Integrated breeding platform - Plant breeding software

IBP India (ICRISAT) - Translating biology: from lessons learnt to new beginnings

March 19, 2015

On 18-20 February 2015, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) was hosting the 5th International Conference on “Next Generation Genomics and Integrated Breeding for Crop Improvement” (NGGIBCI-V) in Hyderabad, India. Dr Jean-Marcel Ribaut, IBP Director, was invited to give the closing lecture, where he presented the factors behind the success of the late Generation Challenge Programme (GCP – parent programme of the IBP), and the lessons that inspire his vision for the Integrated Breeding Platform (IBP).

David Bergvinson, MS Swaminathan, Jean-Marcel Ribaut,
Rajeev Varshney, during the concluding lectures of the
NGGIBCI-V conference, 20 February 2015

This is but one example of close collaboration between the IBP and ICRISAT, a long-standing partner of the GCP and now a certified IBP Regional Hub. Indeed, between ICRISAT’s wide-ranging research activities across crops and regions and their specialty in genomics, and GCP’s mission to use genetic diversity and advanced plant science to improve crops for greater food security in the developing world, the partnership was a natural fit. ICRISAT was the greatest grant recipient of GCP phase II, and quickly got involved in the development of bioinformatics tools and the advent of what would become the Integrated Breeding Platform (IBP).

More specifically, ICRISAT greatly contributed to the development of the Genotypic Data Management System (GDMS) and  the Molecular Breeding Design Tool (MBDT), now core components of the IBP’s Breeding Management System (BMS). It also leads the development of complementary software solutions that will soon be obtainable through their website as well as the IBP portal. These solutions will be available to be used in combination with the BMS to apply more advanced genomics techniques, such as ISMU, a tool designed for genome-wide selection.

Breeding programmes at ICRISAT headquarters and other locations across the African continent have started to adopt the BMS as their primary tool for managing breeding workflow and data management. As Dr Abhishek Rathore, lead on ISMU coding and spokesperson for IBP deployment at ICRISAT, puts it: “The BMS has tools to perform simple crossing and nursery development, as well as for advanced statistical analysis such as Genomic Selection (GS). GS is supported through a user friendly pipeline, called Integrated SNP Mining and Utilisation application (ISMU2.0), developed at ICRISAT –  as a reference point, the previous version, ISMU1.0, can mine for SNPs using next generation sequencing data in even those species that lack the reference genome sequence. In my view, the BMS is emerging as a truly efficient tool for catering to all kinds of data management requirements for breeding programmes of any size and objectives.” ICRISAT have implemented the BMS through an open source cloud-based infrastructure, which enables users to access the BMS on their Local Area Network (LAN), or from anywhere through the Internet, ensuring that all breeding data is secured by firewalls and regular backups.

In the spirit of this continuing partnership, it is expected that the breeders and researchers partnering in the ICRISAT-led project Tropical Legume III will also count as adopters of the BMS at a multi-institutional level. TLIII (2015-2019) is set to focus on strengthening breeding pipelines and seed delivery, to facilitate access to new cultivars by farmers across Sub-Saharan Africa and South & South-East Asia. Crop research project with the human and financial resources to adopt the BMS should find it easier to implement and coordinate their routine breeding activities among partners.

“ICRISAT has been working with GCP since its inception to improve crop productivity for its mandate crops, with major collaborative efforts focusing on the development of large scale genetic, genomics and bioinformatics resources, trait mapping and comparative genomics. Now, as an IBP Regional Hub, we are very committed to disseminate demand-driven solutions and informatics tools such as the BMS to breeders of all levels of breeding capacity. We believe that this will lead to tangible and sustainable gains for small-holder farmers across Asia and Sub-Saharan Africa. Together we can face the real opportunity of reenergising the agricultural sector by enabling access to modern breeding practices”, shares Dr Rajeev Varshney, Research Programme Director-Grain Legumes, and Director of ICRISAT’s Centre of Excellence in Genomics. Dr Varshney was also GCP’s Theme Leader for Comparative and Applied Genomics from 2007 to 2013.

If the GCP experience has taught anything, it is that it takes time and resources to implement and nurture true partnerships, but also that these relationships are vital in rolling-out changes as far-reaching as what the IBP mission intends. “We have established strong bonds over the years, mostly because of the tremendous efforts we’ve put in together in achieving the results we see today with the Tropical Legumes initiative. We also have a common, vested interest in advancing genomics research with the help of dedicated bioinformatics. I am confident that our partnership with ICRISAT will not only benefit us mutually, but also help enable other partners across South Asia and Africa to access the latest technologies and better breeding practices”, concludes Dr Jean-Marcel Ribaut, IBP Director. 

About the Integrated Breeding Platform (IBP)

The IBP aims at improving the efficiency of plant breeding programmes in developing countries of Sub-Saharan Africa and South & South East Asia, by giving plant breeders access to the most recent breeding technologies, breeding materials and related information in a centralised and integrated manner. Ultimately, the goal is to help reduce the time and resources required to develop improved, more resilient crop varieties for farmers in target regions. To help achieve this, IBP Hubs such as ICRISAT provide local technical support and personalised training for the roll-out of the BMS across their region and crop expertise.


See also:

Dr Jean-Marcel Ribaut’s presentation at the NGGIBCI-V conference

About IBP Regional Hubs

About the IBP’s Breeding Management System

GCP’s Legume Research Initiative

Collaboration with ICRISAT in TL1

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