Genetic variation in resistance of the tiger pufferfish Takifugu rubripes to a host-specific monogenean parasite Heterobothrium okamotoi

AbstractParasite resistance traits in aquaculture species often have moderate heritability, indicating the potential for genetic improvements by selective breeding. However, parasite resistance is often synonymous with an undesirable negative correlation with body size. In this study, we first tested the feasibility of genomic selection (GS) on resistance to heterobothriosis, caused by the monogenean parasite Heterobothrium okamotoi, which leads to huge economic losses in aquaculture of the tiger pufferfish Takifugu rubripes. Then, using a simulation study, we tested the possibility of simultaneous improvement of parasite resistance, assessed by parasite counts on host fish (HC), and standard length (SL). Each trait showed moderate heritability (square-root transformed HC: h2 = 0.308 ± 0.123, S.E.; SL: h2 = 0.405 ± 0.131). The predictive abilities of genomic prediction among 12 models, including genomic Best Linear Unbiased Predictor (GBLUP), Bayesian regressions, and machine learning procedures, were also moderate for both transformed HC (0.248‒0.344) and SL (0.340‒0.481). These results confirmed the feasibility of GS for this trait. Although an undesirable genetic correlation was suggested between transformed HC and SL (rg = 0.228), the simulation study suggested the desired gains index can help achieve simultaneous genetic improvements in both traits.

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Correction to: Precocious maturation in male tiger pufferfish Takifugu rubripes: genetics and endocrinology

Fisheries Science ◽

10.1007/s12562-021-01505-w ◽

2021 ◽

Author(s):

Sota Yoshikawa ◽

Hisashi Chuda ◽

Masaomi Hamasaki ◽

Kazushi Kadomura ◽

Toshiyuki Yamada ◽

...

Keyword(s):

Takifugu Rubripes ◽

Tiger Pufferfish

A correction to this paper has been published: https://doi.org/10.1007/s12562-021-01505-w

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Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

Scientific Reports ◽

10.1038/s41598-021-83891-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongwei Yan ◽

Qi Liu ◽

Jieming Jiang ◽

Xufang Shen ◽

Lei Zhang ◽

...

Keyword(s):

Sex Determination ◽

High Throughput Sequencing ◽

Sex Differentiation ◽

Mature Mirnas ◽

Takifugu Rubripes ◽

Sequencing Technology ◽

Non Coding Rna ◽

Differentially Expressed Mirnas ◽

Tiger Pufferfish ◽

Long Non Coding Rna

AbstractAlthough sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

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The Sex-Determining Locus in the Tiger Pufferfish, Takifugu rubripes

Genetics ◽

10.1534/genetics.106.069278 ◽

2007 ◽

Vol 175 (4) ◽

pp. 2039-2042 ◽

Cited By ~ 51

Author(s):

Kiyoshi Kikuchi ◽

Wataru Kai ◽

Ayumi Hosokawa ◽

Naoki Mizuno ◽

Hiroaki Suetake ◽

...

Keyword(s):

Takifugu Rubripes ◽

Tiger Pufferfish

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Genomic prediction for testes weight of the tiger pufferfish, Takifugu rubripes, using medium to low density SNPs

Scientific Reports ◽

10.1038/s41598-021-99829-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sho Hosoya ◽

Sota Yoshikawa ◽

Mana Sato ◽

Kiyoshi Kikuchi

Keyword(s):

Family Structure ◽

Prediction Accuracy ◽

Genetic Relatedness ◽

Predictive Ability ◽

Takifugu Rubripes ◽

Best Linear Unbiased Predictor ◽

Acceptable Range ◽

Best Linear Unbiased ◽

Tiger Pufferfish ◽

Aquaculture Production

AbstractAquaculture production is expected to increase with the help of genomic selection (GS). The possibility of performing GS using only a small number of SNPs has been examined in order to reduce genotyping costs; however, the practicality of this approach is still unclear. Here, we tested whether the effects of reducing the number of SNPs impaired the prediction accuracy of GS for standard length, body weight, and testes weight in the tiger pufferfish (Takifugu rubripes). High values for predictive ability (0.563–0.606) were obtained with 4000 SNPs for all traits under a genomic best linear unbiased predictor (GBLUP) model. These values were still within an acceptable range with 1200 SNPs (0.554–0.588). However, predictive abilities and prediction accuracies deteriorated using less than 1200 SNPs largely due to the reduced power in accurately estimating the genetic relationship among individuals; family structure could still be resolved with as few as 400 SNPs. This suggests that the SNPs informative for estimation of genetic relatedness among individuals differ from those for inference of family structure, and that non-random SNP selection based on the effects on family structure (e.g., site-FST, principal components, or random forest) is unlikely to increase the prediction accuracy for these traits.

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