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Multiplex markers in a plant breeding perspective

Hansen, Mats LU (2000)
Abstract
Plant breeding is largely depending on the repeated selection for desirable traits. This process is both time and labour consuming, making the development of commercial plant varieties a slow and costly activity. By the use of molecular markers, analysis of the genetic constitution of plants can be performed at an early stage, providing a possibility to decrease the time and cost required for selection. In addition, as the precision in selection is increased, less unwanted side effects appear in the following generations of plants. Multiplex molecular marker systems can be used to simultaneously generate many markers in the same assay. Such systems provide efficient tools for the analysis of breeding materials. In this thesis, I have... (More)
Plant breeding is largely depending on the repeated selection for desirable traits. This process is both time and labour consuming, making the development of commercial plant varieties a slow and costly activity. By the use of molecular markers, analysis of the genetic constitution of plants can be performed at an early stage, providing a possibility to decrease the time and cost required for selection. In addition, as the precision in selection is increased, less unwanted side effects appear in the following generations of plants. Multiplex molecular marker systems can be used to simultaneously generate many markers in the same assay. Such systems provide efficient tools for the analysis of breeding materials. In this thesis, I have focused on the use of PCR-based, multiplex marker systems in applied plant breeding. The properties of the two most influential multiplex systems in plant breeding applications, random amplified polymorphic DNA (RAPD) and AFLP, have been evaluated and are discussed in detail.



Although the use of RAPD markers are associated with an increased risk of errors in the analysis, they can be valuable for the rapid identification of markers in bulked segregant analysis (BSA) and subsequent marker-assisted trait selection. At present, however, AFLP is the most attractive inherently multiplex system for use in marker-assisted breeding. This highly multiplex system is very cost-effective in fingerprinting of different plant accessions since information from all polymorphic loci is considered. An optimised set of primer combinations for the generation of as many anonymous AFLP markers in as few assays as possible can be identified, allowing for increased efficiency in marker-assisted breeding. The construction of a linkage map and analysis of quantitative trait loci (QTL) in sugar beet by means of AFLP markers has been performed. Several QTLs for resistance to Cercospora beticola were detected and the results are discussed from a marker-assisted breeding perspective. Different methods for the identification of markers tightly linked to a target gene have previously been described. Linkage disequilibrium mapping is widely accepted as a method for the detection of markers tightly linked to human disease genes. This strategy, which has not previously been employed in plants, was used in an attempt to identify AFLP markers for the gene conferring annual growth habit in beet. Two markers that were strongly associated with annual growth habit were found, indicating the general use of this method for gene mapping in plants.



New demands in plant breeding such as the simultaneous selection for alleles at different QTLs require the implementation of novel marker technologies for increased efficiency and precision. Single nucleotide polymorphism (SNP) markers are based on alterations in single basepairs and are found at high frequency throughout genomes. They provide a source for employing artificial multiplexity to target specific genomic regions in the same assay. Results are presented from the first investigation of SNP occurrence in sugar beet. These are encouraging for the future development of high-throughput marker assays in this economically important crop. (Less)
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author
opponent
  • Prof Andersson, Leif, Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
organization
publishing date
type
Thesis
publication status
published
subject
keywords
Plant biochemistry, plant breeding, SNP, RAPD, molecular markers, AFLP, Växtbiokemi
pages
120 pages
publisher
Department of Biochemistry, Lund University
defense location
Hörsalen, LTH´s kårhus, John Ericssonsv. 3, Lund
defense date
2000-04-28 10:00
external identifiers
  • Other:ISRN: LUNKDL/NK VK-00/1015
ISBN
91-973252-4-4
language
English
LU publication?
yes
id
e9839209-6a52-4df2-8b3d-3dd32cf03d19 (old id 40461)
date added to LUP
2007-07-31 10:23:38
date last changed
2016-09-19 08:45:05
@phdthesis{e9839209-6a52-4df2-8b3d-3dd32cf03d19,
  abstract     = {Plant breeding is largely depending on the repeated selection for desirable traits. This process is both time and labour consuming, making the development of commercial plant varieties a slow and costly activity. By the use of molecular markers, analysis of the genetic constitution of plants can be performed at an early stage, providing a possibility to decrease the time and cost required for selection. In addition, as the precision in selection is increased, less unwanted side effects appear in the following generations of plants. Multiplex molecular marker systems can be used to simultaneously generate many markers in the same assay. Such systems provide efficient tools for the analysis of breeding materials. In this thesis, I have focused on the use of PCR-based, multiplex marker systems in applied plant breeding. The properties of the two most influential multiplex systems in plant breeding applications, random amplified polymorphic DNA (RAPD) and AFLP, have been evaluated and are discussed in detail.<br/><br>
<br/><br>
Although the use of RAPD markers are associated with an increased risk of errors in the analysis, they can be valuable for the rapid identification of markers in bulked segregant analysis (BSA) and subsequent marker-assisted trait selection. At present, however, AFLP is the most attractive inherently multiplex system for use in marker-assisted breeding. This highly multiplex system is very cost-effective in fingerprinting of different plant accessions since information from all polymorphic loci is considered. An optimised set of primer combinations for the generation of as many anonymous AFLP markers in as few assays as possible can be identified, allowing for increased efficiency in marker-assisted breeding. The construction of a linkage map and analysis of quantitative trait loci (QTL) in sugar beet by means of AFLP markers has been performed. Several QTLs for resistance to Cercospora beticola were detected and the results are discussed from a marker-assisted breeding perspective. Different methods for the identification of markers tightly linked to a target gene have previously been described. Linkage disequilibrium mapping is widely accepted as a method for the detection of markers tightly linked to human disease genes. This strategy, which has not previously been employed in plants, was used in an attempt to identify AFLP markers for the gene conferring annual growth habit in beet. Two markers that were strongly associated with annual growth habit were found, indicating the general use of this method for gene mapping in plants.<br/><br>
<br/><br>
New demands in plant breeding such as the simultaneous selection for alleles at different QTLs require the implementation of novel marker technologies for increased efficiency and precision. Single nucleotide polymorphism (SNP) markers are based on alterations in single basepairs and are found at high frequency throughout genomes. They provide a source for employing artificial multiplexity to target specific genomic regions in the same assay. Results are presented from the first investigation of SNP occurrence in sugar beet. These are encouraging for the future development of high-throughput marker assays in this economically important crop.},
  author       = {Hansen, Mats},
  isbn         = {91-973252-4-4},
  keyword      = {Plant biochemistry,plant breeding,SNP,RAPD,molecular markers,AFLP,Växtbiokemi},
  language     = {eng},
  pages        = {120},
  publisher    = {Department of Biochemistry, Lund University},
  school       = {Lund University},
  title        = {Multiplex markers in a plant breeding perspective},
  year         = {2000},
}