bioRxiv Science⌕ Search

Biology subjects

Swain, R.

Publications and source records attributed to Swain, R..

2 recordsLinked to original sources

Optimizing Oyster Breeding with Machine Learning and BigData for Superior Quality

1.Oyster aquaculture is a vital component of global marine ecosystems and food production, yet winter mortality events threaten both ecological stability and economic viability. Traditional selective breeding methods, reliant on phenotypic traits and slow generational cycles, struggle to address these challenges efficiently. This study introduces an innovative approach integrating machine learning with multi-omics data genomics, transcriptomics, and proteomics to optimize oyster breeding for resilience and quality. By analyzing high-resolution datasets encompassing genetic markers, environmental stressors, and survival metrics, our ML models identified key SNPs linked to cold tolerance and disease resistance. Marker-assisted selection (MAS) accelerated breeding cycles, while predictive algorithms achieved 92.4% accuracy in forecasting survival and growth traits. Controlled trials demonstrated a 30% reduction in winter mortality and a 25% improvement in growth rates among ML-selected oyster lineages compared to traditional methods. Additionally, a smartphone-based diagnostic tool was developed to enable real-time monitoring of oyster health, empowering farmers to adapt feeding and environmental strategies dynamically. This research bridges the gap between conventional aquaculture and computational innovation, offering a scalable framework to enhance genetic diversity, sustainability, and yield. By replacing trial-and-error practices with data-driven precision, our approach not only mitigates immediate industry challenges but also establishes a pathway for climate-resilient aquaculture. The fusion of ML with multi-omics technologies marks a transformative shift, enabling breeders to make rapid, evidence-based decisions that harmonize ecological stewardship with commercial demands.

bioinformatics↗

SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity

COVID-19 that emerged as a global pandemic is caused by SARS-CoV-2 virus. The virus genome analysis during disease spread reveals about its evolution and transmission. We did whole genome sequencing of 225 clinical strains from the state of Odisha in eastern India using ARTIC protocol-based amplicon sequencing. Phylogenetic analysis identified the presence of all five reported clades 19A, 19B, 20A, 20B and 20C in the population. The analyses revealed two major routes for the introduction of the disease in India i.e. Europe and South-east Asia followed by local transmission. Interestingly, 19B clade was found to be much more prevalent in our sequenced genomes (17%) as compared to other genomes reported so far from India. The haplogroup analysis for clades showed evolution of 19A and 19B in parallel whereas the 20B and 20C appeared to evolve from 20A. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state in India suggesting it to be one of the major initial points of disease transmission in India during month of March and April. We found that with the time 20A and 20B clades evolved drastically that originated from central Europe. At the same time, it has been observed that 20A and 20B clades depicted selection of four common mutations i.e. 241 C>T (5UTR), P323L in RdRP, F942F in NSP3 and D614G in the spike protein. We found an increase in the concordance of G614 mutation evolution with the viral load in clinical samples as evident from decreased Ct value of spike and Orf1ab gene in qPCR. Molecular modelling and docking analysis identified that D614G mutation enhanced interaction of spike with TMPRSS2 protease, which could impact the shedding of S1 domain and infectivity of the virus in host cells.

genomics↗