Related papers: The Genomic Signature of Crop-Wild Introgression i…
This study explores the application of machine learning-based genetic linguistics for identifying heavy metal response genes in rice (Oryza sativa). By integrating convolutional neural networks and random forest algorithms, we developed a…
Heterosis is the improved or increased function of any biological quality in a hybrid offspring. We have studied yet the largest maize SNP dataset for traits prediction. We develop linear and non-linear models which consider relationships…
Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with…
Precise crop yield prediction is essential for improving agricultural practices and ensuring crop resilience in varying climates. Integrating weather data across the growing season, especially for different crop varieties, is crucial for…
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
We seek models for the genotype evolution of agricultural animals, animals involved in primary production processes. Classical models for genotype evolution have tended to be very simple in order that analytic methods may be employed in…
Crop breeding is crucial in improving agricultural productivity while potentially decreasing land usage, greenhouse gas emissions, and water consumption. However, breeding programs are challenging due to long turnover times,…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen…
A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Development of either drought-resistant or drought-tolerant varieties in rice (Oryza sativa L.), especially for high yield in the context of climate change, is a crucial task across the world. The need for high yielding rice varieties is a…
We apply an empirical, data-driven approach for describing crop yield as a function of monthly temperature and precipitation by employing generative probabilistic models with parameters determined through Bayesian inference. Our approach is…
When setting up field experiments, to test and compare a range of genotypes (e.g. maize hybrids), it is important to account for any possible field effect that may otherwise bias performance estimates of genotypes. To do so, we propose a…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleterious. Therefore, large…
The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population…