Biology subjects

Osorio-Guarin, J. A.

Publications and source records attributed to Osorio-Guarin, J. A..

3 recordsLinked to original sources

bioRxiv2023

Characterising genome composition and large structural variation in banana varietal groups

BackgroundBananas and plantains (Musa spp.) are one of the most important crops worldwide. The cultivated varieties are vegetatively propagated, and their diversity is essentially fixed over time. Nevertheless, millennia of diversification and selection have led to hundreds of edible varieties. M. acuminata and M. balbisiana respectively provided the A and B subgenomes that mostly constitute these varieties. Here we aimed to characterise chromosomal exchanges and structural variation among lineages to understand shared foundational events and identify sources of allelic diversity in introgressed loci for genetic improvement. MethodsWe identified clonal somatic groups among 188 banana and plantain accessions introduced for cropping in Colombia, using admixture, principal component, and phylogenetic analyses. We established a new alignment-based metric, named Relative Averaged Alignment (RAA), to infer subgenome composition (AA, AAB, etc.). We later used comparisons in read coverage along conserved chromosomal windows between the A, B, and S subgenomes to identify introgressions. ResultsIn our panel, we identify ten varietal groups composed of somatic clones, plus three groups of tetraploid accessions. We demonstrated RAA can be used to infer subgenome composition in the total genome and individual chromosomes. We identified 20 introgressions, several newly reported, among the AAB and ABB varieties. We did not observe B-donor introgression in any AA/AAA varietal groups. We identified variation in length in at least two introgressions, a B-donor introgression in chromosome 7 between the "Maoli" and a "Popoulu" subdivisions, and an S-donor (M. schizocarpa) introgression in chromosome 2 in four varietal groups with different compositions (AAA, AAB, ABB, and AA). ConclusionsThe extensive distribution of introgressions and the variation in the length of some introgressions between varieties support that the emergence of many varieties can be attributed to intricate founding events, which encompassed multiple instances of hybridisation and subsequent residual backcrossing. We also showed the contribution of M. schizocarpa to four cultivated varieties, and proposed subdivision-specific intergenomic recombination in chromosome 7 between subgroups Maoli and Popoulu plantains. Introgressed loci over these 20 introgressions likely provide an extensive resource of allelic diversity to further explore their contribution to disease resistance, climatic adaption, etc. and potential for exploiting in breeding and genome editing.

plant biology↗

bioRxiv2020

Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

Anthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently not enough information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum cut-flowers were characterized by transcriptome sequencing technology. For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three varieties that differ in spathe color ( Sasha (white), Honduras (red), and Rapido (purple)). A large number of differentially expressed genes (8,324) that were potentially involved in multiple biological and metabolic pathways were identified, including the flavonoid and anthocyanin biosynthetic pathways. Our results showed that chalcone synthase (CHS) and flavonoid 3-hydroxylase (F3H) were the main genes differentially expressed in the white/red/purple comparison. We also identified a differentially expressed cytochrome P450 in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Additionally, putative MYB-domain protein candidates that could be responsible for the control of the biosynthetic pathway were identified. The results provided basic sequence information for future research on spathe color, which have important implications for breeding strategies in this ornamental. Core ideasO_LIRNA-seq was performed on three anthurium varieties. C_LIO_LIGene expression was compared for developmental stage and spathe color. C_LIO_LIDifferentially expressed unigenes were identified. C_LIO_LIPutative MYB-domain protein candidates of the anthocyanin biosynthetic pathway were identified. C_LI

genomics↗

bioRxiv2018

Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao

As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.

genomics↗