Molecular characterization

molecular characterization
The Genetic Resource Center of IITA possess tens of thousands of germplasm accessions for clonally propagated and seed crops. As a result of the sheer size of these accessions, there is a need to develop strategies which use innovative technologies for characterizing genetic diversity and efficient utilization for germplasm enhancement. Molecular characterization or DNA fingerprinting using molecular markers is an important process that provides valuable data to detect variation at DNA level and to assess genetic diversity in crops and their wild relatives, which in turn helps in selection of diverse parents in crop improvement programs. DNA markers are used to evaluate the genetic variation in gene banks, as well as to identify phylogenetic and molecular structure of crops and their associated wild species. It also plays an important role in developing conservation strategies such as identification of duplicates or mismatches in rationalising ex situ germplasm collections. Molecular markers can also be used to certify varieties, determine the presence or absence of diseases and assess the reproductive biology of species, among other applications.

Current projects


  • Molecular fingerprinting of cocoa germplasm from five countries in West and Central Africa (Nigeria, Ghana, Cameroon, Togo and Cote d'Ivoire) using SNPs for identification of true-to-type genotypes and assessment of genetic diversity.

molecular characterization cocoa
This is a World Cocoa Foundation (WCF) funded project for five years which focuses mainly on fingerprinting 10,000 genotypes from five different countries in West and Central Africa. This five-year project will contribute to the program's overall goal of institutionalizing effective public and private sector models to support sustainable productivity growth and improved food security on diversified cocoa farms in West and Central Africa. The main objective of the project is to improve cocoa productivity through increased availability of better planting materials to farmers. This will ensure removal of mislabeled trees among clones in the Seed Gardens and Breeders' active collections, and provide information on the extent of mislabeling in the Seed Gardens by identifying 'true-to-type' clones. The project will also institutionalize a quality assurance mechanism for clonal identity in the seed gardens by creating the framework to ensure that new plantings in the seed gardens rely on certified clones.



  • Genotyping by sequencing (GBS) of yam genotypes including popular varieties, landraces conserved in international collection and breeding populations such as crossing block materials, mapping population parents and progenies as well as genotypes with historical morphological data for 5-6 years

molecular characterization - yamThis is a CRP RTB complimentary funded project which is aimed at assessing the population structure of Dioscorea rotundata at molecular level. This will allow identifying diverse populations and initiating bi-parental crossing for linkage mapping and QTL analysis. This will also allow for genome wide selection through association of GBS data with historical morphological data for targeted traits to ensure marker assisted breeding in Dioscorea rotundata.

  • Development of a linkage map in Dioscorea alata and identification of QTL (s) for anthracnose disease

This is a USAID funded project which is aimed at saturating the linkage map of Dioscorea alata using additional markers such as EST-SSRs, which were generated from transcriptome analysis of the parents which were diverse for anthracnose disease. This will allow identification of QTL (s) for anthracnose disease in D. alata. In addition, RNASeq technique is being applied to understand the gene (s) expression for anthracnose disease.

  • Identification of molecular markers associated with nitrogen use efficiency in Dioscorea rotundata and D. alata

This is a MAFF funded project which aims to assess the performance of genotypes of Dioscorea rotundata and D. alata at different nutrient levels. The project also aims to assess the genetic diversity to identify diverse parents for nutrient use efficiency and generate mapping population progenies for further linkage mapping and identification of QTL (s). This project also aims to understand the biochemical pathways responsible for nutrient uptake by different genotypes.

  • Genotyping of germplasm including landraces, breeding populations and wild species of Dioscorea using molecular markers such as SSRs

This is an internal IITA activity wherein the genotypes in germplasm collections, core collection and crossing blocks of yam breeding program are genotyped using available genomic and EST-SSRs to assess the genetic diversity and identify diverse parents to initiate fresh crossing programs as well as generate mapping population progenies.

  • Genotype-by-sequencing in cassava, yam, maize
  • Metabolomics in cassava, yam, and banana