Sequencing & Pangenomes

Towards robustness and resiliency: developing a high-quality genome assembly for thermotolerance breeding of Chinook salmon (Oncorhynchus tshawytscha) in New Zealand

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Abstract

Farmed Chinook salmon in Aotearoa New Zealand have at times exhibited reduced survival during marine heatwave events. To assist farmed salmon stocks with adapting to increases in water temperatures, the genetic improvement of thermotolerance traits is a key tool. Genome assemblies are fundamental for understanding the genomic architecture of traits that are relevant for selective breeding. However, as the current reference genome for Chinook salmon is fragmented, comprehensive detection of potential causative variants that can be used to accelerate genetic improvement of thermotolerance is difficult. In addition, preliminary analyses also revealed that large genetic differences exist between New Zealand Chinook salmon populations compared to their Pacific Northwest counterparts. To address these concerns, we have developed a high-quality genome assembly for farmed New Zealand Chinook salmon with excellent contiguity, completeness and accuracy. By harnessing the power of PacBio (62x coverage) sequencing technology, complemented with long Nanopore reads (4x coverage) for scaffolding, our assembled genome (2.52 Gb) approaches a size that coincides with flow cytometry (~2.8 Gb) estimates. Results from our preliminary analyses revealed a higher scaffold N50 (75.51 Mb) and comparable BUSCO completeness (95.3%) score than the current Chinook salmon reference genome. The QV score (49.99) also indicates very good assembly accuracy. These metrics conform with the quality standards set by the Earth Biogenomes Project. Further refinement, through the incorporation of additional ultra-long reads and Hi-C data for scaffolding will be performed to achieve best assembly results. Subsequent genome annotation will also be done to support future genome-wide association analyses. Ultimately, our genome assembly will be used to complement ongoing work to breed for climate-resilient Chinook salmon and support genotyping initiatives for quantitative genetics and comparative genomic studies.

Keywords: 2026

How to Cite:

Ariñez, J., Symonds, J., Scholtens, M., Kenny, N. & Clarke, S., (2026) “Towards robustness and resiliency: developing a high-quality genome assembly for thermotolerance breeding of Chinook salmon (Oncorhynchus tshawytscha) in New Zealand”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286004. doi: https://doi.org/10.31274/wcgalp.23835

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