify restriction fragments to detect length differences. SSRs detect variability in simple sequence repeats. Molecular markers are useful for applications like gene mapping, phylogenetic studies, and analyzing genetic diversity.
QTL
This document discusses quantitative trait loci (QTL) mapping. It begins by defining QTLs as genomic regions containing genes associated with quantitative traits. QTL mapping involves correlating genotypic and phenotypic data from a mapping population to identify these regions. Common mapping populations discussed include recombinant inbred lines, double haploids, and backcrosses. Interval mapping and composite interval mapping are presented as methods for QTL analysis. The goals of QTL mapping are to locate genomic regions influencing traits and estimate the effects of QTLs.
Molecular markers
This document provides an overview of different types of molecular markers that can be used in genetics and plant breeding. It discusses morphological markers that are visible traits, as well as several classes of molecular markers including biochemical markers such as allozymes, and DNA-based markers such as RFLPs, microsatellites, AFLPs, STS, and others. The advantages and disadvantages of each type of marker are described. Morphological markers are influenced by the environment while molecular markers directly reflect genotypes. DNA-based markers allow more precise tracking of genetic material and are not affected by the environment.
QTL MAPPING & ANALYSIS
This document discusses quantitative trait loci (QTL) mapping, which is used to identify genomic regions associated with quantitative or complex traits. It defines QTLs and their characteristics, and describes the basic process of QTL mapping, which involves constructing genetic linkage maps, phenotyping mapping populations for traits of interest, and using statistical analyses to detect associations between trait variation and genetic markers. The document outlines different types of mapping populations, methods for QTL detection like single-marker analysis and interval mapping, and the use of logarithm of odds (LOD) scores to evaluate the strength of evidence for a QTL in a particular genomic region.
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This document discusses QTL mapping in genetic analysis. It begins by defining quantitative traits as traits controlled by multiple genes that show continuous variation, like yield, quality, and disease resistance. Quantitative trait loci (QTL) are the genomic regions associated with quantitative traits. The document outlines the objectives, prerequisites, types of mapping populations, and steps involved in QTL mapping, including phenotyping, genotyping, linkage map construction, and analysis methods like single marker analysis, interval mapping, and composite interval mapping. It discusses merits of QTL mapping in identifying novel genes and limitations. The materials and methods section describes a study that mapped QTLs for salt stress in rice using a mapping population and 50K SNP chip. Results identified 34 Q
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2. Key factors for successful association mapping include choosing diverse germplasm with extensive recombination history, collecting high-quality phenotypic data across environments, genotyping candidate genes and markers, and using statistical methods to account for population structure.
3. Combining association mapping with traditional QTL mapping and the various available software tools allows for rapid dissection and evaluation of complex traits.
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This document discusses quantitative trait loci (QTL) analysis and mapping. It begins with a brief history of genetics and quantitative traits. QTL analysis uses phenotypic and genotypic data to link complex trait variation to genetics. There are several approaches for QTL analysis, including single marker analysis, interval mapping, and association mapping. Interval mapping uses flanking markers and likelihood estimates to more precisely map QTL locations compared to single marker analysis. Composite interval mapping further refines this by using additional markers as cofactors. The accuracy of QTL mapping is influenced by genetic and environmental factors as well as population size and experimental error. QTLs can be confirmed through multiple methods such as stability across environments or using near-isogenic lines.
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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.
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This document discusses quantitative trait loci (QTL) mapping. It begins by explaining that quantitative traits are controlled by multiple genes and the regions of the genome that control these traits are called QTLs. It then describes the process of QTL mapping, which involves constructing a linkage map using molecular markers and identifying genomic regions associated with traits. The key steps involve developing a mapping population, generating a saturated linkage map, phenotyping the population, and using approaches like single marker analysis, interval mapping, and composite interval mapping to detect QTLs.
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This document discusses QTL mapping in genetic analysis. It begins by defining quantitative traits as traits controlled by multiple genes that show continuous variation, like yield, quality, and disease resistance. Quantitative trait loci (QTL) are the genomic regions associated with quantitative traits. The document outlines the objectives, prerequisites, types of mapping populations, and steps involved in QTL mapping, including phenotyping, genotyping, linkage map construction, and analysis methods like single marker analysis, interval mapping, and composite interval mapping. It discusses merits of QTL mapping in identifying novel genes and limitations. The materials and methods section describes a study that mapped QTLs for salt stress in rice using a mapping population and 50K SNP chip. Results identified 34 Q
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This document discusses various cytogenetic techniques for gene location and transfer. It describes techniques for locating genes such as using structural and numerical chromosomal aberrations, chromosome banding, and in situ hybridization. Structural aberrations discussed include deficiencies, inversions, and translocations. Numerical aberrations discussed include aneuploids like trisomics, monosomics, and nullisomics. The document also describes techniques for transferring genes between species such as transferring whole genomes, whole chromosomes, chromosome arms, and through various types of interchanges. Specific examples of using these techniques in plants are provided.
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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.
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molecular markers ,application in plant breeding
1. The document discusses a seminar on applying molecular markers in plant breeding. It defines different types of markers including morphological, cytological, biochemical, and DNA/molecular markers.
2. It describes various molecular marker techniques like RFLP, RAPD, AFLP, and SSR. The techniques differ in characteristics like being dominant or co-dominant.
3. Molecular markers have important applications in plant breeding like marker-assisted selection, genetic diversity analysis, germplasm characterization, variety identification, and gene pyramiding.
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Genomic mapping, concept by kk sahu
Introduction
Genome mapping
History
Genetic mapping
Genetic markers
Linkage mapping
Recombination frequency
Physical mapping
Uses of genomic mapping
Limitation
References
Marker assisted backcross breeding
This document discusses marker-assisted backcrossing (MAB) for introgressing traits from a donor parent into a recipient line. MAB uses DNA markers linked to target genes/QTLs to aid in selection. Markers can be used for foreground selection of target genes, background selection to recover the recipient genome, and recombinant selection to minimize linkage drag. A case study is described where MAB was used over multiple generations to introgress 5 drought resistance QTLs from a donor rice variety into a recipient variety. Through foreground, background, and recombinant selection using DNA markers, lines were developed with the target QTLs and most of the recipient genetic background.
Forward and reverse genetics
This document discusses genetic analysis techniques including gene mapping and quantitative trait locus (QTL) analysis. It provides an overview of the basic requirements for gene mapping such as near isogenic lines and saturated physical maps. It describes the 5 step process for map-based cloning including gene tagging, high resolution mapping, physical mapping, sequencing, and transformation. It also discusses QTL analysis including principal objectives, factors considered, and methods to detect QTL like single marker analysis and interval mapping. Applications of QTL analysis in plant breeding and pre-breeding are mentioned. The key differences between traditional QTL mapping and association mapping are highlighted.
Molecular markers
This document discusses molecular markers and their applications in molecular breeding. It defines molecular breeding as using genetic manipulation at the DNA level to improve plant and animal traits. Quantitative trait loci (QTL) are genomic regions associated with quantitative traits, which are influenced by polygenes and the environment. The document describes different types of molecular markers like restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), expressed sequence tags (ESTs), and single nucleotide polymorphisms (SNPs). It explains how these codominant and dominant markers are used for genetic mapping, diversity studies, and marker-assisted breeding to identify QTL
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QTL mapping and analysis
- 1. QTL Mapping MSc ag (2) year Agriculture Genetics and Plant Breeding Deen Dayal Upadhyaya Gorakhpur University Gorakhpur Submitted by. Shweta Kumari Submitted to Department of Genetics and plant breeding
- 2. Introduction ✩ QTL mapping ✩ QTL mapping is the process to identify the genomic region associated with desirable quantitative trait with the help of DNA marker ✩ In this process DNA markers are tested throughout the genome which are associated with QTLs.
- 3. Quantitative Traits Loci ✩ The loci controlling quantitative traits are called quantitative traits Ioci ( QTL) ✩ the term quantitative traits coined by Genderman. ✩ QTL is the region of genome which control quantitative trait ✩ QTL characteristics ✩ The QTLs are controlled by multiple genes ,each segregating according to Mendel's Law. ✩ These traits also a ected by environment to varying degrees ✩ QTL can show dominant or co-dominant
- 4. Objective of QTL mapping ✩ The basic objective is to detect QTL ✩ To identify the region of genome that a ects the trait of interest ✩ To analyse the e ect of the QTL on the trait ✩ How much variation for the trait is caused by a specific region ✩ What is the gene action associated with the QTL? ✩ Which allele is associated with the favourable e ect.
- 5. Procedure for QTL mapping ✩ Selection of diverse parental lines ✩ Creation of mapping population ✩ Phenotyping of the progeny ✩ Genotyping of the progeny ✩ Construction of linkage map.
- 6. Types of mapping population ✩ Recombinant Inbred line(RIL) ✩ Backcross ✩ F2 population ✩ Double haploid ✩ Near isogenic line(NIL)
- 7. Backcross mapping population ✩ Advantages: It is easier to identify QTL as there are less epistatic and linkage drag e ects; especially useful for crosses with wild species. ✩ Disadvantages: Di cult or impossible in species that are highly heterozygous and outcrossing. ✩ Use: best when inbred lines are available
- 8. F2 mapping Population ✩ Advantage: Fast and easy to construct. ✩ Disadvantage: F3 families are still very heterozygous; so the precision of the estimates can be low (because of the high standard error); can't be replicated
- 9. Recombinant Inbred Line ✩ RILs are produced by continuous selfing progeny of individual member of an F2 population until complete homozygous is achieved ✩ Advantages: fixed lines so can be replicated across many locations and/or years; can eliminate problem of background heterozygosity. ✩ Disadvantages: Can take a long time to produce. (Some species are not amenable)
- 10. Near Isogenic Line ✩ Advantage: Very precise and statistically strong, as background is constant; especially useful for validation experiments. ✩ Disadvantage: Can take time to construct; only useful for specific target QTL
- 11. Doubled Haploid Line ✩ Advantages: 1)Spontaneous chromosome doubling of ✩ Haploid microspores in in vitro culture ✩ 2)Homozygosity achieved in a single step Plants. ✩ Disadvantages: Less recombination between linked markers Not all systems are amenable to in vitro culture
- 12. Methods of QTL Detection ✩ Studying single markers one at a time. ✩ The simplest method for QTL analysis. ✩ Can be done by t-tests or ANOVA. ✩ Does not require a complete linkage map.
- 13. Simple Interval mapping ✩ Two markers at a time (flanking markers). ✩ Based on linkage mapping of markers. ✩ More accurate than single-marker analysis.
- 14. Composite interval mapping ✩ For detection of a QTL more than two markers are used ✩ It is based on linkage mapping of the marker.
- 15. Thank you
- 16. Zoho Show To create beautiful presentations, download Zoho Show from Play Store https://zoho.to/cy7 QTL mapping.pdf (This PDF has been generated using Zoho Show)