bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.10.750604

Genome-wide association study and genetic differentiation analysis reveal the genetic basis of Vibrio harveyi resistance in blackspotted croaker (Protonibea diacanthus)

Sun, S.·Zhong, L.·Yan, L.·Yan, K.·Li, N.·Xu, P.·Cai, W.
View original source ↗Export metadata ↓

Abstract

Vibrio harveyi is a primary causative agent of vibriosis, leading to catastrophic economic losses in the blackspotted croaker (Protonibea diacanthus) aquaculture. However, the genetic architecture underlying its resistance remains poorly understood. In this study, we conducted the first integrated genome-wide association study (GWAS) and genetic differentiation analysis (F_ST) to investigate the genetic basis of V. harveyi resistance. A total of 450 juveniles were challenged, and 300 individuals (comprising 150 resistant and 150 susceptible) were selected for whole-genome resequencing. Genomic heritability (h^2) was estimated at 0.374+/-0.29 for survival time (ST) and 0.237+/-0.185 for survival status (SS), indicating moderate genetic control. Notably, an exceptionally high genetic correlation (r_g = 0.999) was observed between ST and SS, while resistance traits were genetically independent of growth performance (r_g < 0.03). Through the convergence of GWAS and selection sweep signals, a major-effect QTL was identified on chromosome 4. Candidate gene prioritization identified high-confidence targets involved in post-transcriptional regulation and mRNA stability, specifically elavl4 (harboring a top-tier exon variant), rorb, cbpc6, and epn4. Functional enrichment analysis further revealed that resistance is significantly associated with "rRNA processing", "mRNA surveillance pathway", and "nucleocytoplasmic transport", suggesting that efficient RNA metabolic control is a critical determinant of host survival. These findings provide novel insights into the non-canonical immune mechanisms of P. diacanthus and offer robust molecular markers for marker-assisted selection and genomic selection, facilitating the development of disease-resistant strains in the sciaenid industry.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sun, S., Zhong, L., Yan, L., Yan, K., Li, N., Xu, P., Cai, W.. 2026-09-16. Genome-wide association study and genetic differentiation analysis reveal the genetic basis of Vibrio harveyi resistance in blackspotted croaker (Protonibea diacanthus). https://doi.org/10.64898/2026.09.10.750604

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗