Biology subjects

Macaya-Sanz, D.

Publications and source records attributed to Macaya-Sanz, D..

5 recordsLinked to original sources

bioRxiv2024

Population structure limits inferences from genomic prediction and genome-wide association studies in a forest tree

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, assess risks of genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and a replicated common- garden experiment to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and practice assisted migration. We analyzed hierarchical population structure by partitioning phenotypic and genomic (SNP) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60-81%) occurred at the population level and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive ability r > 0.9) but almost as well using climate or geography (r > 0.8). In contrast, genomic prediction within populations was poor (r < 0.2). Similarly, we identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Our results highlight the difficulty of using GWAS to identify causal loci when there is population structure, and the limitations of using genomic information alone to guide assisted migration.

genomics↗

bioRxiv2022

High resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa

Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of seven males and seven females. Genomes of the resulting 49 full-sib families (N=829 offspring) were re-sequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The fourteen parental genetic maps contained 1820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over (CO) regions, where 38,846 CO events in 1,658 gametes were observed. CO events were positively associated with gene density and negatively associated with GC content and long terminal repeats. One of the most striking findings was higher rates of COs in males in 8 out of 19 chromosomes. Regions with elevated male CO rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate CO hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.

genetics↗

bioRxiv2020

Structure of core fungal endobiome in Ulmus minor: patterns within the tree and across genotypes differing in tolerance to Dutch elm disease

Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpotrichiellaceae and Tremellaceae. Surveying a natural population with a gradient of vitality, we found some taxa enriched in declining trees. By combining all surveys and adding a further study in a distant natural population, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.

microbiology↗

bioRxiv2019

A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats

BackgroundSex chromosomes in a wide variety of species share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. They have arisen independently in numerous lineages, providing a conclusive example of convergent evolution. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that facilitate sequence conservation through gene conversion, and contain genes that are crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in particular it is not clear how coding sequence conservation is maintained in the absence of homologous recombination.\n\nResultsHere we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb stretches of highly conserved sequences among the four arms. The closely-related species S. suchowensis also has two copies of a portion of the palindrome arm and provides strong evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR of the closely-related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.\n\nConclusionThe presence of palindromic structures in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

genomics↗

bioRxiv2018

Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery

Biological organisms are complex systems that are composed of functional networks of interacting molecules and macromolecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plants sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to lignin-related lignin-phenotypes across the network layers. The resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.

bioinformatics↗