Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 5, 2025

Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model

Language: Английский

Comparative analysis of genomic prediction models based on body weight trait in large yellow croaker (Larimichthys crocea)

Aquaculture, Journal Year: 2025, Volume and Issue: 599, P. 742125 - 742125

Published: Jan. 7, 2025

Language: Английский

The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme

BMC Genomic Data, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 25, 2025

Abstract Objectives European whitefish ( Coregonus lavaretus L .) is a freshwater salmonid that inhabits cold regions of central and north Europe Siberia. It an important aquaculture species in Finland, selectively bred since 1999. The breeding programme has applied genomic selection uses SNP markers phenotypic data to improve traits such as growth, product quality, fish health. Salmonids are known for chromosomal rearrangements, the current C. reference genome based on individual from Switzerland may deviate Finnish one. Therefore, we have assembled whitefish. This allows us better assess genetic basis enhance accuracy selection. Data description was sequenced using combination Illumina PacBio technologies wtbg2 HiRise software. assembly size 2.94 Gb comprises 6,706 scaffolds with scaffold N50 1.36 Mb.

Language: Английский