- Written by Ivan Dulgerov
Crop Quantitative Genetics
To exploit the vast natural genetic variation in vegetable crops, using quantitative genetics and systems biology approaches, in order to understand plant responses to abiotic stresses and achieve crops with enhanced resilience to stresses as well as improved nutritional properties. The department leader will be the ERA Chair holder – the outstanding scientist Dr. Saleh Alseekh, who has notable publication track record and scientific achievements (more than 120 publications in international peer reviewed journals, including Nature Biotechnology, Nature Communications, Nature Genetics, Molecular Plant, Plant Cell, Trends in Plant Science etc.; and more than 3500 citations). Under his guidance, the research department will scale up the applied research on vegetable breeding in CPSBB and the region. Furthermore, the new CPSBB department will link with Bulgarian and international research organizations, companies, and farmer associations in the field of crop science, creating an ecosystem network that is highly attractive to talented researchers and brings the innovations to end users for the benefit of the society.
2024
- Bortlik J., Lühle J., Alseekh S., Weiste C., Fernie A.R., Dröge-Laser W., Börnke F. (2024)
- DOMAIN OF UNKNOWN FUNCTION581-9 negatively regulates SnRK1 kinase activity. Plant Physiology. 194(3): 1853-1869. (IF 8.005)
- John A., Krämer M., Lehmann M., Kunz H.H., Aarabi .F, Alseekh S., Fernie A.R., Sommer F., Schroda M., Zimmer D., Mühlhaus T., Peisker H., Gutbrod K., Dörmann P., Neunzig J., Philippar K., Neuhaus H.E. (2024)
- Degradation of FATTY ACID EXPORT PROTEIN1 by RHOMBOID-LIKE PROTEASE11 contributes to cold tolerance in Arabidopsis. The Plant Cell. 36(5): 1937-1962. (IF 10.0)
- Stavrakeva K., Metodieva K., Benina M., Bivolarska A., Dimov I., Choneva M., Kokova V., Alseekh S., Ivanova V., Vatov E., Gechev T., Mladenova T., Mladenov R., Todorov K., Stoyanov P., Gyuzeleva D., Popova M., Apostolova E. (2024)
- Metabolic composition of methanolic extract of the Balkan endemic species Micromeria frivaldszkyana (Degen) Velen and Its anti-inflammatory effect on male wistar rats. International Journal of Molecular Sciences. 25(10): 5396. (IF 5.6)
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Steimker J., Tripodi P., Wendenburg R., Tringovska I., Nankar A., Stoeva V., Pasev G., Klemmer A., Todorova V., Bulut M., Tikunov Y., Bovy A., Gechev T., Kostova D., Fernie A.R., Alseekh S. (2024)
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The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites. Current Biology. DOI: https://doi.org/10.1016/j.cub.2024.07.098. (IF 8.1)
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- Timm S., Klaas N., Niemann J., Jahnke K., Alseekh S., Zhang Y., Souza P.L., Hou L.Y., Cosse M., Selinski J., Geigenberger P., Daloso D.M., Fernie A.R., Hagemann M. (2024)
- Thioredoxins o1 and h2 jointly adjust mitochondrial dihydrolipoamide dehydrogenase-dependent pathways towards changing environments. Plant, Cell & Environment. DOI: doi: 10.1111/pce.14899. (IF 7.947)
- Yu Y., Alseekh S., Zhu Z., Zhou K., Fernie A.R. (2024)
- Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants. Plant Biotechnolgy Journal. DOI: doi: 10.1111/pbi.14379. (IF 13.8)
2023
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Aarabi F., Ghigi A., Ahchige M.W., Bulut M., Geigenberger P., Neuhaus H.E., Sampathkumar A., Alseekh S., Fernie A.R. (2023)
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Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation. Plant Physiology. 193(3): 2037-2054. (IF 8.005)
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Alamillo J.M, López C.M, Martínez Rivas F.J, Torralbo F., Bulut M., Alseekh S. (2023)
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Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein and hairy roots: a perfect match for gene functional analysis and crop improvement. Current Opinion in Plant Biology. 79: 102876. (IF 9.396)
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Alseekh S., Karakas E., Zhu F., Wijesingha Ahchige M., Fernie A.R. (2023)
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Plant biochemical genetics in the multiomics era. Journal of Experimental Botany. 74(15): 4293–4307. (IF 7.298)
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- Alseekh S., Fernie A.R. (2023)
- Expanding our coverage: Strategies to detect a greater range of metabolites. Current Opinion in Plant Biology. 73: 102335. (IF 9.396)
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Balparda M., Schmitz J., Duemmel M., Wuthenow I.C., Schmidt M., Alseekh S., Fernie A.R., Lercher M.J., Maurino V.G. (2023)
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Viridiplantae-specific GLXI and GLXII isoforms co-evolved and detoxify glucosone in planta. Plant Physiology. 191(2): 1214-1233. (IF 8.005)
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Bellucci E., Benazzo A., Xu C., Bitocchi E., Rodriguez M., Alseekh S., Di Vittori V., Gioia T., Neumann K., Cortinovis G., Frascarelli G., Murube E., Trucchi E., Nanni L., Ariani A., Logozzo G., Shin JH., Liu C., Jiang .L, Ferreira J.J., Campa A., Attene G., Morrell P.L., Bertorelle G., Graner A., Gepts P., Fernie A.R., Jackson S.A., Papa R. (2023)
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Selection and adaptive introgression guided the complex evolutionary history of the European common bean. Nature Communications. 14(1): 1908. (IF 17.694)
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Bulut M., Alseekh S., Fernie A.R. (2023)
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Natural variation of respiration-related traits in plants. Plant Physiology. 191(4): 2120-2132. (IF 8.005)
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Bulut M., Nunes-Nesi A., Fernie A.R., Alseekh S. (2023)
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Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato. Horticulture Research. 10(12): uhad224. (IF 7.291)
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- Bulut M., Wendenburg R., Bitocchi E., Bellucci E., Kroc M., Gioia T., Susek K., Papa R., Fernie A.R., Alseekh S. (2023)
- A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin. The Plant Journal. 116(4): 1152-1171. (IF 7.091)
- Córdoba S.C., Tong H., Burgos A., Zhu F., Alseekh S., Fernie A.R., Nikoloski Z. (2023)
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nature Communications. 4(1): 4897. (IF 17.694)
- Dziubek D., Poeker L., Siemiątkowska B., Graf A., Marino G., Alseekh S., Arrivault S., Fernie A.R., Armbruster U., Geigenberger P. (2023)
- NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels. Plant Physiology. 194(2): 982-1005. (IF 8.005)
- Fernie A.R., Alseekh S. (2023)
- Phylogenomic discovery of deleterious mutants completes the potato breeding revolution. Molecular Plant. 16(7): 1103-1105. (IF 27.5)
- Gyuzeleva D., Benina M., Ivanova V., Vatov E., Alseekh S., Mladenova T., Mladenov R., Todorov K., Bivolarska A., Stoyanov P. (2023)
- Metabolome profiling of Marrubium peregrinum L. and Marrubium friwaldskyanum boiss reveals their potential as sources of plant-based pharmaceuticals. International Journal of Molecular Sciences. (24)23: 17035. (IF 6.208)
- Hayashi K., Alseekh S., Fernie A.R. (2023)
- Genetic and epigenetic control of the plant metabolome. Proteomics. 13: e2200104. (IF 5.911)
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Julca I., Mutwil-Anderwald D., Manoj V., Khan Z., Lai S.K., Yang L.K., Beh IT., Dziekan J., Lim Y.P., Lim S.K., Low Y.W, Lam Y.I, Tjia S., Mu Y., Tan Q.W., Nuc P., Choo L.M., Khew G., Shining L., Kam A., Tam J.P., Bozdech Z., Schmidt M., Usadel B., Kanagasundaram Y.S, Alseekh S., Fernie A., Li H.Y., Mutwil M. (2023)
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Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. Journal of Integrative Plant Biology. 65(6): 1442-1466. (IF 9.106)
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- Karakas E., Ferrante P., Schafleitner R., Giuliano G., Fernie A.R., Alseekh S. (2023)
- Plant Sample Collection and Shipment for Multi-omic Analyses and Phytosanitary Evaluation. Current Protocols. (12): e952.
- Li X., Tieman D., Alseekh S., Fernie A.R., Klee H.J. (2023)
- Natural variations in the Sl-AKR9 aldo/keto reductase gene impact fruit flavor volatile and sugar contents. The Plant Journal. 115(4): 1134-1150. (IF 7.091)
- López C.M., Alseekh S., Torralbo F., Martínez Rivas F.J., Fernie A.R., Amil-Ruiz F., Alamillo J.M. (2023)
- Transcriptomic and metabolomic analysis reveals that symbiotic nitrogen fixation enhances drought resistance in common bean. Journal of Experimental Botany. 74(10): 3203–3219. (IF 7.298)
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Machens F., Ran G., Ruehmkorff C., Meyer Auf der Heyde J., Mueller-Roeber B., Hochrein L. (2023)
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PhiReX 2.0: A Programmable and Red Light-Regulated CRISPR-dCas9 System for the Activation of Endogenous Genes in Saccharomyces cerevisiae. ACS Synthetic Biology. 12(4): 1046-1057. (IF 5.249)
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Martínez-Rivas F.J., Blanco-Portales R., Serratosa M.P., Ric-Varas P., Guerrero-Sánchez V., Medina-Puche L., Moyano L., Mercado J.A., Alseekh S., Caballero J.L., Fernie A.R., Muñoz-Blanco J., Molina-Hidalgo FJ. (2023)
- FaMYB123 interacts with FabHLH3 to regulate the late steps of anthocyanin and flavonol biosynthesis during ripening. The Plant Journal. 114(3): 683-698. (IF 7.091)
- Naake T., Zhu F., Alseekh S., Scossa .F, Perez de Souza L., Borghi M., Brotman Y., Mori T., Nakabayashi R., Tohge T, Fernie A.R. (2023)
- Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis. Plant Physiology. DOI: doi.org/10.1093/plphys/kiad511. (IF 8.005)
- Perez de Souza L, Fernie A.R. (2023)
- Computational methods for processing and interpreting mass spectrometry-based metabolomics. Computational and Structural Biotechnology Journal. DOI: 10.1042/EBC20230019. (IF 7.271)
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Poplawski P., Alseekh S., Jankowska U., Skupien-Rabian B., Iwanicka-Nowicka R., Kossowska H., Fogtman A., Rybicka B., Bogusławska J., Adamiok-Ostrowska A., Hanusek K., Hanusek J., Koblowska M., Fernie A.R., Piekiełko-Witkowska A. (2023)
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Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell International. 23(1): 2. (IF 6.07)
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- Salem M.A., Aborehab N.M., Abdelhafez M.M., Ismail S.H., Maurice N.W., Azzam M.A., Alseekh S., Fernie A.R., Salama M.M., Ezzat S.M. (2023)
- Salem M.A., El-Shiekh R.A, Aborehab N.M., Al-Karmalawy A.A., Ezzat S.M., Alseekh S., Fernie A.R. (2023)
- Metabolomics driven analysis of Nigella sativa seeds identifies the impact of roasting on the chemical composition and immunomodulatory activity. Food Chemistry. 398: 133906 (IF 9.231)
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Sarnowska E., Kubala S., Cwiek P., Sacharowski S., Oksinska P., Steciuk J., Zaborowska M., Szurmak J.M., Dubianski R., Maassen A., Stachowiak M., Huettel B., Ciesla M., Nowicka K., Rolicka A.T., Alseekh S., Bucior E., Franzen R., Skoneczna A., Domagalska M.A., Amar S., Hajirezaei M.R., Siedlecki J.A., Fernie A.R., Davis S.J., Sarnowski T.J. (2023)
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A non-canonical function of Arabidopsis ERECTA proteins and a role of the SWI3B subunit of the SWI/SNF chromatin remodeling complex in gibberellin signaling. The Plant Journal. 115(3): 788-802. (IF 7.091)
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- Segarra-Medina C., Alseekh S., Fernie A.R., Rambla J.L., Pérez-Clemente R.M., Gómez-Cádenas A., Zandalinas S.I. (2023)
- Abscisic acid promotes plant acclimation to the combination of salinity and high light stress. Plant Physiology and Biochemistry. 3: 108008. (IF 5.437)
- Sreenivasulu N., Alseekh S., Tiozon R.N Jr., Graner A., Martin C., Fernie A.R. (2023)
- Metabolic signatures from genebank collections: An underexploited resource for human health? Annual Review of Food Science and Technology. 14: 183-202. (IF 14.714)
- Sun Y., Alseekh S., Fernie A.R. (2023)
- Plant secondary metabolic responses to global climate change: A meta-analysis in medicinal and aromatic plants. Global Change Biology. 29(2): 477-504. (IF 13.211)
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Wijesingha Ahchige M, Fernie A.R, Alseekh S. (2023)
- PANTOTHENATE KINASE4, LOSS OF GDU2, and TRANSPOSON PROTEIN1 affect the canalization of tomato fruit metabolism. Plant Physiology.192(1): 442-468. (IF 8.005)
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Xie J.Q., Zhou X., Jia Z.C., Su C.F., Zhang Y., Fernie A.R., Zhang J., Du Z.Y., Chen M.X. (2023)
- Alternative splicing, an overlooked defense frontier of plants with respect to bacterial infection. Journal of Agricultural and Food Chemistry. 71(45): 16883–16901. (IF 6.1)
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Zemach I., Alseekh S., Tadmor-Levi R., Fisher J., Torgeman S., Trigerman S., Nauen J., Hayut S.F., Mann V., Rochsar E., Finkers R., Wendenburg R., Osorio S., Bergmann S., Lunn J.E., Semel Y., Hirschberg J., Fernie A.R., Zamir D. (2023)
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Multi-year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity. The Plant Journal. 116(4): 1136-1151. (IF 7.091)
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- Zhao H., He Y., Zhang K., Li S., Chen Y., He M., He F., Gao B., Yang D., Fan Y., Zhu X., Yan M., Giglioli-Guivarc’h N., Hano C., Fernie A.R., Georgiev M.I., Janovska D., Meglic V., Zhou M. (2023)
- Rewiring of the seed metabolome during Tartary buckwheat domestication. Plant Biotechnology Journal. 21(1): 150-164. (IF 13.263)
- Zhang Y., Jaime M.S., Bulut M., Graf A., Fernie A.R. (2023)
- The conditional mitochondrial protein complexes of Arabidopsis thaliana: differences between tissue-type and environmental conditions. Plant Communications. 4(5): 100635. (IF 10.5)
- Zhang Y., Wiese L., Fang H., Alseekh S., Perez de Souza L., Scossa F., Molloy J., Christmann M., Fernie A.R. (2023)
- Synthetic biology identifies the minimal gene set required for Paclitaxel biosynthesis in a plant chassis. Molecular Plant. 16(12): 1951-1961. (IF 27.5)
- Zayed A., Farag M.A., Mehring A., Salem M.A., Ibrahim R.M., Alseekh S., Fernie A.R., Ulber R. (2023)
- Zhu F., Bulut M., Cheng Y., Alseekh S., Fernie A.R. (2023)
- Metabolite-based genome-wide association studies of large-scale metabolome analysis to illustrate alterations in the metabolite landscape of plants upon responses to stresses. Methods in Molecular Biology. 2642: 241-255.
- Zhu F., Sun Y., Jadhav S.S., Cheng Y., Alseekh S., Fernie A.R. (2023)
- The plant metabolic changes and the physiological and signaling functions in the responses to abiotic stress. Methods in Molecular Biology. 2642: 129-150.
- Zhu F., Wen W., Cheng Y., Alseekh S., Fernie A.R. (2023)
- Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways. aBIOTECH. 4(1): 47-56. (IF 3.6)
