Bioinformatics Lab

iita bioscience center - bioinformatics labIn the decade gone by, genome sequencing was not only time consuming but also cost millions of dollars. Today, technological advances have made this task much easier: a whole genome can be sequenced in a few days and costs 100 times cheaper.

The landscape of biology in general and genetics and plant breeding in particular has changed. A few years ago, there barely existed 100s of molecular markers – the tools that geneticists use to find the QTLs/genes that control traits of interest – in many crop species. Now, we are already obtaining high-density genotypic data (1000s to 100,000s) in maize, cassava, and soon yam and banana at a cost of < $ 30 per sample. The technology involves direct re-sequencing of plant populations, a process that generates millions of base-pair reads and requires both high computational power as well as significant bioinformatics skills to tap into these resources.

Presently, IITA scientists have several projects that involve next-generation technologies through outsourcing and multi-partner collaboration. Though these partnerships are helpful in terms of data analysis, we do not want to be dependants forever. Without the development of an in-house bio-informatics capacity IITA science in genetics and breeding is vulnerable and risks becoming uncompetitive. Furthermore enhanced capacity in this area is crucial to fully realizing the value of our genetic resources in underpinning breeding and research directly contributing to food security.

  • Server
  • Workstation
  • Software for sequence analysis
  • Software for linkage and association analysis

 

 

iita bioscience center - molecular biologyGenotyping Services

  • Applied Biosystems Genetic Analyzer for DNA sequencing and fragment analysis
  • This instrument is fluorescence based genetic analyzing system where the genotyping methods are based on the sizing of fluorescently labelled DNA fragments.
    The applied biosystems 3130xl is capable of performing sequencing and fragment analysis of applications like microsatellite or short Tandem Repeats (STR), AFLP, LOH, SNP, rapid sequencing, standard sequencing de novo sequencing and resequencing.
    The sequencer is typically set up for rapid sequencing and fragment analysis but upon request, we can install 50cm array for standard sequencing (≤900bp) and 80cm array for ≥1000bp reads.
    Available data software sequencing analysis Software v5.2 and Genemapper v4.0. The system uses POP7 as well as POP6 but mostly POP7 as its separation matrix.

  • Thermocyclers (Polymerase Chain Reaction – PCR machines) for amplification of short selected fragments of DNA from the genome
  • Quantitative real-time PCR for gene expression analysis
  • Equipment for medium throughput DNA and RNA extraction and analysis including Genogrinder to grind 192 samples in few minutes (2 times 96 well plates);
  • Gel electrophoresis: a wide range of apparatus for analysis and visualization of nucleic acids
  • Spectrophotometers and other analytical instruments

 

 

Cytogenetics

IITA Bioscience Center - cytogenetics, microscope roomCytogenetics is a study which analyzes the structure and function of the cell, especially the chromosomes. Change the chromosome number and/or structure of the chromosomes can cause problems with growth, development and functions.
The Bioscience center has installed micro scope with LED light. You can carry out the observation with fluorescence, for example FISH.


Equipment and Facilities

Working Space

  • Microscope and flow cytometry room

Major Equipments

  • Flow cytometry
  • Light microscope (OLYMPUS)
  • Inverted light microscope for fluorescence observation (Carl Zeiss)

 

 

Tissue culture

iita bioscience center -  cytogeneticsPresently tissue culture based research work is focused on banana and yam. However, other fields of TC such as in-vitro propagation, virus indexing, etc. are being carried out for all clonally propagated crops of IITA including cassava.

Plant tissue culture involves growing plant cells, tissues or organs in artificial nutrient media under sterile conditions in a controlled growth environment and it is widely used in plant science research with several commercial applications. At the IITA Bioscience Centre's plant tissue culture facility, various tissue culture techniques are utilized for micropropagation and In vitro pre-breeding of vegetatively propagated crops. Embryo rescue is being used to increase the progeny from crosses where seeds are difficult to germinate. Anther/ovule culture is also being explored to generate haploid plants for the production of doubled haploids. In vitro polyploid induction using anti mitotic agents is employed for the conversion of banana/plantain diploids to tetraploids for use in the breeding program. Particularly for banana/plantain which has a very low propagation rate (5-10 suckers per year), micropropagation offers a rapid means of generating 'clean' plantlets (over 1000 plantlets from a single shoot tip in 8 months) (Pillay et al. 2011). Tissue culture techniques are also useful for genetic transformations; a method used for incorporating traits into the breeding populations, when such traits are not available in the genetic resources pool of the crop. At IITA, transgenic technologies are used in the improvement of vegetatively propagated crops (Tripathi, 2012). The tissue culture facility is also backed by a cell biology facility for microscopy, cytogenetics and physiology research.

Equipment and Facilities

Working Spaceiita bioscience center - tissue culture

  • Conservation rooms:
  • Transfer rooms:
  • Washing room
  • Media preparation/sterilizing room

Major Equipments

  • Laminar flow hood (x2 workstations)
  • Laminar flow hoods (x1 workstation)
  • Autoclave
  • Refrigerator
  • Plant growth Cabinets
  • Weighing balance
  • PH meters
  • Magnetic stirrers
  • Microwave oven
  • Dispenser
  • Equipment's dryer

 

 

Core utility services

Core services such as ultralow temperature specimen storage; cold room; water purification system; sterilization/autoclave systems, Lyophilisation, Nucleic acid quantification—Nanodrop, Basic bioinformatics, Digital gel imaging etc.