This document provides an overview of the use of molecular markers in plant breeding and crop improvement. It discusses different types of genetic markers including morphological, biochemical, and DNA markers. DNA markers such as RFLPs, AFLPs, RAPDs, SSRs, and SNPs are now widely used due to their abundance. Molecular markers can be used to construct linkage maps, assess genetic diversity, identify cultivars, and facilitate marker-assisted selection by breeders to transfer genes controlling important traits from one plant variety to another. The document highlights several examples of genes for traits like disease resistance being tagged and mapped using molecular markers to accelerate plant breeding efforts.
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
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.
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
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.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
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)
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.”
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.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
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.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
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)
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.”
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.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
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.
Role of Marker Assisted Selection in Plant Resistance RandeepChoudhary2
Topic Role of Marker Assisted Selection in Plant Resistance is described in detail including some case studies.
Types of markers used in genetic engineering and biotechnology are described in detail.
Marker assisted selection is a process whereby a marker (morphological, biochemical or one
based on DNA/RNA variation) is used for indirect selection of a genetic determinant of a trait
of interest. Since the first reported linkage of an agronomically important trait (a quantitative
trait locus affecting seed weight) to a simply controlled gene (seed colour) in common bean by
Sax (1923), it has taken more than 60 years for genetic markers to become a qualified tool for
plant breeding programs. In rice, the Xieyou 218 hybrid was the first to be developed through
MAS to select individuals carrying a bacterial blight-resistant gene. Marker-assisted selection
(MAS) can be applied at the seedling stage, with high precision and reductions in cost. Genetic
mapping of major genes and quantitative traits loci (QTLs) for agricultural traits is increasing
the integration of biotechnology with the conventional breeding process. Traits related to
disease resistance to pathogens and to the quality of some crop products are offering some
important examples of a possible routinary application of MAS. For more complex traits, like
yield and abiotic stress tolerance, a number of constraints have severe limitations on an efficient
utilization of MAS in plant breeding. However, the economic and biological constraints such
as a low return of investment in small-grain cereal breeding, lack of diagnostic markers, and
the prevalence of QTL-background effects hinder the broad implementation of MAS but over
the past 2 decades, a number of R-genes conferring resistance to a diverse range of pathogens
have been mapped in many crops using molecular markers.
Molecular marker and its application in breed improvement and conservation.docxTrilokMandal2
Molecular markers have revolutionized the field of genetics and genomics by providing valuable tools for studying genetic diversity, identifying individuals, and characterizing traits of interest. This review paper aims to explore the applications of molecular markers in breed improvement and conservation. We discuss the various types of molecular markers commonly used, such as microsatellites, single nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs), and many more. Additionally, we examine their applications in genetic diversity assessment, parentage analysis, marker-assisted selection (MAS), and conservation efforts. The paper highlights the importance of molecular markers in accelerating breed improvement programs and enhancing conservation strategies for maintaining genetic diversity within a population.Molecular markers have had a significant impact on breed development and conservation efforts, transforming genetics and offering vital insights into genetic diversity, lineage tracing, and genotype characterization. The importance of molecular markers in improving genetic gains, facilitating breeding programs, and preserving genetic diversity for the long-term sustainability of the animal population has been underlined in this review paper. Emerging advancements in molecular marker technology show enormous potential for improving and conserving breeds. Deeper insights into the genetic basis of complex traits will be provided through GWAS, CRISPR/Cas9, gene editing technologies, and sequencing technologies, resulting in faster genetic gains. Breeders and conservationists will be able to make more informed judgments thanks to these technologies. In conclusion, molecular markers have had a significant impact on breed conservation and enhancement. Their innovations have changed the industry and given both conservationists and breeders vital knowledge. We can pave the road for more effective and sustainable genetic improvement and the preservation of biodiversity for future generations by combining the power of molecular markers with conventional breeding and conservation techniques.
Molecular markers (DNA markers) have entered the scene of genetic improvement in a wide range of horticultural crops. Among the major traits targeted for improvement in horticultural breeding programmes are disease and pest resistance, fruit yield and quality, tree shape, floral morphology, drought tolerance and dormancy. The development of molecular techniques for genetic analysis has led to a great increase in the knowledge of horticultural genetics and understanding and behavior of their genomes. These molecular techniques in particular, molecular markers, have been used to monitor DNA sequence variation in and among the species and create new sources of genetic variation by introducing new and favorable traits from landraces, wild relatives and related species and to fasten the time taken in conventional breeding. Today, markers are also being used for, genetic mapping, gene tagging and gene introgression from exotic and wild species.
Molecular Markers: Indispensable Tools for Genetic Diversity Analysis and Cro...Premier Publishers
Recent progress in molecular biology has led to the development of new molecular tools that offer the promise of making plant breeding faster. Molecular markers are segments of DNA associated with agronomically important traits and can be used by plant breeders as selection tools. Breeders can use marker-assisted selection (MAS) to bypass the traditional phenotype-based selection methods in order to improve crop varieties with pyramiding the desirable traits within short time. Various molecular markers such as RAPD, SSR, ISSR, RFLP, AFLP, SNP, SCAR, CAPS, etc. are extensively used for plant genetic diversity studies and crop improvement biotechnology. These markers are different in characteristic properties, applicability to various plants, unique in the resolving power and also have own advantages and disadvantages. This review article provides a valuable insight into different molecular marker techniques, classification, their advantages, disadvantages, ways of actions, uses of molecular markers in plant genetic diversity analysis and quantitative trait loci (QTL) mapping. It could be helpful for plant scientists and breeders in MAS breeding and crop improvement biotechnology in the post-genomic era.
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
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.
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Advancement of molecular markers and crop improvement in plant breeding
1. Progress in Agricultural Science and Technology
A Report
on
Advancement of molecular markers and crop
improvement in plant breeding
Submitted by:
Ripon Kumar Sikder, PhD Fellow
Institute of Cotton Research, CAAS
ID No. 2017Y90100144
Graduate School of Chinese Academy of Agricultural Sciences
12, Zhongguancun Nadajie, Haidian District, Beijing 100081, P. R. China
2. Page | 1
Introduction
Plant Breeding is a dynamic area of applied science. It relies on genetic variation and uses
selection to gradually improve plants for traits and characteristics. The way of improvement is
the introduction of new genetic material (e.g. genes for disease resistance) from other sources,
such as gene bank accessions and related plant species. Although current breeding practices
have been very successful in producing a continuous range of improved varieties, recent
developments in the field of biotechnology and molecular biology can be employed to enhance
plant breeding efforts and to speed up the creation of cultivars.
Molecular breeding implies molecular marker-assisted breeding (MAB) and is defined as the
application of molecular biotechnologies, specifically molecular markers, in combination with
linkage maps and genomics, to alter and improve plant or animal traits on the basis of genotypic
assays. Genetic markers represent genetic differences between individual organisms or species.
Generally, they do not represent the target genes themselves but act as ‘signs’ or ‘flags’.
Genetic markers that are located in close proximity to genes (i.e. tightly linked) may be referred
to as gene ‘tags’. Such markers themselves do not affect the phenotype of the trait of interest
because they are located only near or ‘linked’ to genes controlling the trait. All genetic markers
occupy specific genomic positions within chromosomes (like genes) called ‘loci’ (singular
‘locus’).
Different Genetic Markers in Plant Breeding
Genetic markers are the biological features that are determined by allelic forms of genes or
genetic loci and can be transmitted from one generation to another, and thus they can be used
as experimental probes or tags to keep track of an individual, a tissue, a cell, a nucleus, a
chromosome or a gene. There are three major types of genetic markers:
(1) Morphological (also ‘classical’ or ‘visible’) markers which themselves are phenotypic traits
or characters. Morphological markers are usually visually characterized phenotypic characters
such as flower color, seed shape, growth habits or pigmentation.
(2) Biochemical markers, which include allelic variants of enzymes called isozymes. Isozyme
markers are differences in enzymes that are detected by electrophoresis and specific staining.
(3) DNA (or molecular) markers, which reveal sites of variation in DNA (Jones et al., 1997;
Winter & Kahl, 1995). DNA markers have developed into many systems based on different
polymorphism-detecting techniques or methods (southern blotting – nuclear acid hybridization,
3. Page | 2
PCR – polymerase chain reaction, and DNA sequencing) (Collard et al., 2005), such as RFLP,
AFLP, RAPD, SSR, SNP, etc.
DNA markers are the most widely used type of marker predominantly due to their abundance.
They arise from different classes of DNA mutations such as substitution mutations (point
mutations), rearrangements (insertions or deletions) or errors in replication of tandemly
repeated DNA (Paterson, 1996a). These markers are selectively neutral because they are
usually located in non-coding regions of DNA. Unlike morphological and biochemical
markers, DNA markers are practically unlimited in number and are not affected by
environmental factors and/or the developmental stage of the plant (Winter & Kahl, 1995).
Apart from the use of DNA markers in the construction of linkage maps, they have numerous
applications in plant breeding such as assessing the level of genetic diversity within germplasm
and cultivar identity (Baird et al., 997; Henry, 1997; Jahufer et al., 2003; Weising et al., 1995;
Winter & Kahl, 1995).
DNA markers may be broadly divided into three classes based on the method of their detection:
(1) hybridization-based; (2) polymerase chain reaction (PCR)-based and (3) DNA sequence-
based (Gupta et al., 1999; Jones et al., 1997; Joshi et al., 1999; Winter & Kahl, 1995).
Essentially, DNA markers may reveal genetic differences that can be visualized by using a
technique called gel electrophoresis and staining with chemicals (ethidium bromide or silver)
or detection with radioactive or colorimetric probes. DNA markers are particularly useful if
they reveal differences between individuals of the same or different species. These markers are
called polymorphic markers, whereas markers that do not discriminate between genotypes are
called monomorphic markers. Polymorphic markers may also be described as co-dominant or
dominant.
Role of Molecular Markers in Crop Improvement
Conventional crop improvement has developed a large number of varieties. Genotypic and
environmental effects produce phenotypic values over genotypes in plants and other living
organisms. Strategies using best phenotypes to infer the best genotypes are commonly less
efficient than the schemes performing progeny tests. These strategies spend more time on
selection, and consequently it is necessary to invest major economic resources.
4. Page | 3
On the other hand, it is convenient to recognize the effects of quantitative or qualitative genes
on phenotypes. In general, it can be assumed that if the substitution effect of an allele on the
phenotypic expression is small, the trait is classified as quantitative, in turn, if the effect is large
the characteristic is considered as qualitative. The selection using molecular markers can be
enhanced, and the efficiency of the molecular marker will be higher if the markers are closely
linked to the genes controlling quantitative and qualitative characters (Appels et al., 1998).
Progress in crop improvement has been reached by manipulating the genetic variation within
populations. Currently, novel molecular tools as the molecular markers have started to
demonstrate their usefulness into practical plant breeding facilitating the identification,
characterization, and manipulation of the genetic variation on important agronomic traits
(Sorrells and Wilson, 1997). Molecular markers are being used for crop improvement to
achieve different objectives such as measuring genetic diversity among corn lines. Results
indicated that when inbreed lines were unrelated, a measurement of relative relationship based
on proportion of homomorphic marker loci, was significantly correlated with a measure of
relationship based on yield. Conversely, when lines were related the correlations were low
(Dudley et al., 1991). Smith and Smith (1989) proposed that problems related to the property
and registration of lines and control of genetic purity in seed production can be solved by use
of molecular markers. SSR markers are being applied to identify and validate pedigree of
genotypes. For this purpose different lines of maize were compared by using SSR and RFLP
technologies and found that SSR markers have potential advantages of reliability,
reproducibility, discrimination, standardization, and cost of effectiveness over RFLPs (Smith
et al., 1997). All these uses have contributed to the modernization of plant improvement;
however, one of the most important uses has been the application of molecular markers to
increase effectiveness of selection. This application called Marker-Assisted Selection (MAS)
and playing important role in crop improvement.
Plant improvement, either by natural selection or through the efforts of breeders, has always
relied upon creating, evaluating and selecting the right combination of alleles. The
manipulation of a large number of genes is often required for improvement of even the simplest
of characteristics (Flavell, 1995). With the use of molecular markers it is now a routine to trace
valuable alleles in a segregating population and mapping them. These markers once mapped
enable dissection of the complex traits into component genetic units more precisely (Hayes,
1993), thus providing breeders with new tools to manage these complex units more efficiently
in a breeding program.
5. Page | 4
The very first genome map in plants was reported in maize (Helentjaris et al., 1986 and
Gardiner et al. 1993), followed by rice (McCouch et al. 1988), Arabidopsis (Chang et al., 1988
and Nam et al., 1989) etc. using RFLP markers. Maps have since then been constructed for
several other crops like potato, barley, banana, members of Brassicaceae, etc (Winter et al.,
1995). Once the framework maps are generated, a large number of markers derived from
various techniques are used to saturate the maps as much as is possible. Microsatellite markers,
especially STMS markers, have been found to be extremely useful in this regard. Owing to
their quality of following clear Mendelian inheritance, they can be easily used in the
construction of index maps, which can provide an anchor or reference point for specific regions
of the genome. About 30 microsatellites have already been assigned to five linkage groups in
Arabidopsis, while their integration into the genetic linkage maps is still in progress in rice,
soybean, maize, etc. The very first attempt to map microsatellites in plants was made by Zhao
and Kochert (Zhao et al., 1992) in rice using (GGC)n, followed by mapping of (GA)n and
(GT)n by Tanksley et al and (GA/AG)n, (ATC) 10 and (ATT) 14, by Panaud et al., 1995 in
rice. The most recent microsatellite map has been generated by Milbourne et al., 1998 for
potato. Similar to microsatellites, looking at the pattern of variation, generated by
retrotransposons, it is now proposed that apart from genetic variability, these markers are ideal
for integrating genetic maps (Ellis et al., 1998).
Once mapped, these markers are efficiently employed in tagging several individual traits that
are extremely important for a breeding program like yield, disease resistance, stress tolerance,
seed quality, etc. A large number of monogenic and polygenic loci for various traits have been
identified in a number of plants, which are currently being exploited by breeders and molecular
biologists together, so as to make the dream of marker-assisted selection come true. Tagging
of useful genes like the ones responsible for conferring resistance to plant pathogen, synthesis
of plant hormones, drought tolerance and a variety of other important developmental pathway
genes, is a major target. Such tagged genes can also be used for detecting the presence of useful
genes in the new genotypes generated in a hybrid program or by other methods like
transformation, etc. RFLP markers have proved their importance as markers for gene tagging
and are very useful in locating and manipulating quantitative trait loci (QTL) in a number of
crops. The very first reports on gene tagging were from tomato (Paterson et al., 1988, Weller
et al., 1988 and Williamson, 1994), availing the means for identification of markers linked to
genes involved in several traits like water use efficiency (Martin et al., 1989), resistance
to Fusarium oxysporum (the 12 gene) (Sarfatti et al., 1989), leaf rust resistance genes LR 9 and
6. Page | 5
24 (Schachermayr et al., 1994 and Schachermayr et al., 1995), and root knot nematodes
(Meliodogyne sp.) (mi gene) (Klein-Lankhorst et al., 1991 and Messeguer et al., 1991).
Recently, Xiao et al., 1998 have shown the utility of RFLP markers in identifying the trait
improving QTL alleles from wild rice relative O. rufipogon.
Allele-specific associated primers have also exhibited their utility in genotyping of allelic
variants of loci that result from both size differences and point mutations. Some of the genuine
examples of this are the waxy gene locus in maize (Shattuck-Eidens et al., 1991), the Glu D1
complex locus associated with bread making quality in wheat (D’Ovidio et al., 1994),
the Lr1 leaf rust resistance locus in wheat (Feuillet et al., 1995), the Gro1 and H1 alleles
conferring resistance to the root cyst nematode Globodera rostochiensis in potato (Niewohner
et al., 1995), and allele-specific amplification of polymorphic sites for detection of powdery
mildew resistance loci in cereals (Mohler et al., 1996). A number of other traits have been
tagged using ASAPs in tomato, lettuce, etc. (Olson et al., 1989, Klein-Lankhorst et al., 1991
and Paran et al., 1991). Besides ASAPs, AFLP and SSR markers have been identified to be
associated with quantitative resistance to Globodera pallida (stone) in tetraploid potato, which
can be very well employed in marker-assisted selection (Bradshaw et al., 1998).
STMS markers have displayed a potential use as diagnostic markers for important traits in plant
breeding programs, e.g. (AT) 15 repeat has been located within a soybean heat shock protein
gene which is about 0.5 cM from (Rsv) a gene conferring resistance to soybean mosaic virus
(Yu et al., 1994). Several resistance genes including peanut mottle virus (Rpv), phytopthera
(Rps3) and Javanese rootknot nematode are clustered in this region of the soybean genome.
Similar to specific markers like RFLPs, STMS and ASAPs, arbitrary markers like RAPDs have
also played important role in saturation of the genetic linkage maps and gene tagging. Their
use in mapping has been especially important in systems, where RFLPs have failed to reveal
much polymorphism that is so very important for mapping. One of the first uses of RAPD
markers in saturation of genetic maps was reported by Williams et al (Williams et al., 1991).
They have proven utility in construction of linkage maps among species where there has been
inherent difficulty in producing F2 segregating populations and have large genome size, e.g.
conifers (Carlson et al., 1991 & Chaparoo et al., 1992). RAPD markers in near isogenic lines
can be converted into SCARs and used as diagnostic markers. SCAR/STS marker linked to the
translocated segment on 4 AL of bread wheat carrying the Lr28 gene has been tagged by Naik et
al., 1998. Recently, ISSRs, which too belong to the arbitrary marker category, but are found to
7. Page | 6
be devoid of many of the drawbacks shared by RAPD class of markers, have been employed
as a reliable tool for gene tagging. An ISSR marker (AG) 8YC has been found to be linked
closely (3.7 ± 1.1 cM) to the rice nuclear restorer gene, RF1 for fertility. RF1 is essential for
hybrid rice production and this marker would be useful not only for breeding both restorer and
maintainer lines, but also for the purity management of hybrid rice seeds (Akagi et al., 1996).
Similarly ISSR marker (AC)8 YT has been found to be linked to the gene for resistance to
fusarium wilt race 4 in repulsion at a distance of 5.2 cM in chickpea (Ratnaparkhe et al., 1998).
Apart from mapping and tagging of genes, an important utility of RFLP markers has been
observed in detecting gene introgression in a backcross breeding program (Jena et al., 1990),
and synteny mapping among closely related species (Gale et al., 1998). Similar utility of STMS
markers has been observed for reliable pre-selection in a marker assisted selection backcross
scheme (Ribaut et al 1997). Apart from specific markers, DAMD-based DNA fingerprinting
in wheat has also been useful for monitoring backcross-mediated genome introgression in
hexaploid wheat (Somers et al., 1996).
In plant breeding, MAS is a relatively new concept, nevertheless the original selection concept
has not changed, that is, the purpose of the selection is to search and preserve the best
genotypes, but using molecular markers. MAS can be used for manipulating both qualitative
and quantitative traits. A highly saturated marker linkage map is necessary for effective marker
based selection. Basically, MAS consists of identifying association between molecular markers
and genes controlling agronomic traits, and using these to improve lines or populations
(Dudley, 1993). Otherwise, based on the heritability of molecular markers, which is essentially
100 %, when the selection is performed for a low heritable trait, it will be more effective and
potentially less expensive than phenotypic selection (Winter and Kahl, 1995). Concerning
MAS applied to qualitative traits, Huang et al. (1997) using DNA marker-assisted selection
developed rice lines containing two, three, and four resistance genes to the bacterial blight
pathogen (Xanthomonas oryzae pv. orizae). Moreover, these researchers consider that a way
to maintain resistance in rice for long time is use of pyramiding, nevertheless the accumulation
of resistant genes and the epistasis and/or the masking effect of genes can be difficult or
impossible to manipulate in conventional plant improvement. A molecular marker was detected
in wheat associated with GBSS 4a locus, which affects the texture for Udon noodles.
Application of this result can reduce breeding cost for production of wheat varieties with this
characteristic (Briney et al., 1998).
8. Page | 7
With respect to the application of MAS for selecting quantitative traits, some researchers have
used molecular markers to locate loci associated with quantitative characters. Osmotic
adjustments were identified to assist the selection for drought tolerance in rice by use of
molecular markers linked to root traits (Nguyen et al., 1997). Likewise in maize quantitative
trait loci (QTLs) for yield components under two water conditions and for drought tolerance
were detected by using molecular markers (Frova et al., 1999). In wheat utilizing RFLP
markers Shah et al. (1999) determined important association with QTLs influencing
characteristics such as plant height, 1000 kernel weight, and kernel number. spike-1
. On the
other hand, in maize crop QTLs have been detected for plant height and European corn borer
tunneling length (Lee et al., 1991), other morphological traits with polygenic control have also
been studied in corn for example; Godshalk et al. (1990) identified loci linked to grain yield,
moisture, ear height, and root lodging.
Marker-Based Breeding and Conventional Breeding: Challenges and Perspectives
Marker-assisted breeding became a new member in the family of plant breeding as various
types of molecular markers in crop plants were developed during the 1980s and 1990s. The
extensive use of molecular markers in various fields of plant science, e.g. germplasm
evaluation, genetic mapping, map-based gene discovery, characterization of traits and crop
improvement, has proven that molecular technology is a powerful and reliable tool in genetic
manipulation of agronomically important traits in crop plants. Compared with conventional
breeding methods, MAB has significant advantages:
MAB can allow selection for all kinds of traits to be carried out at seedling stage and
thus reduce the time required before the phenotype of an individual plant is known. For
the traits that are expressed at later developmental stages, undesirable genotypes can be
quickly eliminated by MAS. This feature is particularly important and useful for some
breeding schemes such as backcrossing and recurrent selection, in which crossing with
or between selected individuals is required.
MAB can be not affected by environment, thus allowing the selection to be performed
under any environmental conditions (e.g. greenhouse and off-season nurseries). For
low-heritability traits that are easily affected by environments, MAS based on reliable
markers tightly linked to the QTLs for traits of interest can be more effective and
produce greater progress than phenotypic selection.
9. Page | 8
MAB using co-dominance markers (e.g. SSR and SNP) can allow effective selection of
recessive alleles of desired traits in the heterozygous status. No selfing or test crossing
is needed to detect the traits controlled by recessive alleles, thus saving time and
accelerating breeding progress.
For the traits controlled by multiple genes/QTLs, individual genes/QTLs can be
identified and selected in MAB at the same time and in the same individuals, and thus
MAB is particularly suitable for gene pyramiding. In traditional phenotypic selection,
however, to distinguish individual genes/loci is problematic as one gene may mask the
effect of additional genes.
Genotypic assays based on molecular markers may be faster, cheaper and more accurate
than conventional phenotypic assays, depending on the traits and conditions, and thus
MAB may result in higher effectiveness and higher efficiency in terms of time,
resources and efforts saved.
However, MAS and MABC were and are primarily constrained to simply-inherited traits, such
as monogenic or oligogenic resistance to diseases/ pests, although quantitative traits were also
involved (Collard and Mackill, 2008; Segmagn et al., 2006; Wang and Chee, 2010). The
application of molecular markers in plant breeding has not achieved the results as expected
previously in terms of extent and success (e.g. release of commercial cultivars). Improvement
of most agronomic traits that are of complicated inheritance and economic importance like
yield and quality is still a great challenge for MAB including the newly developed GS. The
application of molecular technologies to plant breeding is still facing the following drawbacks
and/or challenges:
Not all markers are breeder-friendly and not all markers can be applicable across
populations due to lack of marker polymorphism or reliable marker-trait
association.
False selection may occur due to recombination between the markers and the genes/
QTLs of interest.
Imprecise estimates of QTL locations and effects result in slower progress than
expected.
A large number of breeding programs have not been equipped with adequate
facilities and conditions for a large-scale adoption of MAB in practice.
10. Page | 9
The methods and schemes of MAB must be easily understandable, acceptable and
implementable for plant breeders, unless they are not designed for a large scale use
in practical breeding programs.
Higher startup expenses and labor costs.
With a long history of development, especially since the fundamental principles of inheritance
were established in the late 19th
and early 20th
centuries, plant breeding has become an
important component of agricultural science, which has features of both science and arts.
Conventional breeding methodologies have extensively proven successful in development of
cultivars and germplasm. However, subjective evaluation and empirical selection still play a
considerable role in conventional breeding. Scientific breeding needs less experience and more
science. MAB has brought great challenges, opportunities and prospects for conventional
breeding. As a new member of the whole family of plant breeding, however, MAB, as
transgenic breeding or genetic manipulation does, cannot replace conventional breeding but is
and only is a supplementary addition to conventional breeding. High costs and technical or
equipment demands of MAB will continue to be a major obstacle for its large-scale use in the
near future, especially in the developing countries (Collard and Mackill, 2008; Ribaut et al.,
2010). Therefore, integration of MAB into conventional breeding programs will be an
optimistic strategy for crop improvement in the future. It can be expected that the drawbacks
of MAB will be gradually overcome, as its theory, technology and application are further
developed and improved.
Conclusion
Molecular markers as new tools in crop improvement have demonstrated usefulness, especially
with genes controlling qualitative traits, whereas successful results are inconsistent with
application to quantitative characteristics. However, the value, ease, and cost of measurement,
and nature of genetic control of agronomic traits will determine the way in which molecular
markers may be effectively used in a breeding program. In addition, these new tools will have
a better opportunity for demonstrating their true values for crop improvement, when the
techniques used by molecular genetics reach a higher degree of automation; then it will be
possible to use molecular markers leading to a new “green revolution” in the world of
agriculture.
11. Page | 10
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