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.
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:
Previous lab members:
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:
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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Education / Academic experience:
Main supervisor to the following doctoral students:
1. Fernanda Leiva. PhD student at the Department of Plant Breeding, SLU, 2019 – ongoing.
2. Mustafa Zakieh. PhD student at the Department of Plant Breeding, SLU, 2019 – ongoing.
3. Su Myat Noe. Licentiate student at the Department of Plant Breeding, SLU, 2022 – ongoing.
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.
2023
Thuraga, V., Martinsson, U. D., Vetukuri, R. R., & Chawade, A. (2023). Delineation of Genotype X Environment Interaction for Grain Yield in Spring Barley under Untreated and Fungicide-Treated Environments. Plants, 12(4), 715. https://doi.org/10.3390/plants12040715
2022
Roitsch, T., Himanen, K., Chawade, A., Jaakola, L., Nehe, A., & Alexandersson, E. (2022). Functional phenomics for improved climate resilience in Nordic agriculture. Journal of Experimental Botany, 73(15), 5111–5127. https://doi.org/10.1093/jxb/erac246
Sundararajan, P., Kalyandurg, P. B., Liu, Q., Chawade, A., Whisson, S. C., & Vetukuri, R. R. (2022). Spray-Induced Gene Silencing to Study Gene Function in Phytophthora (Vol. 2536, pp. 459–474). https://doi.org/10.1007/978-1-0716-2517-0_27
Koc, A., Odilbekov, F., Alamrani, M., Henriksson, T., & Chawade, A. (2022). Predicting yellow rust in wheat breeding trials by proximal phenotyping and machine learning. Plant Methods, 1–11. https://doi.org/10.1186/s13007-022-00868-0
Malin, I., Lindstedt, M., Sandby, S., Zeller, K. S., Se, L., Chawade, A., … Forreryd, A. S. (2022). ( 12 ) United States Patent, 2.
Phuke, R. M., He, X., Juliana, P., Kabir, M. R., Roy, K. K., Marza, F., … Singh, P. K. (2022). Identification of Genomic Regions and Sources for Wheat Blast Resistance through GWAS in Indian Wheat Genotypes. Genes, 13(4). https://doi.org/10.3390/genes13040596
Lan, Y., Chawade, A., Kuktaite, R., & Johansson, E. (2022). Climate Change Impact on Wheat Performance—Effects on Vigour, Plant Traits and Yield from Early and Late Drought Stress in Diverse Lines. International Journal of Molecular Sciences, 23(6). https://doi.org/10.3390/ijms23063333
Lan, Y., Chawade, A., Kuktaite, R., & Johansson, E. (2022). Climate Change Impact on Wheat Performance — Effects on Vigour , Plant Traits and Yield from Early and Late Drought Stress in Diverse Lines. https://doi.org/10.3390/ijms23063333
Leiva, F., Zakieh, M., Alamrani, M., Dhakal, R., Henriksson, T., Singh, P. K., & Chawade, A. (2022). Phenotyping Fusarium head blight through seed morphology characteristics using RGB imaging. Frontiers in Plant Science, 13(October), 1–13. https://doi.org/10.3389/fpls.2022.1010249
Alemu, A., Brantestam, A. K., & Chawade, A. (2022). Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production. Frontiers in Plant Science, 13(March), 1–15. https://doi.org/10.3389/fpls.2022.844450
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
Selga, C., Chrominski, P., Carlson-Nilsson, U., Andersson, M., Chawade, A., & Ortiz, R. (2022). Diversity and population structure of Nordic potato cultivars and breeding clones. BMC Plant Biology, 22(1), 1–12. https://doi.org/10.1186/s12870-022-03726-2
Chaudhary, A., Chaurasia, P. K., Kushwaha, S., Chauhan, P., Chawade, A., & Mani, A. (2022). Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions. International Journal of Biological Macromolecules, 220(July), 743–753. https://doi.org/10.1016/j.ijbiomac.2022.08.100
He, X., Kabir, M. R., Roy, K. K., Marza, F., Chawade, A., Duveiller, E., … Singh, P. K. (2022). Genetic dissection for head blast resistance in wheat using two mapping populations. Heredity, 128(6), 402–410. https://doi.org/10.1038/s41437-021-00480-3
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
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