Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting.
Sandell, F. L., Holzweber, T., Street, N. R., Dohm, J. C., & Himmelbauer, H.
Plant Biotechnology Journal, 22(5): 1312–1324. 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267
Paper
doi
link
bibtex
abstract
@article{sandell_genomic_2024,
title = {Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting},
volume = {22},
copyright = {© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
issn = {1467-7652},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14267},
doi = {10.1111/pbi.14267},
abstract = {Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.},
language = {en},
number = {5},
urldate = {2024-04-19},
journal = {Plant Biotechnology Journal},
author = {Sandell, Felix L. and Holzweber, Thomas and Street, Nathaniel R. and Dohm, Juliane C. and Himmelbauer, Heinz},
year = {2024},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267},
keywords = {betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour},
pages = {1312--1324},
}
Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.
ABI5 binding proteins: key players in coordinating plant growth and development.
Vittozzi, Y., Krüger, T., Majee, A., Née, G., & Wenkel, S.
Trends in Plant Science. April 2024.
Publisher: Elsevier
Paper
doi
link
bibtex
@article{vittozzi_abi5_2024,
title = {{ABI5} binding proteins: key players in coordinating plant growth and development},
issn = {1360-1385},
shorttitle = {{ABI5} binding proteins},
url = {https://www.cell.com/trends/plant-science/abstract/S1360-1385(24)00065-7},
doi = {10.1016/j.tplants.2024.03.009},
language = {English},
urldate = {2024-04-09},
journal = {Trends in Plant Science},
author = {Vittozzi, Ylenia and Krüger, Thorben and Majee, Adity and Née, Guillaume and Wenkel, Stephan},
month = apr,
year = {2024},
pmid = {38584080},
note = {Publisher: Elsevier},
keywords = {AFP (ABI5 binding protein), abscisic acid, flowering regulation, microprotein, seed germination},
}
NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion in Arabidopsis.
Lathe, R. S., McFarlane, H. E., Kesten, C., Wang, L., Khan, G. A., Ebert, B., Ramírez-Rodríguez, E. A., Zheng, S., Noord, N., Frandsen, K., Bhalerao, R. P., & Persson, S.
Proceedings of the National Academy of Sciences, 121(15): e2321759121. April 2024.
Publisher: Proceedings of the National Academy of Sciences
Paper
doi
link
bibtex
abstract
@article{lathe_nks1elmo4_2024,
title = {{NKS1}/{ELMO4} is an integral protein of a pectin synthesis protein complex and maintains {Golgi} morphology and cell adhesion in {Arabidopsis}},
volume = {121},
url = {https://www.pnas.org/doi/10.1073/pnas.2321759121},
doi = {10.1073/pnas.2321759121},
abstract = {Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.},
number = {15},
urldate = {2024-04-12},
journal = {Proceedings of the National Academy of Sciences},
author = {Lathe, Rahul S. and McFarlane, Heather E. and Kesten, Christopher and Wang, Liu and Khan, Ghazanfar Abbas and Ebert, Berit and Ramírez-Rodríguez, Eduardo Antonio and Zheng, Shuai and Noord, Niels and Frandsen, Kristian and Bhalerao, Rishikesh P. and Persson, Staffan},
month = apr,
year = {2024},
note = {Publisher: Proceedings of the National Academy of Sciences},
pages = {e2321759121},
}
Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.
Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization.
Hoermayer, L., Montesinos, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhava, P., Caballero-Mancebo, S., Benková, E., Heisenberg, C., Dagdas, Y., Majda, M., & Friml, J.
Developmental Cell. April 2024.
Paper
doi
link
bibtex
abstract
@article{hoermayer_mechanical_2024,
title = {Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization},
issn = {1534-5807},
url = {https://www.sciencedirect.com/science/article/pii/S1534580724001771},
doi = {10.1016/j.devcel.2024.03.009},
abstract = {Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.},
urldate = {2024-04-12},
journal = {Developmental Cell},
author = {Hoermayer, Lukas and Montesinos, Juan Carlos and Trozzi, Nicola and Spona, Leonhard and Yoshida, Saiko and Marhava, Petra and Caballero-Mancebo, Silvia and Benková, Eva and Heisenberg, Carl-Philip and Dagdas, Yasin and Majda, Mateusz and Friml, Jiří},
month = apr,
year = {2024},
keywords = {ablation, cell division, cell division plane, cell expansion, mechanical forces, microscopy, microtubules, plant development},
}
Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.