Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing

Abstract

Cost-effective genotyping can be achieved by sequencing PCR amplicons. Short 3–10 base primers can arbitrarily amplify thousands of loci using only a few primers. To improve the sequencing efficiency of the multiple arbitrary amplicon sequencing (MAAS) approach, we designed new primers and examined their efficiency in sequencing and genotyping. To demonstrate the effectiveness of our method, we applied it to examining the population structure of the small freshwater fish, medaka (Oryzias latipes). We obtained 2987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. We also attempted to reconstruct the genetic backgrounds of a commercial orange mutant strain, Himedaka, which has caused a genetic disturbance in wild populations. Our admixture analysis focusing on Himedaka showed that at least two wild populations had genetically been contributed to the nuclear genome of this mutant strain. Our genotyping methods and results will be useful in quantitative assessments of genetic disturbance by this commercially available strain.

Utilizing ISSRseq genotyping to assist growth selection in tomato grouper (Cephalopholis sonnerati) without broodstock information

“…Our study has demonstrated that ISSRseq can infer the parentage (lineage) relationships of fish fry even without broodstock information, showcasing its potential for marker‐assisted selection. Furthermore, although ISSRseq markers, like RADseq, do not require prior genomic information, they can still be mapped to a reference genome when available (Fujimoto et al, 2022; Lee et al, 2019). This allows further exploration of whether they originate from genic regions and are related to specific gene functions.…”

“…This allows further exploration of whether they originate from genic regions and are related to specific gene functions. This potential may be further exploited in the future (Fujimoto et al, 2022; Lee et al, 2019).…”