Biology subjects

Lopez, M.-E.

Publications and source records attributed to Lopez, M.-E..

5 recordsLinked to original sources

bioRxiv2022

DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)

O_LIEnvironmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes especially at the level of DNA methylation. DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. C_LIO_LIWe investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable environmental conditions at DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. C_LIO_LIThese findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses. C_LI

plant biology↗

bioRxiv2020

Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

genetics↗

bioRxiv2019

Modeling the Switching behavior of Functional Connectivity Microstates (FCμstates) as a Novel Biomarker for Mild Cognitive Impairment

It is evident the need for designing and validating novel biomarkers for the detection of mild cognitive impairment (MCI). MCI patients have a high risk of developing Alzheimers disease (AD), and for that reason the introduction of novel and reliable biomarkers is of significant clinical importance. Motivated by recent findings about the rich information of dynamic functional connectivity graphs (DFCGs) about brain (dys)function, we introduced a novel approach of identifying MCI based on magnetoencephalographic (MEG) resting state recordings.\n\nThe activity of different brain rhythms {{delta}, {theta}, 1, 2, {beta}1, {beta}2, {gamma}1, {gamma}2} was first beamformed with linear constrained minimum norm variance in the MEG data to determine ninety anatomical regions of interest (ROIs). A dynamic functional connectivity graph (DFCG) was then estimated using the imaginary part of phase lag value (iPLV) for both intra-frequency coupling (8) and also cross-frequency coupling pairs (28). We analyzed DFCG profiles of neuromagnetic resting state recordings of 18 Mild Cognitive Impairment (MCI) patients and 20 healthy controls. We followed our model of identifying the dominant intrinsic coupling mode (DICM) across MEG sources and temporal segments that further leads to the construction of an integrated DFCG (iDFCG). We then filtered statistically and topologically every snapshot of the iDFCG with data-driven approaches. Estimation of the normalized Laplacian transformation for every temporal segment of the iDFCG and the related eigenvalues created a 2D map based on the network metric time series of the eigenvalues (NMTSeigs). NMTSeigs preserves the non-stationarity of the fluctuated synchronizability of iDCFG for each subject. Employing the initial set of 20 healthy elders and 20 MCI patients, as training set, we built an overcomplete dictionary set of network microstates (nstates). Afterward, we tested the whole procedure in an extra blind set of 20 subjects for external validation.\n\nWe succeeded a high classification accuracy on the blind dataset (85 %) which further supports the proposed Markovian modeling of the evolution of brain states. The adaptation of appropriate neuroinformatic tools that combine advanced signal processing and network neuroscience tools could manipulate properly the non-stationarity of time-resolved FC patterns revealing a robust biomarker for MCI.

neuroscience↗

bioRxiv2019

Single-step genome-wide association study for resistance to Piscirickettsia salmonis in rainbow trout (Oncorhynchus mykiss)

One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteria Piscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait. The objectives of this study were to i) identify the genomic regions associated with resistance to P. salmonis; and ii) identify candidate genes associated with the trait. We experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 57 K SNP array. Resistance to P. salmonis was defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 {+/-} 0.04 and 0.34 {+/-} 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located on Omy27 was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited by P. salmonis during infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance to P. salmonis through artificial selection in the current rainbow trout population. Furthermore, our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance to P. salmonis in O. mykiss.

genomics↗

bioRxiv2019

Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

1.Domestication of Atlantic salmon started approximately forty years ago, using both artificial and natural selection strategies. Such selection methods are likely to have imposed distinctive selection signatures on the salmon genome. Therefore, identifying differences in selection signatures may give insights into the mechanism of selection and candidate genes of biological and productive interest. Here, we used two complementary haplotype-based statistics, the within-population integrated Haplotype Score test (|iHS|) and the cross-population Extended Haplotype Homozygosity test (XP-EHH) to compare selection signatures in four populations of Atlantic salmon with a common genetic origin. Using |iHS| we found 24, 14, 16 and 26 genomic regions under selection in Pop-A, Pop-B, Pop-C, and Pop-D, respectively. While using the XP-EHH test we identified 27, 25 and 15 potential selection regions in Pop-A/Pop-B, Pop-A/Pop-C and Pop-A/Pop-D, respectively. These genomic regions harbor important genes such igf1r and sh3rf1 which have been associated with growth related traits in other species. Our results contribute to the detection of candidate genes of interest and help to understand the evolutionary and biological mechanisms for controlling complex traits under selection in Atlantic salmon.

genetics↗