How diversity arises and what is the relative role of allopatric and ecological divergence are among the most persistent questions in evolution and ecology. Here, we assessed whether ecological divergence has enhanced the diversification of the Neotropical alpine plant complex Espeletia, also known as frailejones. This genus has one of the highest diversification rates ever reported and is distributed in the world’s fastest evolving biodiversity hotspot, the Páramo (Neotropical alpine grasslands at elevations of c. 2800–4700 m). Our goal was to determine whether ecology plays a role in divergence within the Espeletia complex by quantifying genome-wide patterns of ecological divergence. We characterized 162 samples of the three most common and contrasting ecotypes (distinct morphotypes occupying particular habitats) co-occurring in six localities in the northern Andes using Genotyping by Sequencing. Contrasting ecotypes were caulescent cloud forest populations, caulescent populations from wind-sheltered and well-irrigated depressions and acaulescent populations from wind-exposed drier slopes. We found high polymorphism with a total of 1,273 single nucleotide polymorphisms (SNPs) that defined the relationships among nine genetic clusters. We quantified allelic associations of these markers with localities and habitats using 18 different general and mixed-effects statistical models that accounted for phylogenetic distance. Despite that these models always yielded more SNPs associated with the localities, markers associated with the habitat types were recovered too. We found strong evidence for isolation-by-distance (IBD) across populations despite rampant gene flow, as expected for plant groups with limited seed dispersal. Contrasts between populations of different habitat types showed that an isolation-by-environment (IBE) trend emerged and masked the IBD signal. Maximum likelihood estimation of the number of migrants per generation (N_em) among ecotypes confirmed the IBE pattern. This result illustrates the importance of mountains’ environmental variation at a local scale in generating rapid morphological radiations and maintaining multiple adaptations in a fast-evolving ecosystem like the Páramo.

Common bean is an important but often a disease-susceptible legume crop of temperate, subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue (RGH) cloning has proven to be an efficient tool for identifying markers and R (resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes (BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr (bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364×G19833. A genetic map was constructed with a total of 264 markers, among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

Agraz (Vaccinium meridionale Swartz) is a shrub native to the Neotropical region of South America, including Colombia, Ecuador, Venezuela, and Peru. Known for its edible fruits valued for their nutritional, nutraceutical, and medicinal properties, the species remains underexplored despite its potential. This research aimed to investigate the genetic diversity and population structure of agraz in Colombia, focusing on native individuals from Santander and commercial individuals from Boyacá and Cundinamarca, providing insights that can support conservation and genetic improvement efforts. Methods: In this study, genotyping by sequencing (GBS) was used to analyze genetic variation and population structure in V. meridionale. The sequencing data were aligned to the V. corymbosum cv. Draper v1.0 reference genome. The obtained single-nucleotide polymorphisms (SNPs) were employed to evaluate genetic diversity, population differentiation, and inbreeding coefficients, with measures such as expected heterozygosity and F-statistics providing insights into population structure and genetic composition across regions. Results: A total of 12,910 SNPs were obtained, and the results revealed moderate genetic diversity within the agraz populations, characterized by an expected heterozygosity (He) of 0.3586. A negative Fis value indicated an excess of heterozygosity and low genetic differentiation among the sampled regions. Population structure analysis identified three distinct subpopulations, with Subpopulation 3 exhibiting the most unique genetic composition. Conclusions: This study provides the first genetic diversity analysis of V. meridionale in Colombia using the GBS approach. The findings contribute to the understanding of the species’ genetic variability and offer valuable information for conservation strategies, genetic improvement and breeding programs to enhance its agricultural potential and ensure the sustainable utilization of agraz resources.