Biology subjects

Blommaert, J.

Publications and source records attributed to Blommaert, J..

6 recordsLinked to original sources

bioRxiv2025

Selective breeding and production strategies to support snapper farming in the warming waters of New Zealand's South Island

Diversifying aquaculture species is essential for building resilience in the face of climate change, particularly as warming oceans challenge existing production systems. In New Zealands Marlborough Sounds, rising sea temperatures are making salmon farming increasingly difficult, highlighting the need for climate-adapted alternatives. This study evaluated the aquaculture performance of selectively bred F4 versus unselected F1 Australasian snapper (Chrysophrys auratus) across two rearing environments: sea pens in the Marlborough Sounds and a land-based system in Nelson. Approximately 1,000 F4 and 1,000 F1 snapper were reared from 4 to 30 months of age in each system. At 30 months, selectively bred snapper showed improved growth-body length increased by 1.7% (land-based) and 4.8% (ocean-based), and body weight by 9.8% and 14.2%, respectively compared with F1 snapper. Survival was also significantly higher, with selected snapper outperforming controls by 84.2% in the land-based and 60.8% in the ocean-based system. Mortality peaked in the first winter across both systems, with size-selective patterns in sea pens informing minimum stocking sizes. These findings offer important insights for refining husbandry and selective breeding practices. They are not only relevant for New Zealand but also for global aquaculture sectors seeking robust species suited to changing marine environments.

zoology↗

bioRxiv2025

Integrating genomics, machine learning, and computer vision to understand growth traits in selectively bred snapper (Chrysophrys auratus)

Genomic prediction of complex traits is limited when phenotype records are restricted and when using linear models. Increasing the amount of phenotypic data with high-throughput, image-based phenotyping could result in better genomic prediction and stronger signals in variant detection. Here, we analysed phenotypic and genomic data from a selectively bred cohort of the Australasian snapper (Chrysophrys auratus) to identify genetic variants associated with growth traits. We used a high-throughput phenotyping pipeline to extract 13 measurements of size from images. Phenotypic correlations among image-derived and manually measured traits (weight, fork length), together with heritabilities, were analysed. All measurements were significantly positively correlated with each other, and heritability ranged from 0.20-0.38. Genome-wide association studies (GWAS) identified 28 growth-associated SNPs, while GBLUP was used to predict phenotypes, and XGBoost machine-learning models were used to jointly predict phenotypes and report important variants. Both GBLUP (mean R2 = 0.50) and XGBoost (mean R2 = 0.77) performed well on the training data, but performance dropped on testing sets (both = 0.11), which decreased further when accounting for genetic relatedness (both = 0.06). Despite this, approximately 20% of the genetic variance for growth traits was captured by the models, and feature importance from XGBoost reflected signals seen in GWAS. Our findings highlight the utility of integrating computer vision-based phenotyping with GWAS, GBLUP, and ML for trait prediction. Despite detecting shared biological signals as GWAS, genomic prediction faces challenges with population structure and relatedness that are inherent in breeding programmes of mass spawning species, including many aquatic species. Article summaryIncorporating genetic information into selective breeding programmes can accelerate gains but may also miss gene interactions in complex traits. Machine learning approaches, such as decision trees, can capture those relationships and potentially improve genomic predictions. We used high-throughput computer vision phenotyping to uncover biological signal for genetic growth variants involved in the Australasian snapper. Both types of models captured 18-40% of the genetic variation, but the prediction accuracies were hampered by the population structure in this cohort of mass-spawning fish.

genomics↗

bioRxiv2022

The swan genome and transcriptome: its not all black and white

The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.

genomics↗

bioRxiv2021

Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size

Eukaryotic genomes vary greatly in size due to variation in the proportion of non-coding DNA, a pattern that emerges both in comparisons at a larger taxonomic scale and at the level of individuals within a species. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of intraspecific genome size variation among Eukaryotes, displaying almost 2-fold variation within a geographic population. Here we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short-reads of 15 individuals from the same geographic population. We identified large, contiguous copy number variable regions (CNVs), which exhibited significant coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were mainly composed of tandemly repeated satellite DNA, with only few interspersed genes or other sequences, and were characterized by an elevated GC-content. Judging from their distributions across contigs, some CNVs are fragments of accessory (B-)chromosomes while others resemble large insertions to normal chromosomes. CNV patterns in offspring of two parents with divergent genome size, and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Our study provides unprecedented insights into genome size evolution at microevolutionary time scales and thus paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

evolutionary biology↗

bioRxiv2020

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of >55% compared to the genome-wide density of <10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesise that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the "toxic-Y" effect in Drosophila. Furthermore, Haldanes rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldanes rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.

evolutionary biology↗

bioRxiv2019

Sensorimotor functional connectivity in unilateral cerebral palsy: influence of corticospinal tract wiring pattern and clinical correlates

In children with unilateral cerebral palsy (uCP), the corticospinal tract (CST) wiring patterns may differ (contralateral, ipsilateral or bilateral), partially determining motor deficits. However, the impact of such CST wiring on functional connectivity remains unknown. Here, we explored differences in functional connectivity of the resting-state sensorimotor network in 26 uCP with periventricular white matter lesions (mean age (SD): 12.87m (4.5), CST wiring: 9 contralateral, 9 ipsilateral, 6 bilateral) compared to 60 healthy controls (mean age (SD): 14.54 (4.8)), and between CST wiring patterns. Functional connectivity from each M1 to three bilateral sensorimotor regions of interest (primary sensory cortex, dorsal and ventral premotor cortex) and the supplementary motor area was compared between groups (healthy controls vs. uCP; and healthy controls vs. each CST wiring group). Results from the seed-to-voxel analyses from bilateral M1 were compared between groups. Additionally, relations with upper limb motor deficits were explored. Aberrant sensorimotor functional connectivity seemed to be CST-dependent rather than specific from all the uCP population: in the dominant hemisphere, the contralateral CST group showed increased connectivity between M1 and premotor cortices, whereas the bilateral CST group showed higher connectivity between M1 and somatosensory association areas. These results suggest that functional connectivity of the sensorimotor network is CST wiring-dependent, although the impact on upper limb function remains unclear.

neuroscience↗