Biology subjects

Reyes-Herrera, P. H.

Publications and source records attributed to Reyes-Herrera, P. H..

4 recordsLinked to original sources

bioRxiv2023

Pleistocene dispersion supports a unique native diversity in the Colombian avocado germplasm

Genomic characterization of ex-situ collections optimizes the utilization of genetic resources, identifies redundancies among accessions, captures cryptic variation, establishes reference collections, and ultimately assists pre-breeding and breeding efforts. However, the integration of population genomic analyses is often lacking when studying the biodiversity of crop gene pools. Here, we present modern classification and machine learning approaches to characterize and harness the genebank of an agrobiodiversity hotspot on Persea americana Mill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide. We selected 144 accessions from the Colombian National genebank and 240 materials from local plantations in the Colombian Northwest Andes. We genotyped them using a strategy based on reduced representation sequencing. We included available sequences of genotypes from known avocado races, Mexican, Guatemalan, and West Indian, to discover SNPs, analyze the population structure and identify possible new genetic groups in Colombian germplasm. We detected a population structure suggestive of a new fourth race in Colombia, with a possible genetic substructure related to geographical origin (Andean and Caribbean). Hybrid determination and ABC modeling suggested rampant inter-race geneflow. They supported the hypothesis of the high mobility of native avocado trees from Central America to Northern South America starting in the Pleistocene. Our study supports that Colombia might be a new diversity center for P. americana. Genotypes of the two newly identified Colombian groups can be used as parents in plant breeding strategies to generate cultivars adapted to specific ecogeographical regions of Colombia.

plant biology↗

bioRxiv2022

Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America

The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019, Foc TR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified as Foc TR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences of Foc TR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the Colombian Foc TR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 available Foc TR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin of Foc TR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny.

genomics↗

bioRxiv2020

Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species

Genotype-by-sequencing (GBS) is a widely used cost-effective technique to obtain large numbers of genetic markers from populations. Although a standard reference-based pipeline can be followed to analyze these reads, a reference genome is still not available for a large number of species. Hence, several research groups require reference-free approaches to generate the genetic variability information that can be obtained from a GBS experiment. Unfortunately, tools to perform de-novo analysis of GBS reads are scarce and some of the existing solutions are difficult to operate under different settings generated by the existing GBS protocols. In this manuscript we describe a novel algorithm to perform reference-free variants detection and genotyping from GBS reads. Non-exact searches on a dynamic hash table of consensus sequences allow to perform efficient read clustering and sorting. This algorithm was integrated in the Next Generation Sequencing Experience Platform (NGSEP) to integrate the state-of- the-art variants detector already implemented in this tool. We performed benchmark experiments with three different real populations of plants and animals with different structures and ploidies, and sequenced with different GBS protocols at different read depths. These experiments show that NGSEP has comparable and in some cases better accuracy and always better computational efficiency compared to existing solutions. We expect that this new development will be useful for several research groups conducting population genetic studies in a wide variety of species.

bioinformatics↗

bioRxiv2020

Inheritance of Rootstock Effects in Avocado ( Persea americana Mill.) cv. Hass

Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. Yet, the interconnection of both genotypes obscures individual contributions to phenotypic variation (i.e. rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as model fruit tree. We characterized 240 rootstocks from 8 avocado cv. Hass orchards in three regions of the province of Antioquia, in the northwest Andes of Colombia, using 13 microsatellite markers (simple sequence repeats - SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, eco-physiological, and fruit yield and quality traits) in the scions for three years (2015-2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a genetic prediction model in order to calculate narrow-sense heritabilities (h2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (R2) that oscillated between 0.58 and 0.74 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e. total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), while the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock-scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in Hass avocado. They also reinforce the utility of SSR markers for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work reinforces the importance of considering the rootstock-scion interaction to broaden the genetic basis of fruit tree breeding programs, while enhancing our understanding of the consequences of grafting.

plant biology↗