Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
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.
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
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.
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
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.
Targeted Induced Local Lesions IN Genome. Mutations (Single base pair substitution) are created by traditionally used chemical mutagens. Identify SNPs and / or INDELS in a gene / genes of interest from a mutagenized population.
It comprises on mating designs used in plant breeding programs. 6 basic mating designs are briefly explained in it with their requirements as well limiting factors...
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.
it cover almost all content in cis/intragesis, right from introduction definition, explanation, production of marker free transgenic, intragenic vector construction, regulatory guide lines, current and future status, limitation, advantage over existing technique, swot analysis etc
its very useful for your seminar and presentations. it contain lot of picture, table, figure for your easy understanding
thank you
Mahesh
Molecular Marker and It's ApplicationsSuresh Antre
Molecular (DNA) markers are segments of DNA that can be detected through specific laboratory techniques. With the advent of marker-assisted selection (MAS), a new breeding tool is now available to make more accurate and useful selections in breeding populations.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
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.
Targeted Induced Local Lesions IN Genome. Mutations (Single base pair substitution) are created by traditionally used chemical mutagens. Identify SNPs and / or INDELS in a gene / genes of interest from a mutagenized population.
It comprises on mating designs used in plant breeding programs. 6 basic mating designs are briefly explained in it with their requirements as well limiting factors...
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.
it cover almost all content in cis/intragesis, right from introduction definition, explanation, production of marker free transgenic, intragenic vector construction, regulatory guide lines, current and future status, limitation, advantage over existing technique, swot analysis etc
its very useful for your seminar and presentations. it contain lot of picture, table, figure for your easy understanding
thank you
Mahesh
Presentation by Jacob van Etten.
CCAFS workshop titled "Using Climate Scenarios and Analogues for Designing Adaptation Strategies in Agriculture," 19-23 September in Kathmandu, Nepal.
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)
this presentation is about the molecular markers as we all know the molecular markers are the DNA sequences it can be easily detected and its inheritance is easily monitored.so the main basics of the molecular markers is the polymorphic nature so it can used as molecular markers.and this will gives you the idea about AFLP, RFLP, RAPD, SNPS,ETC.
In this presentation, we will delve into the principles of QTL mapping and explore various strategies for mapping QTLs in plants. We will also discuss the advantages and limitations, and provide insights into how QTL mapping is advancing our understanding of genetics.
Advances in host plant resistance and identification of broad-based stable so...ICRISAT
Host Plant Resistance is the most effective and economical management option for Fusarium wilt (Fusarium udum Butler) of pigeonpea (Figure 1) either alone or as a major component of IDM. The disease can cause yield losses of up to 100% in susceptible cultivars. ICRISAT has developed large numbers of high yielding wilt resistant lines by selecting them under high disease pressure in field screening. These resistant lines if found to possess stable resistance across locations, could be utilized in pigeonpea disease resistance breeding program.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
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.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
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
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
11. QTL mapping
• genotype and phenotype individuals
• look for statistical correlation between
genotype and phenotype
12. Genetic Linkage maps
Genetic Linkage maps (also called meiotic maps) rely
on the naturally occurring process of recombination
for determination of the relative order, and distances
between polymorphic markers.
The statistical analysis of the segregating data is then
used to convert the recombination fraction into an
additive unit of distance measured in centiMorgan
(cM), with 1 cM representing a 1% probability that
a recombination has occurred between two markers
on a single chromosome.
13. Several linkage maps based on intraspecific crosses between upland
cottons have been reported (Shappley et al. 1998, Ulloa
and Meredith 2000, Zuo et al. 2000, Ulloa et al. 2002), but all the maps
were characterized with low marker coverage of the
genome. As molecular polymorphism is limited within ( G. hirsutum L).
Therefore, in this study we are interested to using interspecific hybrids
between G. hirsutum L. and G. barbadense L., as an efficient source for
polymorphism.
14. 4 . Selection of parental varieties
The cotton map will be developed from an interspecific cross between
G. barbadense and G. hirsutum. Polymorphic parental varieties will be
selected among previous studied genotypes.
These parental varieties will be crossed to obtain the F1 generation.
5 . Generation of segregating population
An F1 plant will be selfed to generate the F2 segregating population.
The DNA of the different individual plants representing the F2 population
will be analyzed using the different marker types ( SSR and AFLP ).
The pattern of inheritance of these genetic markers among the F2
Individuals will be examined.
1 . Selection of cotton accessions among the collection available at the
Cotton Research Institute (CRI)
2 . Isolation and purification of genomic DNA from the different accessions.
3 . Fingerprinting of cotton accessions using different molecular markers
(AFLP , SSR and ISSR).
15. 7 . Bulked Segregant Analysis
To rapidly find markers closely linked to the trait of interest
(earliness ), two bulked samples will be prepared for the trait.
Screening for differences between the pooled DNA samples for
the trait will be performed using the different molecular markers.
6 . Screening of Morphological Traits
Morphological trait of interest particularly date of flowering will be
scored for the individual plants of the segregating population.
8 . Analysis of Segregation and Map construction
The segregation of all the studied markers ( molecular and
Morphological ) will be analyzed among the F2 individuals.
The goodness of fit to the expected 3:1 Mendelian ratio for
each segregating locus will be tested by chi-square test and
the linkage analysis between loci determined according to
the maximum likelihood method.
The linkage map will be constructed using the MAPMAKER
version 2.0 software.
16.
17. Marker Distance
Line1
Line2
Line3
Line4
Line5
Line6
Line7
Line8
Line9
Line10
Line11
Line12
Line13
Line14
Line15
Line16
_3_0363_ 0 A B B A A A B A B B A B B B B B
_1_1061_ 0.8 A B B A A A B A B B A A A B B A
_3_0703_ 1.5 B A A B B B A B A A B B B B B B
_1_1505_ 1.5 B A A B B B A B A B B B B B B B
_1_0498_ 1.5 B B B B B B B B B B B B B B B A
_2_1005_ 3.8 A B B A A A B A B A A B B B B B
_1_1054_ 3.8 A A A A A A A A A B A A A A A A
_2_0674_ 6 A B B A A A B A B A A A A A A B
_1_0297_ 8.8 A A B B B B B A A A A A A A A B
_1_0638_ 10.7 A A B B B B B A A B A A A A A A
_1_1302_ 11.4 B A A A B B A A A B A B B B B A
_1_0422_ 11.4 B A A A B B A A A B A B B B B A
_2_0929_ 15.3 A B B B A A B B B A B A A A A B
_3_1474_ 15.4 A B B B A A B B B A B A A A A A
_1_1522_ 17.3 A B B B A A B B B A B A A A A A
_2_1388_ 17.3 A A A A A A A A A A A A A A A A
_3_0259_ 18.1 B B B B B B B B B B B A A A A A
_1_0325_ 18.1 B B B B B B B B B B B A A A A A
_2_0602_ 20.8 A A B A A A A B A B A A A A A A
_1_0733_ 23.9 B B B B B B B B B B B A A A A A
_2_0729 23.9 B B B B B B B B B B B A A A A A
_1_1272_ 23.9 A B B B A A B B B B B B B B B B
_2_0891_ 26.1 A A A A A A A A A B A A A A A A
_2_0748_ 26.6 B B B B B B B B B A B B B B B B
_3_0251_ 27.4 A B A A A B A A A B A A A B A A
_1_0997_ 35.5 B B A A A B B B B B B B B B B B
_1_1133_ 41.8 B B A A A B B B B A B A A A A A
_2_0500_ 42.5 A A A A A A A A A B A B B B B B
_3_0634_ 43.3 B B B B B B B B B A B A A A A A
0
10
5Disease
severity
19. Introduction
Drought is one of the most common
abiotic stressor limiting crops productivity
throughout the world.
Therefore, breeding and selection for high-
yielding crops under drought stress is a
major objective of crop breeders working
under unfavorable environments.
20. The construction of a molecular linkage map represents the
first step in the genetic dissection of a target trait of interest.
Both, genetic linkage maps and QTL maps are useful in durum
wheat improvement because they provide useful tools for
studying genome structure, evolution, identifying or
manipulating chromosome segments QTL (quantitative trait
loci) controlling important agronomic traits.
21. Objectives
1. To develop a QTL map of Egyptian durum wheat through the
application of different DNA markers (SSR, RAPD, AFLP,
EST and SCoT) and an F2 segregating population obtained
from an intraspecific cross between two durum varieties
(Baniswif-1 and Souhag-2).
2. To tag QTLs controlling yield and drought tolerance-related
traits: root length, plant height, spike length, number of
branches/plant, number of spike/plant, number of
spikelets/spike, number of kernel/spike, thousand kernel
weight, fresh weight, dry weight and total amino acids.
22. Mapping Population used (F2, RIL, DH, BC, ….)
Type of markers employed (AFLP, SSR, EST, SNP,
DArT, ……)
Percentage of Genome Coverage
Traits of Interest (QTL Results)
23. Mapping population
Methodology
Two polymorphic varieties (Baniswif -1 and Sohag-2) were selected
among the germplasm available at Wheat Research Dept., Crop
Research Institute, ARC, Egypt.
These two varieties were used to develop an F2 mapping population
comprising 76 plants from the intraspecific cross.
24. The parents and F2 plants were grown in the year 2009 at one of the Agricultural
Genetic Engineering Research Institute experimental fields.
The F2 plants were grown in two replicates in a randomized complete block design.
25. Trait measurements
Data for:
- Root length, plant height as described by De Vita et al., 2007.
- Number of spikelets/spike, number of kernel/spike and thousand
kernel weight as described by Nacite et al., 1992.
- Spike length, number of branches/plant, number of spike/plant as
described by Diab et al., 2007.
- Fresh weight, dry weight and total amino acids as described by
Abebe et al., 2003.
26. DNA isolation
DNA was isolated from the two parents and the 76 F2 plants using DNAeasy
Plant Mini Kit (Qiagen, Santa Clarita, CA).
DNA markers
A preliminary screen of polymorphism between the two parental
genotypes was performed using 42 RAPD, 56 SSR, 32 AFLP, 20 EST and 26
SCoT primers and/or primer combinations.
Only 1 RAPD, 15 SSR, 11 AFLP and 10 SCoT primers revealed discernible
polymorphic patterns.
Therefore, analysis of segregation among the 76 F2 individuals was
performed using these polymorphic primers and/or primer combinations.
27. RAPD amplification was performed as described by Williams et al. (1990)
with minor modifications.
RAPD analysis
RAPD profile of the two parental genotypes as revealed by different primers
M P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 M P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2
28. SSR analysis
SSR analyses was performed as described by Hussein et al. (2003).
Table : SSR Primer name, primer sequence and Chromosome.
29. SSR profile of the two parental genotypes as revealed by different
primers
M P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2
30. EST analysis
EST analyses were performed as described by Adawy (2007).
Table : EST primer code, gene name, primer sequences and expected PCR
product.
31. EST profiles of the two parental genotypes as revealed by different primers
32. AFLP analysis
AFLP analyses was performed
using 11 AFLP primer
combinations according to the
protocol of Vos et al. (1995) with
minor modifications.
AFLP® Analysis System II
(Invitrogen, USA) was employed .
AFLP profile of the two parental
genotypes as revealed by different
primer combinations
34. Start Codon Targeted (SCoT) Polymorphism analysis
SCoT is a novel method for generating plant DNA markers.
This method was developed based on the short conserved
region flanking the ATG start codon in plant genes.
SCoT uses single 18-mer primers in polymerase chain
reaction (PCR) and an annealing temperature of 50°C.
PCR amplicons are resolved using standard agarose gel
electrophoresis.
35. SCoT Analysis
SCoT analyses were
performed as described
by Collard and Mackil
(2009).
Table : SCoT primers and their sequences
36. SCoT profiles of the two parental genotypes as revealed by different
primers
M P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2 P1 P1 P2 P2
37. Genetic linkage map construction and QTL detection
The markers that showed polymorphism between the parental lines were
used to construct the genetic linkage map.
Linkage analysis and map construction were performed by using Map
Manager QTX V1.4 (Manly and Cudmore, 1997) using the Kosambi
function with a minimum LOD score of 3.0 followed by ripple command
for each linkage group to check the final order of markers.
The association between phenotype and genotype was investigated using
single point analysis (SPA), using QTL cartographer (Wang, et al. 2004).
Significance levels of 5%, 1%, 0.1% and 0.01% were used to declare a QTL.
38. Trait measurements
Results
Phenotypic and physiological data
of root length, plant height, spike
length, number of branches/plant,
number of spike/plant, number of
spikelets/spike, number of
kernel/spike, thousand kernel
weight, fresh weight, dry weight
and total amino acids traits for the
76 F2 plants derived from the
intercross between Baniswif-1 and
Sohag-2.
39. Trait measurements
Phenotypic and physiological data
of root length, plant height, spike
length, number of branches/plant,
number of spike/plant, number of
spikelets/spike, number of
kernel/spike, thousand kernel
weight, fresh weight, dry weight
and total amino acids traits for the
76 F2 plants derived from the
intercross between Baniswif-1 and
Sohag-2.
40. Statistics and normality
test of traits
The Mean, Variance, Standard
Deviation, Coefficient of Variation,
Skewness and Kurtosis values for
root length, plant height, spike length,
number of branches/plant, number of
spike/plant, number of spikelets/spike,
number of kernel/spike, thousand
kernel weight, fresh weight, dry weight
and total amino acids are presented
in Figure.
41. All traits showed normal
distribution and large
amount of variation.
High kurtosis value were
observed for No. of Kernel/
spike (NKS) and Total Amino
Acids (TAA) and a large
skewness value was
obtained for No. of Kernel/
spike (NKS)
42. Primer, sequence, number of total bands and polymorphic bands as
revealed by RAPD analysis.
RAPD patterns of the
two parents and F2
individuals derived
from the cross
BaniSwif-1 and
Sohag-2 as revealed
by primer OP-C4. M
is the standard DNA
marker 100 bp
ladder, P1 (cv. Bani
Swif -1) and P2 (cv.
Sohag-2).
RAPD analysis
M P1 P1 P2 P2 F2 individulas
43. Primer code, Primer
name, primer sequence,
chromosome and
marker size as detected
by SSR
SSR analysis
44. SSR patterns of the two parents and F2 individuals derived from the cross BaniSwif
-1 and Sohag-2 as revealed by primer S8. M is the standard DNA marker 100 bp
ladder, P1 (cv. BaniSwif -1) and P2 (cv. Sohag-2).
45. Primer combinations, selective nucleotides, number of total bands, polymorphic bands
and percentage of polymorphism as detected by AFLP primer combinations.
AFLP analysis
46. AFLP patterns of the two parents and F2 individuals derived from the cross Baniswif -
1 and Sohag-2 as revealed by primercomb. 3/6. M is the standard DNA marker
100bp ladder, P1 (cv. Baniswif -1) and P2 (cv. Sohag-2).
47. SCoT analysis
Primer name, primer sequence, number of total bands, polymorphic bands and
percentage of polymorphism as detected by SCoT
48. SCoT patterns of the two parents and F2 individuals derived from the cross Baniswif -
1 and Sohag-2 as revealed by primer S4. M is the standard DNA marker 100bp
ladder, P1 (cv. Baniswif -1) and P2 (cv. Sohag-2).
49. Distribution of molecular
markers, assignment and
centiMorgan (cM)
coverage across the 14
linkage groups of the
genetic map used in QTL
mapping.
50. Molecular linkage
groups of durum wheat
(intercross between
Baniswif-1 and Sohag-2)
showing positions of
QTL influencing root
length, plant height,
spike length, number of
branches/plant, number
of spike/plant, number
of spikelets/spike,
number of kernel/spike,
thousand kernel weight,
fresh weight, dry weight
and total amino acids.
Map distances between
adjacent markers are in
cM
``
51. All 56 SSR primer pairs preliminary
screened on the two parents, were
previously mapped on the durum
wheat chromosomes.
However, only 15 SSRs primers
revealed polymorphic patterns
between the two parents. These
primer pairs were applied to the F2
individuals.
Assignment of linkage groups
to the chromosomes
52. Based on the presence of these SSR
markers, eight linkage groups (LG) were
assigned to chromosomes, i.e., LG1, LG3,
LG5, LG6, LG7, LG9, LG13 and LG14 were
assigned to chromosomes 1B, 3B, 5B,
6A, 6B, 7A, 3A and 2B, respectively.
The nine SSR markers used to assign
eight chromosomes are highlighted in
the linkage groups shown in the figure.
Assignment of linkage groups
to the chromosomes
53. QTL analysis
A total of 74 QTL at significance
level of 5%, 1%, 0.1% and 0.01%
have been identified for the 11 traits
on twelve linkage groups (1, 2, 3, 4,
5, 6, 7, 8, 9, 12, 13 and 14).
Among these QTLs, 3 QTL for RL, 11
QTL for PH, 7 QTL for SL, 3 QTL for
NBP, 3 QTL for NSP, 8 QTL for NSS,
15 QTL for NKS, 10 QTL for TKW,
4 QTL for FW, 5 QTL for DW and 5
QTL for TAA were identified.
54. Some genomic regions were found
where QTL for different traits
overlapped on linkage groups 2, 4, 6,
7, 8, 9, 13 and 14.
The linkage groups 6, 7 and 8 showed
the most overlapped traits.
Correlation between Traits
55. For example, QTL for spike length,
number of branches/plant, number
of spike/plant, number of
spikelets/spike and thousand kernel
weight were mapped to the same
chromosomal location.
Similarly, QTL for spike length, number
of kernel/spike, thousand kernel
weight and total amino acids were
mapped to identical genomic region.
56. Correlation between traits
Correlation coefficient among Root Length, Plant height, Spike length, Number of branches/plant, Number of
spike/plant, Number of spikelets/spike, Number of Kernel/spike, Thousand kernel weight, Fresh Weight, Dry
Weight and Total Amino Acids traits in F2 segregating population.
Positive
correlation
Negative
correlation
No
correlation
58. Conclusion
A genetic map comprising 114 molecular markers located on 14
linkage groups and spanning a total of 2040.9cM, was constructed.
This map was useful in detecting 74 significant QTLs related to high
productivity and drought tolerance (including : root length, plant
height, spike length, number of branches/plant, number of
spike/plant, number of spikelets/spike, number of kernel/spike,
thousand-kernel weight, fresh weight, dry weight and total amino
acids), and promises to provide a better understanding of the durum
wheat crop and enhancing breeding programs through MAS.
On the other hand, the constructed linkage map contains RAPD, SSR,
SCoT and AFLP markers that were not mapped collectively in any
other durum wheat maps.