Methylomes as key features for predicting recombination in some plant species.

Knowing how chromosome recombination works is essential for plant breeding. It enables the design of crosses between different varieties to combine desirable traits and create new ones. This is because the meiotic crossovers between homologous chromatids are not purely random, and various strategies have been developed to describe and predict such exchange events. Recent studies have used methylation data to predict chromosomal recombination in rice using machine learning models. This approach proved successful due to the presence of a positive correlation between the CHH context cytosine methylation and recombination rates in rice chromosomes. This paper assesses the question if methylation can be used to predict recombination in four plant species: Arabidopsis, maize, sorghum, and tomato. The results indicate a positive association between CHH context methylation and recombination rates in certain plant species, with varying degrees of strength in their relationships. The CG and CHG methylation contexts show negative correlation with recombination. Methylation data was key effectively in predicting recombination in sorghum and tomato, with a mean determination coefficient of 0.65 ± 0.11 and 0.76 ± 0.05, respectively. In addition, the mean correlation values between predicted and experimental recombination rates were 0.83 ± 0.06 for sorghum and 0.90 ± 0.05 for tomato, confirming the significance of methylomes in both monocotyledonous and dicotyledonous species. The predictions for Arabidopsis and maize were not as accurate, likely due to the comparatively weaker relationships between methylation contexts and recombination, in contrast to sorghum and tomato, where stronger associations were observed. To enhance the accuracy of predictions, further evaluations using data sets closely related to each other might prove beneficial. In general, this methylome-based method holds great potential as a reliable strategy for predicting recombination rates in various plant species, offering valuable insights to breeders in their quest to develop novel and improved varieties.

Prediction of crossover recombination using parental genomes.

Meiotic recombination is a crucial cellular process, being one of the major drivers of evolution and adaptation of species. In plant breeding, crossing is used to introduce genetic variation among individuals and populations. While different approaches to predict recombination rates for different species have been developed, they fail to estimate the outcome of crossings between two specific accessions. This paper builds on the hypothesis that chromosomal recombination correlates positively to a measure of sequence identity. It presents a model that uses sequence identity, combined with other features derived from a genome alignment (including the number of variants, inversions, absent bases, and CentO sequences) to predict local chromosomal recombination in rice. Model performance is validated in an inter-subspecific indica x japonica cross, using 212 recombinant inbred lines. Across chromosomes, an average correlation of about 0.8 between experimental and prediction rates is achieved. The proposed model, a characterization of the variation of the recombination rates along the chromosomes, can enable breeding programs to increase the chances of creating novel allele combinations and, more generally, to introduce new varieties with a collection of desirable traits. It can be part of a modern panel of tools that breeders can use to reduce costs and execution times of crossing experiments.

Methylation in the CHH Context Allows to Predict Recombination in Rice.

DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.

Diferenciación genética de las poblaciones de Felis catus en los municipios de Restrepo y Darién del Valle del Cauca, Colombia / Genetic differentiation of Felis catus populations in the municipalities Restrepo and Darién of Valle del Cauca, Colombia

Los genes implicados en los rasgos del pelaje de los gatos son útiles para el análisis de la estructura genética que presentan sus poblaciones. El objetivo de este trabajo fue determinar si existe diferenciación genética entre las poblaciones de gato doméstico de los municipios de Restrepo y Darién, los cuales se encuentran separados por el "Lago Calima". Para esto se estimaron las frecuencias alélicas de diversos marcadores del pelaje y se determinó si estas poblaciones presentaban diferencias significativas en su estructura génica o si se encontraban en equilibrio Hardy­Weinberg, además, se realizó una comparación con otras poblaciones inventariadas en el Valle del Cauca. Posteriormente, se llevó a cabo un análisis de componentes principales (ACP-Biplot), para conocer la correlación entre las frecuencias alélicas y los aportes de cada una de ellas a la variabilidad. También se realizó una prueba de Mantel para estimar si existía correlación entre los índices de fijación (FST) y las distancias geográficas. La prueba de Mantel mostró que el gen Orange es el único que muestra una correlación positiva entre los índices de diferenciación FST y las distancias geográficas. La comparación de las poblaciones de interés con las del Valle del Cauca, evidenció que los genes que aportaron más a la variabilidad fueron Dilution (19,08%), Long hair (16,09%), Agouti (16,06%) e Inhibitor (14,04%). Sin embargo, se encontró que las poblaciones de Restrepo y Darién tienen perfiles genéticos similiares y se comportan como una sola según los valores del equilibrio Hardy-Weinberg y los FST. Debido a que no hay diferencias significativas entre las poblaciones estudiadas, se concluye que, aunque el Lago Calima sea una barrera geográfica, no tiene un efecto significativo en la diferenciación genética entre las poblaciones de gatos de Restrepo y Darién.

The genes involved in cat coat traits are useful for the analysis of genetic structure within a population. The objective of this paper was to determine if any genetic differences exist among domestic cat populations from the municipalities of Restrepo and Darien, which are separated by Calima Lake. To analyze population structure, we estimated allelic frequencies of several coat markers, tested for alignment with the Hardy-Weinberg equilibrium, and compared our populations of interest to others from the Valle del Cauca region. Subsequently, we performed a principal components analysis (PCA-Biplot) to determine the correlation between allelic frequencies and their contributions to variability. A Mantel test was also used to estimate possible correlation among differentiation indexes (FST) and geographic distances. We performed the Mantel test on the Orange gene and identified a positive correlation among differentiation indexes (FST) and geographical distances. After comparing our populations of interest to others in the Valle del Cauca, we observed that the genes with the greatest contribution to variability were Dilution (19,08%), Long hair (16,09%), Agouti (16,06%) and Inhibitor (14,04%). However, we also found that the Restrepo and Darien populations of interest had similar genetic profiles, and aligned with the Hardy-Weinberg equilibrium, and the FST. Due to the absence of significant differentiation between the populations studied, we conclude that Calima Lake does not have a significant effect on any differentiation between the cat populations of Restrepo and Darien.