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Aakash Chawade

I am an Associate Professor of Genetics and Breeding Informatics (Docent) and a group leader of Genomics and Phenomics group at the Department of Plant Breeding at SLU. The overall research goal of my group is to combine genetics, genomics and phenomics to develop novel understanding and breeding tools for key agronomic traits in plants. Ongoing research projects involve cereal crops, potato, sugar beet, faba bean and green peas. We are also interested in developing novel methods and data analysis pipelines for analysis of omics and high-throughput plant phenotyping data using multivariate statistics and machine learning. I have published over 70 peer-reviewed articles in international journals and own three patents.

Teaching

Deputy head of the department "GU ansvarig".

Lectures in plant breeding, bioinformatics, basic statistics and high-throughput phenotyping in undergraduate, MSc and Phd courses.

Research

Ongoing research projects involve cereal crops, potato, sugar beet, faba bean and peas. We are developing methods for low cost genomic selection in cereals, peas and sugar beet in close collaboration with breeding programs in Sweden and in Bangladesh and Zambia in collaboration with CIMMYT. In wheat, we are developing genetic markers for the diseases yellow rust, Fusarium head blight and Septoria tritici blotch resistance. In barley we are studying resistance to economically important diseases, tolerance to abiotic stresses and traits suitable for Northern latitudes. Additionally, we are developing methods for high-throughput phenotyping and machine learning. These techniques generate large amount of data requiring software pipelines for efficient data processing and analysis. Thus, we are developing open source software for efficient data analysis. We work in close collaboration with stakeholders.

Current lab members:

Payam Delfani (Researcher)
Vishnukiran Thuraga (Postdoc)
Aditi Bhandari (Postdoc)
Johanna Åstrand (Industry Postdoc)
Su Myat Noe (Licentiate student)
Vaishnavi Losari (Licentiate student)

Previous lab members:

Mustafa Zakieh (Phd student, 2019-2023), Fernanda Leiva (Phd student, 2019-2023), Admas Alemu (Postdoc, 2020-2023), Ajit Nehe (Postdoc, 2021-2023), Siim Samuel Sepp (Master thesis student, 2021-2022), Rishap Dhakal (Master thesis student, 2021-2022), Alexander Koc (Phd student, 2018-2022),Firuz Odilbekov (Researcher, 2019-2020), David Gaikpa (Research Assistant, 2020), Dhananjay Kumar (Postdoc, 2018-2020), Firuz Odilbekov (Postdoc 2016-2018), Marwan Alamrani (Research Assistant, 2019-2021), Marwan Alamrani (Master thesis student, 2019-20), Djailey Gruijters (Erasmus exchange student, 2019), Johan Lundmark (Master thesis student, 2020) Jonathan Kunst (Erasmus exchange student, 2019), Behnaz Sirooeinejad (visiting Phd student, 2019), Chiara Delvento (Master thesis student, 2019), Rita Armoniené (Postdoc, 2016-2017), Alexander Koc (MSc thesis student, 2017), Salvatore Caruso (Erasmus exchange student, 2016)

Ongoing projects:

Developing low cost genomic selection methods. Project homepage
Developing automated phenotyping methods Project homepage
Identifying molecular mechanisms underlying resistance to Septoria tritici blotch, Fusarium Head Blight and yellow rust in wheat
Pre-breeding for wheat blast resistance for Bangladesh
Identifying novel quantitative trait loci (QTL) and SNP markers in wheat
Project leader of the BalticWheat network comprising of researchers from 10 organizations in 7 countries with focus on sustainable wheat production in the Baltic region. Project homepage

Open Source software:

1. Specalyzer: An online tool for interactive analysis of phenomics data: http://www.specalyzer.org

2. Delexplorer: An online tool for interactive analysis of omics data. http://www.delexplorer.org

3. Normalyzer: An online tool for rapid evaluation of normalization methods for omics datasets: http://quantitativeproteomics.org/normalyzer

4. Dinosaur: An open source peptide MS feature detector: https://github.com/fickludd/dinosaur

5. NormalyzerDE: Online tool for normalization of omics data. http://quantitativeproteomics.org/normalyzerde

Research Funding (current & previous):
Carl Tryggers Foundation, Crafoord Foundation, Einar & Inga Nilsson foundation, Jordbruksverket (Swedish Board of Agriculture), Lantmännen research foundation, Nilsson-Ehle Foundation, Partnerskap Alnarp, PlantLink, SLF, SLU, STINT, Swedish Institute, VR, SLU Grogrund

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ResearchGate

Background

Education / Academic experience:

Associate Professor of genetics and breeding informatics (2018 - Current), SLU
Assistant Professor of genetics and breeding informatics (2015-2018), SLU
Researcher (2014-2016), Lund University
Post Doc in computational proteomics (2012-2014), Lund University
PhD in Biology (2006-2011), University of Gothenburg
Masters in Bioinformatics (2003-2005), University of Skövde
BSc in Genetics, Microbiology, Chemistry (1997-2000), Osmania University, India

Supervision

Main supervisor to the following doctoral students:

1. Su Myat Noe. Licentiate student at the Department of Plant Breeding, SLU, 2022 – ongoing.

2. Fernanda Leiva. PhD student at the Department of Plant Breeding, SLU, 2019 – 2023.

3. Mustafa Zakieh. PhD student at the Department of Plant Breeding, SLU, 2019 – 2023.

4. Alexander Koc. PhD student at the Department of Plant Breeding, SLU, 2018 – 2022.

Assistant Supervisor to the following doctoral students:

1. Poorva Sundarajan. PhD student at the Department of Plant Breeding, SLU, 2021 – Ongoing). Main supervisor Dr. Ramesh Vetukuri

2. Sbatie Lama. PhD student at the Department of Plant Breeding, SLU, 2019-ongoing. Main Supervisor Docent Ramune Kuktaite.

3. Yuzhou Lan. PhD student at the Department of Plant Breeding, SLU, 2019-ongoing. Main supervisor Prof. Eva Johansson.

4. Mohamed Mambu Luseni student at the Department of Plant Protection, SLU, 2018-ongoing. Main Supervisor Prof. Laura Grenville-Briggs Didymus

5. Hannah Ohm student at the Department of Plant Breeding, SLU, 2019-ongoing. Main supervisor Docent Per Hofvander.

6. Catja Selga. PhD student at the Department of Plant Breeding, SLU, 2016 – 2021). Main supervisor Prof. Rodomiro Ortiz

7. Jakob Wilfors. PhD student at the Department of Immunotechnology, Lund University, 2016 – 2020). Main Supervisor Docent. Fredrik Levander, Lund University.

Supervised several MSc thesis students.