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

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

Scientific Reports ◽

10.1038/s41598-020-77069-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Zijie Lin ◽

Sho Hosoya ◽

Mana Sato ◽

Naoki Mizuno ◽

Yuki Kobayashi ◽

...

Keyword(s):

Body Size ◽

Genomic Selection ◽

Simulation Study ◽

Economic Losses ◽

Takifugu Rubripes ◽

Parasite Resistance ◽

Best Linear Unbiased Predictor ◽

Monogenean Parasite ◽

Best Linear Unbiased ◽

Tiger Pufferfish

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 studies with pre-selected markers reveal dominance effects influencing growth traits in Eucalyptus nitens

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab363 ◽

2021 ◽

Author(s):

Bala R Thumma ◽

Kelsey R Joyce ◽

Andrew Jacobs

Keyword(s):

Inbreeding Depression ◽

Prediction Accuracy ◽

Basic Density ◽

Predictive Ability ◽

Best Linear Unbiased Prediction ◽

The Other ◽

Eucalyptus Nitens ◽

Linear Unbiased Prediction ◽

Best Linear Unbiased ◽

Unbiased Prediction

Abstract Genomic selection (GS) is being increasingly adopted by the tree breeding community. Most of the GS studies in trees are focused on estimating additive genetic effects. Exploiting the dominance effects offers additional opportunities to improve genetic gain. To detect dominance effects, trait relevant markers may be important compared to non-selected markers. Here we used pre-selected markers to study the dominance effects in a Eucalyptus nitens (E. nitens) breeding population consisting of open-pollinated (OP) and controlled-pollinated (CP) families. We used 8221 trees from six progeny trials in this study. Of these, 868 progeny and 255 parents were genotyped with the E. nitens marker panel. Three traits; diameter at breast height (DBH), wood basic density (DEN) and kraft pulp yield (KPY) were analysed. Two types of genomic relationship matrices based on identity-by-state (IBS) and identity-by-descent (IBD) were tested. Performance of the genomic best linear unbiased prediction (GBLUP) models with IBS and IBD matrices were compared with pedigree-based additive best linear unbiased prediction (ABLUP) models with and without the pedigree reconstruction. Similarly, the performance of the single-step GBLUP (ssGBLUP) with IBS and IBD matrices were compared with ABLUP models using all 8221 trees. Significant dominance effects were observed with the GBLUP-AD model for DBH. The predictive ability of DBH is higher with the GBLUP-AD model compared to other models. Similarly, the prediction accuracy of genotypic values is higher with GBLUP-AD compared to the GBLUP-A model. Among the two GBLUP models (IBS and IBD), no differences were observed in predictive abilities and prediction accuracies. While the estimates of predictive ability with additive effects were similar among all four models, prediction accuracies of ABLUP were lower than the GBLUP models. The prediction accuracy of ssGBLUP-IBD is higher than the other three models while the theoretical accuracy of ssGBLUP-IBS is consistently higher than the other three models across all three groups tested (parents, genotyped, non-genotyped). Significant inbreeding depression was observed for DBH and KPY. While there is a linear relationship between inbreeding and DBH, the relationship between inbreeding and KPY is non-linear and quadratic. These results indicate that the inbreeding depression of DBH is mainly due to directional dominance while in KPY it may be due to epistasis. Inbreeding depression may be the main source of the observed dominance effects in DBH. The significant dominance effect observed for DBH may be used to select complementary parents to improve the genetic merit of the progeny in E. nitens.

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Metabolomic Spectra For Phenotypic Prediction of Malting Quality In Spring Barley

10.21203/rs.3.rs-1113863/v1 ◽

2021 ◽

Author(s):

Xiangyu Guo ◽

Ahmed Jahoor ◽

Just Jensen ◽

Pernille Sarup

Keyword(s):

Prediction Accuracy ◽

Cross Validation ◽

Spring Barley ◽

Predictive Ability ◽

Malting Quality ◽

Least Squares Regression ◽

Training Population ◽

Prediction Ability ◽

Rate Of Increase ◽

Best Linear Unbiased

Abstract The objectives were to investigate prediction of malting quality (MQ) phenotypes in different locations using information from metabolomic spectra, and compare the prediction ability using different models and different sizes of training population (TP). A total of 2,667 plots of 564 malting spring barley lines from three years and two locations were included. Five MQ traits were measured in wort produced from each individual plot. Metabolomic features (MFs) used were 24,018 NMR intensities measured on each wort sample. Models involved in the statistical analyses were a metabolomic best linear unbiased prediction (MBLUP) model and a partial least squares regression (PLSR) model. Predictive ability within location and across locations were compared using cross-validation methods. The proportion of variance in MQ traits that could be explained by effects of MFs was above 0.9 for all traits. The prediction accuracy increased with increasing TP size but when the TP size reached 1,000, the rate of increase was negligible. The number of components considered in the PLSR models can affect the performance of PLSR models and 20 components were optimal. The accuracy of individual plots and line means using leave-one-line-out cross-validation ranged from 0.722 to 0.865 and using leave-one-location-out cross-validation ranged from 0.517 to 0.817.In conclusion, it is possible to carry out metabolomic prediction of MQ traits using MFs, the prediction accuracy is high and MBLUP is better than PLSR if the training population is larger than 100. The results have significant implications for practical barley breeding for malting quality.

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GWAS findings improved genomic prediction accuracy of lipid profile traits: Tehran Cardiometabolic Genetic Study

Scientific Reports ◽

10.1038/s41598-021-85203-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mahdi Akbarzadeh ◽

Saeid Rasekhi Dehkordi ◽

Mahmoud Amiri Roudbar ◽

Mehdi Sargolzaei ◽

Kamran Guity ◽

...

Keyword(s):

Lipid Profile ◽

Genetic Study ◽

Prediction Accuracy ◽

Significant Snps ◽

Snp Markers ◽

Linear Unbiased Prediction ◽

Genetic Prediction ◽

Heritability Estimation ◽

Precise Prediction ◽

Best Linear Unbiased

AbstractIn recent decades, ongoing GWAS findings discovered novel therapeutic modifications such as whole-genome risk prediction in particular. Here, we proposed a method based on integrating the traditional genomic best linear unbiased prediction (gBLUP) approach with GWAS information to boost genetic prediction accuracy and gene-based heritability estimation. This study was conducted in the framework of the Tehran Cardio-metabolic Genetic study (TCGS) containing 14,827 individuals and 649,932 SNP markers. Five SNP subsets were selected based on GWAS results: top 1%, 5%, 10%, 50% significant SNPs, and reported associated SNPs in previous studies. Furthermore, we randomly selected subsets as large as every five subsets. Prediction accuracy has been investigated on lipid profile traits with a tenfold and 10-repeat cross-validation algorithm by the gBLUP method. Our results revealed that genetic prediction based on selected subsets of SNPs obtained from the dataset outperformed the subsets from previously reported SNPs. Selected SNPs’ subsets acquired a more precise prediction than whole SNPs and much higher than randomly selected SNPs. Also, common SNPs with the most captured prediction accuracy in the selected sets caught the highest gene-based heritability. However, it is better to be mindful of the fact that a small number of SNPs obtained from GWAS results could capture a highly notable proportion of variance and prediction accuracy.

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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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37 Sibs: an R toolkit for computation of relatedness measures using large pedigrees

Journal of Animal Science ◽

10.1093/jas/skaa054.074 ◽

2020 ◽

Vol 98 (Supplement_3) ◽

pp. 41-42

Author(s):

B Victor Oribamise ◽

Lauren L Hulsman Hanna

Keyword(s):

Family Structure ◽

Genetic Relatedness ◽

Current User ◽

Memory Allocation ◽

Relationship Matrix ◽

Additive Effects ◽

Numerator Relationship Matrix ◽

Significant Difference ◽

R Packages ◽

User Friendly

Abstract Without appropriate relationships present in a given population, identifying dominance effects in the expression of desirable traits is challenging. Including non-additive effects is desirable to increase accuracy of breeding values. There is no current user-friendly tool package to investigate genetic relatedness in large pedigrees. The objective was to develop and implement efficient algorithms in R to calculate and visualize measures of relatedness (e.g., sibling and family structure, numerator relationship matrices) for large pedigrees. Comparisons to current R packages (Table 1) are also made. Functions to assign animals to families, summary of sibling counts, calculation of numerator relationship matrix (NRM), and NRM summary by groups were created, providing a comprehensive toolkit (Sibs package) not found in other packages. Pedigrees of various sizes (n = 20, 4,035, 120,000 and 132,833) were used to test functionality and compare to current packages. All runs were conducted on a Windows-based computer with an 8 GB RAM, 2.5 GHz Intel Core i7 processor. Other packages had no significant difference in runtime when constructing the NRM for small pedigrees (n = 20) compared to Sibs (0 to 0.05 s difference). However, packages such as ggroups, AGHmatrix, and pedigree were 10 to 15 min slower than Sibs for a 4,035-individual pedigree. Packages nadiv and pedigreemm competed with Sibs (0.30 to 60 s slower than Sibs), but no package besides Sibs was able to complete the 132,833-individual pedigree due to memory allocation issues in R. The nadiv package was closest with a pedigree of 120,000 individuals, but took 37 min to complete (13 min slower than Sibs). This package also provides easier input of pedigrees and is more encompassing of such relatedness measures than other packages (Table 1). Furthermore, it can provide an option to utilize other packages such as GCA for connectedness calculations when using large pedigrees.

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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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