Biology subjects

Rendon-Anaya, M.

Publications and source records attributed to Rendon-Anaya, M..

5 recordsLinked to original sources

bioRxiv2025

Species-specific genetic routes to a shared phenotype: convergent adaptation of beans to European long days

The loss of photoperiod sensitivity was a key prerequisite for the adaptation of common bean (Phaseolus vulgaris) and scarlet runner bean (P. coccineus) to European environments. While the genetic architecture of this trait has been studied for decades, primarily through QTL mapping in RILs and NILs, its molecular basis remains incompletely resolved. Here, we combine whole-genome resequencing of over 200 P. vulgaris accessions spanning Mesoamerican, Andean, and European origins with 130 P. coccineus cultivars from Mesoamerica and Europe. Phenotyping under controlled long-day conditions revealed distinct distributions of photoperiod sensitivity across species and gene pools. Genome-wide association and haplotype analyses identified single nucleotide variants strongly linked to flowering under long days. Consistent with prior studies, signals of selection reflect independent domestication events in the Americas. Importantly, we detect species-specific selection on core photoperiod regulators, demonstrating that both species achieved similar adaptive outcomes via functionally convergent genetic routes. By explicitly accounting for major loci shaping growth habit in our analyses, we were able to unmask additional genomic regions contributing to flowering responses in European cultivars. Together, these results show that adaptation to long-day environments occurred through stepwise, species-specific genomic innovations, first during domestication in the Americas and later under European cultivation. Our findings highlight the role of pathway-level convergent evolution in shaping complex domestication traits and underscore the potential of parallel genomic strategies for crop adaptation.

plant biology↗

bioRxiv2023

Haplotype differences in common bean accessions confer the capacity to flower under Scandinavian summer conditions.

The capacity to flower under long days has been a major pre-requisite for the adaptation of the common bean to European climates. The complexity of such adaptation has been studied, mostly under the optics of QTL mapping, but still the genetic basis of the trait remains elusive. In the current study we sequenced a collection of >200 accessions of P. vulgaris of Mesoamerican, Andean and European origin, for which the flowering capacity under long days during the summer season in Sweden was evaluated. Our variant calling strategy allowed us to identify 16.9e6 SNPs and 38.6e3 long structural variants. Furthermore, we observed gene-pool specific selective sweeps that correspond to the independent domestication events in the Americas. GWAS and haplotype structure tests identified single nucleotide and structural variants strongly associated to the capacity to flower under long days, particularly in chromosome 1.

plant biology↗

bioRxiv2021

Conserved genomic landscapes of differentiation across Populus speciation continuum

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as a progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (nucleotide diversity and recombination rate) and among-species (relative and absolute divergence) summary statistics of diversity and divergence. We observe highly conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e., the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.

evolutionary biology↗

bioRxiv2021

Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of [~]500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

evolutionary biology↗

bioRxiv2019

The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that [~]39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent \"tuning knobs\" in the genome adaptive landscapes of given species.\n\nSIGNIFICANCE STATEMENTAvocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocados more recent genomic evolutionary history.

genomics↗