Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

Montanari, Sara; Ritchie, Peter A.; Wellenreuther, Maren

doi:10.1093/g3journal/jkac016

Cited by 10 publications

(5 citation statements)

References 59 publications

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“…As for the other species reported in this array, only GBS could be used for high-throughput genotyping in trevally so far ( Valenza-Troubat et al . 2022a , 2022b ). This SNP array is easier to use and yields more accurate data than was previously obtained with GBS, hence it represents a step forward in the application of genomics for selection and conservation of this promising aquaculture species.…”

Section: Discussionmentioning

confidence: 99%

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

Montanari

Deng

Koot

et al. 2023

G3: Genes, Genomes, Genetics

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Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, 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.

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Section: Discussionmentioning

confidence: 99%

“…Furthermore, the application of the SNP array to inform selective breeding of trevally ( Valenza-Troubat et al . 2022a , 2022b ), as demonstrated for snapper, holds immense future potential, e.g. to infer the relatedness of broodstock lines and to inform the selection of suitable outbred parents for new lines.…”

Section: Discussionmentioning

confidence: 99%

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

Montanari

Deng

Koot

et al. 2023

G3: Genes, Genomes, Genetics

Self Cite

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“…mtDNA sequencing) is necessary to confidently resolve whether these represent two distantly related trevally populations or that a different species was instead caught in Australia, this finding indicates that the SNP array can assist in both wild population management and fisheries assessment. Furthermore, application of the SNP array to inform the selective breeding of trevally [37,57], as demonstrated for snapper, holds immense future potential, e.g. to infer relatedness of broodstock lines and to inform the selection of suitable outbred parents for new lines.…”

Section: Discussionmentioning

confidence: 99%

“…Another scenario is that the Australian fishes have been misidentified and they belong to another described or even unknown carangid species in that region. As for the other species reported in this array, GBS was previously used for high-throughput genotyping in trevally [37,57], hence the ease of use of this SNP array and the accuracy of the data represent a step forward in the genomic-assisted selection and conservation for this promising aquaculture species.…”

Section: Trevallymentioning

confidence: 99%

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

Montanari

Deng

Koot

et al. 2022

Preprint

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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.

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“…The former has been applied to an important New Zealand fish stock; Trevally (Pseudocaranx georgianus); a promising new aquaculture species. In the study the genome of this species showed that warmer months are best for maximising breeding time, size and family based selection can work if pedigree structure and inbreeding risks are closely monitored, and lastly selection for body length results in concomitant increases in height and weight where all three contribute to trait selection that is of large importance for aquaculture (Valenza-Troubat, Montanari, et al, 2022). A scan of the literature showed that there is a slow uptake of genetics into aquaculture all over the world where in New Zealand it is increasingly becoming a more important conversation.…”

Section: Genomics In Aquaculturementioning

confidence: 99%

Genome assembly of Parapercis colias (Blue cod/Rāwaru); An endemic marine fish species of New Zealand

Jackson

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Fishery stocks are important resources for communities and nations, but many have been heavily exploited and become vulnerable to collapse. The aim of fisheries science is to understand the nature and structure of fish stocks to ensure fishing pressure can be adjusted to sustainable levels. Genetic methods have made many important contributions to fisheries management, however the development has been limited on whole genome sequencing techniques that are much more powerful and promising than what is currently being used. Technical advances in genetic approaches would provide an invaluable resource to the improvement and development of New Zealand fisheries and aquaculture species. Blue cod / Rāwaru (Parapercis colias) is a popular commercial, recreational and customary fishery in New Zealand. Rāwaru is an endemic marine fish species to New Zealand where it has more recently been considered for aquaculture development. Rāwaru fisheries have been heavily exploited and experienced several fisheries closures in the past, this has led to management changes in how it can be caught. To support Rāwaru fisheries science, the goal of this thesis research is to produce the first whole genome assembly for the species and compare its genome structure to other fish species with whole genome sequences available. Three assemblies were initially generated, one using Illumina short-read sequences (32x coverage) with the assembler Masurca, another using Pacific Biosciences HiFi long-read sequences (10x coverage) with the assembler Peregrine, and a third assembly using Pacific Biosciences HiFi data in combination with Hi-C data generated on a PacBio system, using the assembler Hifiasm. Completeness statistics of these assemblies were compared to determine the best assembly to be used for annotation and downstream analyses. The Illumina assembly produced a BUSCO completeness score of 85.80% and an N50 of 35.3Kb, the Peregrine assembly produced a BUSCO score of 97.70% and an N50 of 551.4Kb and lastly the Hifiasm assembly produced a BUSCO score of 96% and an N50 value of 348.7Kb. The final genome assembly that was subsequently used in future analyses was the Peregrine assembly. The final genome assembly is 643 MB long and consists of 3,535 scaffolds. Within the final genome assembly Repetitive elements covered 36.17% of the genome. In comparison to 6 other New Zealand fish species; King Tarakihi, Tarakihi, Barracouta, Blue moki, Butter fish and Kahawai, Rāwaru has the second largest repetitive element percentage behind Barracouta. Rāwaru also has the second largest genome within this group of species. This is consistent with the trend; as genome size increases so does the proportion of repetitive elements. A P-value of 0.0006 and a Pearsons correlation coefficient of R=0.96 confirmed this trend for repetitive elements. Rāwaru also has the second largest proportion of genes in comparison to the other 6 New Zealand species with 22,842 protein coding genes. There is however, no correlation with genome size and number of genes as well as genome size and gene length also where a P-value of 0.57 and Pearsons correlation coefficient of R=0.2656 confirmed this for number of genes and a P value of 0.7689 and Pearsons correlation coefficient of R= -0.1374104 confirmed this for gene length. This is the first time the Rāwaru genome has been assembled and annotated where 22,842 genes were annotated through maker and 22,720 of those genes were annotated through BLAST where a filtering methods of 5 blast hits and genes with the highest bit score were represented in the annotation. Interproscan was also used to annotate the genome of this Rāwaru where there were 82.8% GO terms were identified for genes predicted and 99.5% of gene models were produced with a balstp annotation. More than 98% of the Rāwaru genes were functionally annotated. No exon statistics could be provided as no transcriptomics data was used in this thesis. This thesis provides a valuable resource to assist in the studies of population genomics, conservation, fisheries management and eco evolutionary comparative studies in other teleost fish both endemic to New Zealand and globally.

show abstract

Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

Cited by 10 publications

References 59 publications

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

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

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

Genome assembly of Parapercis colias (Blue cod/Rāwaru); An endemic marine fish species of New Zealand

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