Genomic selection for heterobothriosis resistance concurrent with body size in the tiger pufferfish, Takifugu rubripes

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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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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Applying the Spatial EBLUP to Place-Based Policing. Simulation Study and Application to Confidence in Police Work

Applied Spatial Analysis and Policy ◽

10.1007/s12061-020-09333-8 ◽

2020 ◽

Vol 13 (4) ◽

pp. 901-924

Author(s):

David Buil-Gil ◽

Angelo Moretti ◽

Natalie Shlomo ◽

Juanjo Medina

Keyword(s):

Spatial Autocorrelation ◽

Random Effects ◽

Simulation Study ◽

Small Area ◽

Police Work ◽

Best Linear Unbiased Predictor ◽

Spatial Random Effects ◽

Area Estimation ◽

Best Linear Unbiased ◽

Estimation Models

Abstract There is growing need for reliable survey-based small area estimates of crime and confidence in police work to design and evaluate place-based policing strategies. Crime and confidence in policing are geographically aggregated and police resources can be targeted to areas with the most problems. High levels of spatial autocorrelation in these variables allow for using spatial random effects to improve small area estimation models and estimates’ reliability. This article introduces the Spatial Empirical Best Linear Unbiased Predictor (SEBLUP), which borrows strength from neighboring areas, to place-based policing. It assesses the SEBLUP under different scenarios of number of areas and levels of spatial autocorrelation and provides an application to confidence in policing in London. The SEBLUP should be applied for place-based policing strategies when the variable’s spatial autocorrelation is medium/high, and the number of areas is large. Confidence in policing is higher in Central and West London and lower in Eastern neighborhoods.

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

Fisheries Science ◽

10.1007/s12562-019-01342-y ◽

2019 ◽

Vol 85 (6) ◽

pp. 1019-1025 ◽

Cited By ~ 2

Author(s):

Dong In Kim ◽

Sho Hosoya ◽

Naoki Mizuno ◽

Kotaro Ito ◽

Risa Ieda ◽

...

Keyword(s):

Genetic Variation ◽

Takifugu Rubripes ◽

Monogenean Parasite ◽

Tiger Pufferfish

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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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Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

BMC Genomics ◽

10.1186/s12864-021-07723-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaolei Zhang ◽

Ming Lu ◽

Aiai Xia ◽

Tao Xu ◽

Zhenhai Cui ◽

...

Keyword(s):

Phenotypic Variation ◽

Genetic Basis ◽

Molecular Breeding ◽

Best Linear Unbiased Predictor ◽

Maize Line ◽

Maize Varieties ◽

Outer Covering ◽

High Heritability ◽

Best Linear Unbiased ◽

Variation Explained

Abstract Background The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk outer covering the ear. Although several quantitative trait loci (QTL) underlying husk morphology variation have been reported, the genetic basis of husk traits between teosinte and maize remains unclear. Results A linkage population including 191 BC2F8 inbred lines generated from the maize line Mo17 and the teosinte line X26–4 was used to identify QTL associated with three husk traits: i.e., husk length (HL), husk width (HW) and the number of husk layers (HN). The best linear unbiased predictor (BLUP) depicted wide phenotypic variation and high heritability of all three traits. The HL exhibited greater correlation with HW than HN. A total of 4 QTLs were identified including 1, 1, 2, which are associated with HL, HW and HN, respectively. The proportion of phenotypic variation explained by these QTLs was 9.6, 8.9 and 8.1% for HL, HN and HW, respectively. Conclusions The QTLs identified in this study will pave a path to explore candidate genes regulating husk growth and development, and benefit the molecular breeding program based on molecular marker-assisted selection to cultivate maize varieties with an ideal husk morphology.

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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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A method for reducing inbreeding with Best Linear Unbiased Prediction

Proceedings of the British Society of Animal Production (1972) ◽

10.1017/s030822960002362x ◽

1993 ◽

Vol 1993 ◽

pp. 33-33

Author(s):

B Grundy ◽

WG Hill

Keyword(s):

Best Linear Unbiased Prediction ◽

Breeding Value ◽

Best Linear Unbiased Predictor ◽

Linear Unbiased Prediction ◽

Genetic Merit ◽

Selection Decisions ◽

Best Linear Unbiased ◽

Estimated Breeding Value ◽

Commercial Environment ◽

Unbiased Prediction

An optimum way of selecting animals is through a prediction of their genetic merit (estimated breeding value, EBV), which can be achieved using a best linear unbiased predictor (BLUP) (Henderson, 1975). Selection decisions in a commercial environment, however, are rarely made solely on genetic merit but also on additional factors, an important example of which is to limit the accumulation of inbreeding. Comparison of rates of inbreeding under BLUP for a range of hentabilities highlights a trend of increasing inbreeding with decreasing heritability. It is therefore proposed that selection using a heritability which is artificially raised would yield lower rates of inbreeding than would otherwise be the case.

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Genomic selection in French dairy cattle

Animal Production Science ◽

10.1071/an11119 ◽

2012 ◽

Vol 52 (3) ◽

pp. 115 ◽

Cited By ~ 63

Author(s):

D. Boichard ◽

F. Guillaume ◽

A. Baur ◽

P. Croiseau ◽

M. N. Rossignol ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Genomic Selection ◽

Reference Population ◽

Specific Reference ◽

Nucleotide Polymorphisms ◽

Genomic Evaluation ◽

Linear Unbiased Prediction ◽

Best Linear Unbiased ◽

Estimated Breeding Values ◽

Restricted Use

Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.

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Simulation study of development and elimination dynamics of bottlenecks in task of location of railway emergency facilities

Transport of the Urals ◽

10.20291/1815-9400-2021-1-103-107 ◽

2021 ◽

pp. 103-107

Author(s):

Andrey Alexandrovich Sukhov ◽

Keyword(s):

Simulation Study ◽

Simulation Modeling ◽

Economic Losses ◽

Operational Environment

The paper studies the influence of a transport accident on operation of a polygon, compares theoretical and practical variants of operational environment progress. With the use of simulation modeling the author has thoroughly analysed the process of train situation progress and has determined the economic losses from forced delays of trains of various categories, which can be recommended for the application at solving the task of location of emergency trains on polygons.

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