Publications

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4 Publications visible to you, out of a total of 6
Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics

Abstract (Expand)

Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities … associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.

Authors: Núria Tous, Sofia Marcos, Farshad Goodarzi Boroojeni, Ana Pérez de Rozas, Jürgen Zentek, Andone Estonba, Dorthe Sandvang, M. Thomas P. Gilbert, Enric Esteve-Garcia, Robert Finn, Antton Alberdi, Joan Tarradas

Date Published: 6th Sep 2022

Publication Type: Peer Review

Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance

Abstract (Expand)

Polyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids … often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being “dominant.” Such “genome dominance” can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k‐mer–based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans‐acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent‐specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.

Authors: Marek Glombik, Dario Copetti, Jan Bartos, Stepan Stoces, Zbigniew Zwierzykowski, Tom Ruttink, Jonathan F. Wendel, Martin Duchoslav, Jaroslav Dolezel, Bruno Studer, David Kopecky

Date Published: 4th Aug 2021

Publication Type: Journal Article

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.

Abstract (Expand)

The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. … However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.

Authors: M. Montoliu-Nerin, M. Sanchez-Garcia, C. Bergin, M. Grabherr, B. Ellis, V. E. Kutschera, M. Kierczak, H. Johannesson, A. Rosling

Date Published: 28th Jan 2020

Publication Type: Journal Article

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays.

Abstract (Expand)

BACKGROUND: Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to … guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize. RESULTS: We produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping. CONCLUSIONS: We demonstrate MAGIC maize's value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers.

Authors: M. Dell'Acqua, D. M. Gatti, G. Pea, F. Cattonaro, F. Coppens, G. Magris, A. L. Hlaing, H. H. Aung, H. Nelissen, J. Baute, E. Frascaroli, G. A. Churchill, D. Inze, M. Morgante, M. E. Pe

Date Published: 11th Sep 2015

Publication Type: Journal Article

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