Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis

Abstract

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.

Evolutionary history of the extant amphioxus lineage with shallow-branching diversification

“…The PCR was carried out with genomic DNA as template (95 °C for 3 min, 95 °C for 30 sec x35, 55 °C for 30 sec, 72 °C for 30 sec). The amplicons were directly sequenced as described previously 54 . Amplification of two DNA fragments that cover the full length of the mitogenomic DNA excluding the cox1 region was performed by PCR (95 °C for 3 min and 95 °C for 30 sec x35, 68 °C for 15 min) with primer sets shown in Supplementary Table S1 .…”

Comparison of the detection of 3 endangered frog species by eDNA and acoustic surveys across 3 seasons

“…We extracted DNA from ethanol-preserved toes with the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). From this DNA, we amplified and sequenced a partial region of the mitochondrial genome that included the NADH dehydrogenase subunit 5 (ND5) following the method described by Igawa et al (2015). The oligonucleotide primers we used for amplification and sequencing are provided in Table S1.…”

Cells from subcutaneous tissues contribute to scarless skin regeneration in Xenopus laevis froglets

“…Our method should be useful for analyzing cell fate in phenomena other than skin regeneration, so long as it can be used with a non‐GFP‐labeled donor and a genetically GFP‐labeled recipient (tissues grafted from a JG‐hybrid donor to a J‐strain recipient will be immunologically rejected). Since several inbred X. tropicalis strains are being established (Igawa et al, ), this method should be applicable to X. tropicalis as well. Combining an inbred strain and a hybrid between the inbred strain and the transgenic line should prove to be a powerful tool for analyzing cell fates in Xenopus and in other biological resources.…”