Biology subjects

Bassil, N. V.

Publications and source records attributed to Bassil, N. V..

7 recordsLinked to original sources

bioRxiv2025

A Single Genomic Region Controls Primocane Fruiting in Tetraploid Blackberry

The fresh-market blackberry (Rubus subgenus Rubus) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 ([~]33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus Hillquist genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3' UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus, and deliver diagnostic markers that can be immediately deployed in breeding programs.

genetics↗

bioRxiv2025

Inhibition of pro-atherogenic trimethylamine production by human gut bacteria is not determined by varying chlorogenic acid content in highbush blueberries

Elevated blood levels of trimethylamine N-oxide (TMAO) are linked to increased risk of atherosclerosis. TMAO is produced when gut bacteria metabolize quaternary amines such as choline to trimethylamine (TMA), which is converted to TMAO in the liver. Chlorogenic acid (CGA), a phenolic abundant in blueberries, inhibits TMA production. Blueberries may be a TMA- (and TMAO)-lowering food. CGA content in blueberries varies significantly. It remains unclear whether variations in CGA levels influence the TMA-lowering activity of different cultivars. We investigated the impact of blueberry CGA content on inhibition of choline-d9 conversion to TMA-d9 in our upper gastrointestinal and in vitro human fecal model. Preliminary experiments indicated near-total inhibition of TMA-d9 production when whole blueberries were tested. Blueberry pulp and sugars recapitulated this complete inhibition, whereas blueberry skins and a fiber had more moderate inhibition. We proceeded with skins (to avoid interferences from sugar-rich pulp, which would not be present in the colon in vivo) from 20 highbush blueberry genotypes, chosen for extremes in CGA content. CGA in whole berries was 2.6-146 mg/100 g fresh weight, while CGA in skins was 13.6-975 mg/100 g fresh weight. No differences were observed in TMA-d9 production among the 4 highest and 4 lowest CGA genotypes in kinetic curves or area under the curve (AUC) values when skin digesta were fermented with choline-d9. However, significant differences were observed between all genotypes compared to blank digesta, with [~]19.4.% reduction in TMA-d9 AUCs, indicating that skins provides similar TMA-lowering benefits across genotypes. Levels of free CGA in fermenta of skin digesta were 0.05-0.3 M, >1000-fold lower than the minimum effective dose we observed for pure CGA in vitro, suggesting that blueberry CGA content is not a crucial factor for lowering TMA. Fiber also does not account for most of the inhibitory activity of blueberry skins. Studies are needed to confirm this in vitro study and understand how blueberries inhibit TMA and potentially TMAO production in vivo.

microbiology↗

bioRxiv2023

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

genomics↗

bioRxiv2022

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programmes, and managing wild populations and germplasm collections. Amongst available genotyping tools, SNP arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share SNP markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal SNP array, including both closely and distantly related species, was explored. The performance of the SNP array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the SNP array as a technique to further reduce costs was evaluated. SNP performance was generally high, and species-specific SNPs proved suitable for diverse applications. The multi-species SNP-array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

genetics↗

bioRxiv2019

Target Capture Sequencing Unravels Rubus Evolution

BackgroundRubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification.\n\nResultsTarget capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) x Subg. Idaeobatus (raspberries) and Subg. Idaeobatus x Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene.\n\nConclusionsRubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research.

evolutionary biology↗

bioRxiv2019

Pyrus Communis chromosome scale assembly

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

bioinformatics↗

bioRxiv2019

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

plant biology↗