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Aakash Chawade

Aakash Chawade
I am an Associate Professor of Genetics and Breeding Informatics (Docent) and a group leader at the Department of Plant Breeding at SLU. The overall research goal of my lab 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 65 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 at SLU.

 

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 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.  Additonally, 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:

  • Admas Alemu (Postdoc)
  • Ajit Nehe (Postdoc)
  • Vishnukiran Thuraga (Postdoc)
  • Alexander Koc (Phd student)
  • Fernanda Leiva (Phd student)
  • Mustafa Zakieh (Phd student)
  • Rishap Dhakal (Master thesis student)
  • Siim Samuel Sepp (Master thesis student)

Previous lab members:

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

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

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

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.

Selected publications

2022

Juliana, P., He, X., Marza, F., Islam, R., Anwar, B., Poland, J., … Singh, P. K. (2022). Genomic Selection for Wheat Blast in a Diversity Panel, Breeding Panel and Full-Sibs Panel. Frontiers in Plant Science, 12(January), 1–18. https://doi.org/10.3389/fpls.2021.745379

 

2021

de Ävila, R. I., Carreira Santos, S., Siino, V., Levander, F., Eriksson, D., Chawade, A., … Zeller, K. S. (2021). Unravelling cocktail effects of complex chemical mixtures using integrated -omics: a case study with agricultural fungicides. Toxicology Letters, 350, S236–S237. https://doi.org/10.1016/S0378-4274(21)00787-6

Roy, K. K., Reza, M. M. A., Muzahid-E-Rahman, M., Anwar, M. B., Kishowar-E-Mustarin, Kabir, M. R., … Singh, P. K. (2021). Evaluation of elite bread wheat lines for resistance to blast disease in Bangladesh. Euphytica, 217(7), 1–17. https://doi.org/10.1007/s10681-021-02883-z

Leiva, F., Vallenback, P., Ekblad, T., Johansson, E., & Chawade, A. (2021). Phenocave: An Automated, Standalone, and Affordable Phenotyping System for Controlled Growth Conditions. Plants, 10(9), 1817. https://doi.org/10.3390/plants10091817

Zakieh, M., Gaikpa, D. S., Sandoval, F. L., Alamrani, M., Henriksson, T., Odilbekov, F., & Chawade, A. (2021). Characterizing Winter Wheat Germplasm for Fusarium Head Blight Resistance Under Accelerated Growth Conditions. Frontiers in Plant Science, 12(August).

Alemu, A., Brazauskas, G., Gaikpa, D. S., Henriksson, T., Islamov, B., Jørgensen, L. N., … Chawade, A. (2021). Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat. Frontiers in Genetics, 12(May), 1–15. https://doi.org/10.3389/fgene.2021.661742

Kanta, K., Mostofa, R., Reza, A., Anwar, B., Rezaul, K. M., Kumar, P., … Chawade, A., Kumar, P. (2021). Evaluation of elite bread wheat lines for resistance to blast disease in Bangladesh. Euphytica, 0123456789. https://doi.org/10.1007/s10681-021-02883-z

He, X., Juliana, P., Kabir, M. R., Roy, K. K., Islam, R., Marza, F., … Singh, P. K. (2021). Screening and Mapping for Head Blast Resistance in a Panel of CIMMYT and South Asian Bread Wheat Germplasm. Frontiers in Genetics, 12(May). https://doi.org/10.3389/fgene.2021.679162

Selga, C., Koc, A., Chawade, A., & Ortiz, R. (2021). A bioinformatics pipeline to identify a subset of snps for genomics-assisted potato breeding. Plants, 10(1), 1–14. https://doi.org/10.3390/plants10010030

Bharti, A., Paritosh, K., Mandla, V. R., Chawade, A., & Vivekanand, V. (2021). Gis application for the estimation of bioenergy potential from agriculture residues: An overview. Energies, 14(4), 1–15. https://doi.org/10.3390/en14040898

Singh, P. K., Gahtyari, N. C., Roy, C., Roy, K. K., He, X., Tembo, B., … Chawade, A. (2021). Wheat Blast: A Disease Spreading by Intercontinental Jumps and Its Management Strategies. Frontiers in Plant Science, 12(July), 1–21. https://doi.org/10.3389/fpls.2021.710707

Sharma, M., Kaushik, P., & Chawade, A. (2021). Frontiers in the Solicitation of Machine Learning Approaches in Vegetable Science Research. Sustainability, 13(15), 8600. https://doi.org/10.3390/su13158600

Maurya, N. S., Kushwaha, S., Chawade, A., & Mani, A. (2021). Transcriptome profiling by combined machine learning and statistical R analysis identifies TMEM236 as a potential novel diagnostic biomarker for colorectal cancer. Scientific Reports, 11(1), 1–11. https://doi.org/10.1038/s41598-021-92692-0

He, X., Azzimonti, G., Sánchez-Vidaña, M. del R., Pereyra, S. A., Sansaloni, C., Hernández-Anguiano, A. M., Chawade, A., Singh, P. K. (2021). Mapping for Adult-Plant Resistance Against Septoria Tritici Blotch in a Common Wheat Line Murga. Phytopathology®, PHYTO-05-20-017. https://doi.org/10.1094/phyto-05-20-0172-r

 

2020 and older

Google Scholar

 

Links

Interviews:

1.      Swedish radio (Sverigesradio P1). Interviewed for how to produce enough food in the changing climate. In Swedish. 26th November 2021

Så får vi tillräckligt med mat i en varmare värld med torka och översvämningar

2.      Lantbruksnytt. Interview: “Value of genbank germplasm for disease resistance. 25 Dec 2021. 

3.      Lantbruksnytt. Interview: “Drones can be used for fungicide applications”.27 May 2021

Popular Science articles in media:

1.      Producing cold tolerant oats for autumn sowing in Sweden. SeedQuest. June 16 2011

2.      Vetesorterna som ska klara ett extremt klimat. July 10 2019.

3.      Drönare ersätter personal. Land Lantbruk Nr. 10. 5 March 2020

4.      Smart växtförädling minskar behovet av bekämpningsmedel. May 2021

5.      Utvärdering av odlingsförsök med drönare ska testas. February 2021

6.      Billig teknik ger kunskap om framtidens höstvete. February 2021

7.      Roten till tillväxt och avkastning. Grodden. Nr. 1 February 2021

8.      Tekniken överlägsen det mänskliga ögat. Jordbruksaktuellt. 19 March 2021 

9.      Drönare och AI – nya aktörer i fält. Arvensis. October 2021.

10.  Gener som skyddar gamla vetesorter mot sjukdom kartlagda och fria att utnyttja. December 2021

11.  Fusariumresistent vete med snabbare förädlingsmetod. December 2021

12.  Phenocave mäter tillväxten automatiskt i växtförsök. December 2021

Invited Speaker

“Best practices for industry-academic collaboration” (2021) Lantmännen, Helsingborg.

Invited talk: "Resistance breeding in wheat". PlantLink (2020)

Invited talk: "Challenges and opportunities for analysis of omics data". Statistics@SLU seminar series (2020)

Invited talk: "Bildanalysmetoder som ett hjälpmedel för växtförädlare".Teknik för att säkra hög utsädeskvalitet. Gröna möten, Skara (2019)

Invited talk: "Distansundervisning". Utbildningskonferens. SLU. Lund (2019).

Invited talk: "Winter wheat pre-breeding with integrated omics". International plant and molecular biology conference, Paris (2018)

Invited talk: ”Regional variation i resistens mot svartpricksjuka hos höstvetesorter”. Meddelande från södra jordbruksförsöksdistriktet, Nr 70. Rapport från växtodlings- och växtsyddsdagarna i Växjö (2017).

Invited talk: "Spektralanalys för gradering av svampsmitta i vete" in the one day seminar "Smarta lösningar med ny sensorteknik och bildanalys - seminarium med fokus på växtskydd" (2017), Alnarp

Invited talk:  "Precision breeding with omics" at the 5th Plant Genomics and gene editing congress (2017), Amsterdam

Invited talk: “Disease resistance breeding using omics” at joint CPSC-PlantLink workshop 2016, Copenhagen, Denmark

Invited talk: “Challenges in denovo transcriptome assembly in polyploids”, PlantLink Server talks 2014, Lund, Sweden

Invited talk: cold tolerance at Nordic Oat conference, 2008, Gothenburg, Sweden


Contact

Senior Lecturer at the Institutionen för växtförädling
Telephone: +4640415328
Postal address:
Växtförädling, Box 190
234 22 LOMMA
Visiting address: Sundsvägen 10, Alnarp