Physical mapping technologies for identification and characterization of mutated genes contributing to crop quality


To accelerate crop breeding programmes through the application of physical mapping and complementary genomic approaches; and the characterization and utilization of induced mutants for improvement of crop quality with the objective of increasing agricultural sustainability, food security, economic stability, and alleviating local quality-related food problems.

  • To promote crop improvement with the production of quality trait mutants and to maximize the application of genetic, cytogenetic, and molecular stocks, linkage maps, and germplasm for crop improvement;
  • To foster relationships, transfer knowledge, technology, and genetic resources between all research groups for their mutual benefit between and among developing countries;
  • To generate physically maps and cytological and molecular markers to characterize quality trait variation with the aim of utilization;
  • To encourage distribution and dissemination of basic information, genetic, cytogenetic, and molecular stocks on an unrestricted basis;
  • To develop guidelines on methods for the application of molecular cytogenetics to plant breeding.


There are many important aspects of 'crop quality'. Quality products give the farmer a competitive market advantage and high added value, which will result in increased farm income. Public health is improved by access to better quality diet. Following is a list of a few of the many characters that can define 'crop quality': post-harvest characters, sprouting, nutritional, bread making, stress-related, processing, colour, taste, texture, sanitary, amino acid composition, protein, micronutrients, vitamins, secondary metabolites, nutraceuticals, fibres-cellulose-lignin, oils, waxes, and starches.

Physical mapping can provide an effective approach to manipulate the various quality characters, including the transfer of genes between varieties and even species. The technology is applicable to seeded as well as non-seed propagated crops. A particular advantage is that genetic polymorphisms and large segregating populations are not required for physical mapping.

Physical mapping technologies provide new tools for the rapid advancement of breeding programs and are highly applicable to neglected crops in developing countries. Furthermore, they open new opportunities for developing modern approaches to plant improvement research. In the past twenty years, major investments in several model species have been made, advancing our understanding of plant genomics. Utilizing classical breeding, mutation technology, markers and molecular cytogenetic techniques, considerable progress has been made in our ability to manipulate genes and gene complexes. However, plant breeders are still some distance from being able to utilize all the genomic information, and a better understanding of genome structures and variation (spontaneous and induced) to carry out the sort of directed gene manipulation is required. It has been well established that the utilization of mutagens can be a very important approach for manipulating many crop characters including quality. Future advances in our ability to improve production and quality will become more dependent on the utilization of many technologies. A more thorough understanding of gene expression, gene interactions, and physical location will improve our ability to manipulate and control genes, and directly lead to crop improvement.

The improvement of yield and quality traits, as well as the reduction of post-harvest losses in agricultural crops is hampered by the lack of information on the genes underlying these characters. Genetic linkage maps of various densities are being constructed in most of the crops, providing markers that may be used for marker-assisted breeding. Less attention has been paid to physical mapping and the physical location of genes of interest remains unknown. Yet, it is recognized that the expression of a gene depends on its physical location in a genome, which defines its interaction with other genes and DNA sequences. Gene location may be changed due to spontaneous or induced mutations as well as recombination in intra- and interspecific hybrids. Physical mapping is needed for efficient transfer of genes between varieties and species and may provide effective approach to manipulate various plant characters.

This CRP addresses the problems associated with physical placement of a gene or gene complex in a chromosome. An understanding of the physical organization of genomes and chromosomes is important to the utilization of induced mutations for plant improvement. The work plan applies the technology involved in accessing the genetic and physical position of quality genes in various crop genomes, build towards using physical map information and develop suitable cytological and molecular markers to screen for specific traits in crop improvement breeding programs.


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Project Officer:

P.J.L. Lagoda