Development and evaluation of a high-throughput single nucleotide polymorphism multiplex assay for assigning pedigrees in common carp

Abstract

Accurate pedigree information is critical when managing animal breeding programmes and ensure the highest rate of genetic gain. The abundance of available genomic data and the development of high-throughput genotyping platforms have facilitated the use of single nucleotide polymorphisms (SNPs) as the best DNA markers for genomic selection studies. Furthermore, the superior qualities of SNPs compared with those of microsatellite markers allow standardization between laboratories, which is crucial for developing an international set of markers for use in traceability studies. The objective of this study was to develop a high-throughput SNP array to assign common carp pedigrees accurately. A 48-SNP array was developed based on the Fluidigm genotyping platform, and a phylogenetic analysis was performed to distinguish different pedigrees. A likelihood-based approach was used to infer parental pairs, and the pair with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) was assigned. The SNP genotypes of the offspring and candidate parents tested were collected, and 94% of the offspring were assigned to the most-likely parent pair, which was consistent with the actual pedigree records. Using this SNP assay will allow implementation of offspring testing at large commercial farms where improved accuracy of pedigree assignments and genetic evaluations will increase genetic gains in the common carp aquaculture industry.

Molecular Parentage Analysis in Aquaculture: Principles, Applications, and Challenges: A Review

“…Microsatellites are the marker of choice for parentage analysis [20], because they are easily scorable, codominant, and highly polymorphic markers [21]. Microsatellites have been used for the parentage analysis in more than 20 aquaculture species, such as salmon [22], Asian seabass [12] [23], common carp [24], rainbow trout [13], European sea bass [25], and sea bream [26].…”

Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming

“…Current results already provide valuable insight for fish farmers. First, knowing genetic divergences between domesticated fish stocks paves the way (i) to develop accurate pedigree assignment (e.g., [55]) and (ii) to compare genetic specificities and aquaculture potential (sensu [56]; e.g., growth rate, filet yielding), which can ultimately lead to genomebased selection (e.g., [57]).…”

Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp

“…Researchers have also developed a relatively low-throughput SNP array, including 48 SNPs, for accurate and cost-competitive pedigree assignment in common carp. 41 Genetic maps are powerful for chromosome-level assembly and fine-mapping of quantitative trait loci (QTL) for economically important traits. Many versions of genetic maps have been published for common carp with various marker types and uneven marker densities.…”

“…This SNP panel has provided a powerful tool for genetic investigations of common carp and the relatives. Researchers have also developed a relatively low‐throughput SNP array, including 48 SNPs, for accurate and cost‐competitive pedigree assignment in common carp 41 …”