A training event on Genome-Wide Association Studies (GWAS) for the South Asia Nitrogen Hub (SANH)

In the week of 7^th-11^th of June 2021 Aberdeen partners delivered a planned training event called SANH BAAP GWAS Training Workshop. It ran for four hours every day for a week and was attended by 25 trainees and three trainers.

SANH is a £17M GCRF project funded by UKRI with 22 partners in the UK and every country in South Asia that is tackling the human and environmental damage caused by nitrogen. SBS professors Jo Smith and Adam Price are heavily involved in work packages addressing the use of nitrogen on farms and the associated ammonia and greenhouse gas emissions (Jo Smith) and genetic solutions for improved nitrogen use efficiency in rice and wheat (Adam Price).

The purpose of the workshop was to teach SANH staff and students the genetic analysis of the Bengal and Assam Aus Panel (BAAP) that is being heavily used for mapping nitrogen use efficiency in rice in SANH work package 2.1b. Taking part in the training were the following SANH partners; Indian Institute of Rice Research (3 people), the National Rice Research Institute (India) (2), Indian Agricultural Research Institute (Delhi) (1), the Bangladesh Rice Research Institute (4), the University of Agriculture, Faisalabad (4), Aligarh Muslim University (1) and the University of Aberdeen (4), plus non-SANH participants from Assam Agricultural University (4), the University of Durham (1) and the University of Nottingham (1). Of the 25 “trainees” 13 were women while 10 were students and 15 staff. The workshop was delivered by Dr Tony Travis (employed on SANH project) and Professor Adam Price (WP2.1b joint lead) and they were assisted by recent Aberdeen PhD graduate Dr Caijin Chen. 

Topics covered included using Bio-Linux to handle large data files, GWAS, identifying quantitative trait loci, identifying accurately where loci are and using bioinformatics to identify good quality candidate genes.  The original plan for the workshop was a live event in Aberdeen for 10 trainees, but because of COVID it was conducted online allowing more people to attend.

In order to host the event live, however, considerable information technology hurdles related to cyber security and remote access had to be tackled.  Together we overcame those and did not lose a single participant. We had a remarkably interactive and productive event which the organisers considered to have been massively successful and enjoyable. Good luck hunting genes everyone!

Of the workshop, one SANH participant wrote:

“The workshop was very interesting, informative, comprehensive and thought provoking. It was meticulously organized with timely document sharing, notes and recordings. The interpretations were exemplary and really added to the understanding of GWAS from the total GWAS analysis to landing over a gene / SNP.  The bioinformatics part was very well explained, and we could in fact do it together hands-on with you all simultaneously.  The workshop was made very friendly and comfortable by sharing all notes in advance and giving time before, during break and after workshop for issue resolving and associated question answer sessions. Feeling confident of executing GWAS data analysis after the workshop.”

Another SANH partner wrote:

“Thank you for arranging such an important training for us. Special thanks to University of Aberdeen to facilitate us this GWAS workshop and share the knowledge. ……. Although it was a virtual training, but we never feel so as Professor Tony teaches us by taking control of our computer when we could not follow. We are very happy to attain such training. Thanks to all.”