TY - THES A1 - de Abreu e Lima, Francisco Anastacio T1 - Experimental validation of hybrid performance predictive models in Zea mays L. Y1 - 2017 ER - TY - JOUR A1 - de Abreu e Lima, Francisco Anastacio A1 - Willmitzer, Lothar A1 - Nikoloski, Zoran T1 - Classification-driven framework to predict maize hybrid field performance from metabolic profiles of young parental roots JF - PLoS one N2 - Maize (Zea mays L.) is a staple food whose production relies on seed stocks that largely comprise hybrid varieties. Therefore, knowledge about the molecular determinants of hybrid performance (HP) in the field can be used to devise better performing hybrids to address the demands for sustainable increase in yield. Here, we propose and test a classification-driven framework that uses metabolic profiles from in vitro grown young roots of parental lines from the Dent x Flint maize heterotic pattern to predict field HP. We identify parental analytes that best predict the metabolic inheritance patterns in 328 hybrids. We then demonstrate that these analytes are also predictive of field HP (0.64 >= r >= 0.79) and discriminate hybrids of good performance (accuracy of 87.50%). Therefore, our approach provides a cost-effective solution for hybrid selection programs. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0196038 SN - 1932-6203 VL - 13 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - de Abreu e Lima, Francisco Anastacio A1 - Li, Kun A1 - Wen, Weiwei A1 - Yan, Jianbing A1 - Nikoloski, Zoran A1 - Willmitzer, Lothar A1 - Brotman, Yariv T1 - Unraveling lipid metabolism in maize with time-resolved multi-omics data JF - The plant journal N2 - Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high-oil line By804 in two distinct time-series experiments. The integrative analysis based on high-dimensional regularized regression yielded lipid-transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co-localization of lipid-transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 x By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl-lipid classes. Therefore, the proposed approach provides high-confidence candidates for experimental testing in maize and model plant species. KW - Zea mays KW - lipid metabolism KW - omics KW - GFLASSO KW - QTL Y1 - 2018 U6 - https://doi.org/10.1111/tpj.13833 SN - 0960-7412 SN - 1365-313X VL - 93 IS - 6 SP - 1102 EP - 1115 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Rodriguez Cubillos, Andres Eduardo A1 - Tong, Hao A1 - Alseekh, Saleh A1 - de Abreu e Lima, Francisco Anastacio A1 - Yu, Jing A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat JF - Heredity N2 - Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. Y1 - 2018 U6 - https://doi.org/10.1038/s41437-017-0030-5 SN - 0018-067X SN - 1365-2540 VL - 120 IS - 5 SP - 463 EP - 473 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - de Abreu e Lima, Francisco Anastacio A1 - Leifels, Lydia A1 - Nikoloski, Zoran T1 - Regression-based modeling of complex plant traits based on metabolomics data JF - Plant Metabolomics N2 - Bridging metabolomics with plant phenotypic responses is challenging. Multivariate analyses account for the existing dependencies among metabolites, and regression models in particular capture such dependencies in search for association with a given trait. However, special care should be undertaken with metabolomics data. Here we propose a modeling workflow that considers all caveats imposed by such large data sets. KW - Metabolomics KW - Plants KW - Trait KW - Regression KW - Prediction KW - Modeling KW - R programing language KW - R software packages Y1 - 2018 SN - 978-1-4939-7819-9 SN - 978-1-4939-7818-2 U6 - https://doi.org/10.1007/978-1-4939-7819-9_23 SN - 1064-3745 SN - 1940-6029 VL - 1778 SP - 321 EP - 327 PB - Humana Press Inc. CY - New York ER -