Software

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

B Jayashree¹ , Praveen T Reddy¹ , Y Leeladevi¹ , Jonathan H Crouch³ , V Mahalakshmi⁴ , Hutokshi K Buhariwalla⁵ , KE Eshwar² , Emma Mace⁶ , Rolf Folksterma⁷ , S Senthilvel² , Rajeev K Varshney² , K Seetha² , R Rajalakshmi¹ , VP Prasanth¹ , Subhash Chandra¹ , L Swarupa¹ , P SriKalyani¹ and David A Hoisington²

¹Bioinformatics and Biometrics Unit, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India

²Applied Genomics Laboratory, ICRISAT, Patancheru 502 324, Andhra Pradesh, India

³International Wheat and Maize Improvement Centre (CIMMYT), Apdo. Postal 6-641, 06600 México, D.F., México

⁴3-6-502, Satguru Apts, Himayat Nagar, Hyderabad 500029, Andhra Pradesh, India

⁵c/o International Wheat and Maize Improvement Centre (CIMMYT), Apdo. Postal 6-641, 06600 México, D.F., México

⁶Hermitage Research Station, Queensland Department of Primary Industries and Fisheries, Yangan Rd, via Warwick Q 4370 Australia

⁷De Ruiter Seeds Benelux, P.O. Box 1050, 2660 BB Bergschenhoek, The Netherlands

author email corresponding author email

BMC Bioinformatics 2006, 7:383doi:10.1186/1471-2105-7-383

Published:	17 August 2006

Abstract

Background

With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.

Results

A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.

Conclusion

A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp webcite.