Aquaculture 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-F
, principal components, or random forest) is unlikely to increase the prediction accuracy for these traits.
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Studies using genome-wide single nucleotide polymorphisms (SNPs) have become commonplace in genetics and genomics, due to advances in high-throughput sequencing technologies. Since the numbers of ...required SNPs and samples vary depending on each research goal, genotyping technologies with high flexibility in the number of SNPs/samples and high repeatability have been intensively investigated. For example, the ultrahigh-multiplexed amplicon sequencing, Ion AmpliSeq, has been used as a high-throughput genotyping method mainly for diagnostic purposes. Here, we designed a custom panel targeting 3,187 genome-wide SNPs of fugu, Takifugu rubripes, and applied it for genotyping farmed fugu to test its feasibility in aquaculture studies. We sequenced two libraries consisting of different pools of individuals (n = 326 each) on the Illumina MiSeq sequencer. Consequently, over 99% target regions (3,178 SNPs) were amplified and 2,655 SNPs were available after filtering steps. Strong correlation was observed in the mean depth of coverage of each SNP between duplicate runs (r = 0.993). Genetic analysis using these genotype data successfully detected the known population structure and the sex determining locus of fugu. These results show the method is superior in repeatability and flexibility, and suits genetic studies including molecular breeding, such as marker assisted and genomic selection.
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Extant ‘fishes’ belong to jawless, cartilaginous, actinopterygian, or sarcopterygian fish lineages. They comprise a non-monophyletic group of vertebrates from which tetrapods are excluded, and they ...are therefore paraphyletic. Recent advances in whole-genome sequencing have shed light on phylogenetic relationships, divergence times among major fish lineages, and the molecular basis of phenotypic diversity. This review encompasses the diversity of extant fishes and explores the variation in genomic organization and its evolutionary origins. This review begins with evaluating available genomic sequence resources with a focus on literally complete (‘telomere-to-telomere’) sequencing. Next, it discusses among-lineage variations in genomic contents, considering karyotype reports, genome sizes, and whole-genome duplication events. Additionally, we investigate three families of protein-coding genes, visual opsins, aquaporins (Aqps), and Hox genes, as they offer insights into morphological and physiological differences among major fish lineages. Overall, our technical basis of analyzing fish genomes and the knowledge of genomic organization provide valuable insights into our vertebrate-wide understanding of how molecular mechanisms specifying variable phenotypes are encoded in genomic sequence information.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Spermatogonial stem cells (SSCs) support continuous production of sperm throughout the male's life. However, the biological characteristics of SSCs are poorly understood in animals exhibiting ...seasonal reproduction, even though most wild animals are seasonal breeders. During the spermiation season in rainbow trout, the lumen of the testes contains only spermatozoa and scattered type A spermatogonia (ASG) along the walls of the testicular lobules. These few remaining ASG, designated “residual ASG,” are the only germ cells capable of supporting the next spermatogenesis, suggesting that the residual ASG are true SSCs. However, whether residual ASG can behave as SSCs in any teleost species is unknown. In this study, we attempted to clarify the biological characteristics of SSCs associated with seasonal reproduction in rainbow trout using spermatogonial transplantation. We found that the stem cell activity was clearly regulated seasonally during the annual reproductive cycle. Although the residual ASG exhibited moderate transplantability and colony-forming ability at the beginning of the spermiation season, these parameters decreased dramatically later and remained low until the next spermatogenesis was initiated. Furthermore, no clear correlations were observed between these qualitative changes and previously described morphologic characteristics of ASG or plasma sex steroid levels. Our results suggest that the biological properties of SSC populations in rainbow trout are seasonally regulated by a novel mechanism. Summary Sentence Stem cell activity of type A spermatogonia drastically changes during the annual reproductive cycle in adult rainbow trout.
Parasite 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: h
= 0.308 ± 0.123, S.E.; SL: h
= 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 (r
= 0.228), the simulation study suggested the desired gains index can help achieve simultaneous genetic improvements in both traits.
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Large-scale release of hatchery-produced seeds has been conducted in order to restore worldwide fishery production; however, concerns exist regarding the genetic effects of hatchery stock on wild ...fish populations, due to the reduced genetic variation often associated with hatchery-reared fish. Therefore, it is important that fish seeds used in stock enhancement possess sufficient genetic diversity to mitigate their genetic impact on wild fish populations. To promote genetic diversity of artificial seeds, seed production should be performed using a sufficiently large broodstock; however, maintenance of large broodstocks requires significant investments with respect to space, labor, and other associated costs. In order to circumvent the need for these investments, the present study proposed a means of producing gametes that possess a large amount of genetic diversity using only a small number of surrogate-broodstock through spermatogonial transplantation. We previously established spermatogonial transplantation methodology capable of producing functional eggs and sperm derived from donor-type A spermatogonia (ASGs). It was expected that if ASGs isolated from testes of different donor individuals were mixed prior to their transplantation into the peritoneal cavity of a single recipient, the resulting recipient would produce gametes derived from several donor individuals. To determine the feasibility of this scenario, mixed donor ASGs derived from vasa-GFP, vasa-DsRed and hsc-GFP transgenic rainbow trout (Oncorhynchus mykiss) were transplanted into triploid recipients. At 20 days post-transplantation, approximately 80% of recipients possessed donor ASGs derived from all three strains within their gonads and mean numbers of incorporated ASGs derived from each donor strain were nearly equal. At 100 days post-transplantation, incorporated donor ASGs proliferated within the gonads of both male and female recipients, and some had differentiated into oocytes within recipient ovaries. Furthermore, in order to ascertain whether incorporated donor ASGs derived from the three strains could differentiate into functional gametes, gametes collected from mature male and female recipients were used in artificial insemination with gametes obtained from wild-type fish of the opposite sex. Phenotypic analysis of F1 offspring revealed that functional sperm and eggs derived from three donor strains were successfully produced in the gonads of individual recipients. These results suggested that individual recipients that received ASGs from multiple donors were capable of producing gametes with different genetic backgrounds. Therefore, it was concluded that the method of spermatogonial transplantation outlined in the present study could serve as a novel and efficient method of producing fish seeds with increased genetic diversity for use in stock enhancement. PUBLICATION ABSTRACT
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus
that has undergone explosive ...radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two
species,
Temminck & Schlegel and
Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two
are likely the same, but the genes used for the similar phenotype in
and distantly related fishes are not the same. Meanwhile,
, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since
, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to
, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.
Schizophyllan is a triple helical β-1,3-
-glucan, and shows the cooperative order-disorder transition in the aqueous solution at the triple helix state. In this paper, the solvent stabilizing effects ...of two carboxylic acids, acetic acid and citric acid, on the cooperative order-disorder transition of aqueous schizophyllan solution were investigated from DSC and SEC-MALS measurements. The transition temperature (T
) was shifted to higher temperature with increasing the molar fraction of carboxylic acid in the mixture (x). The transition enthalpy (ΔH
) was increased with increasing x. These solvent stabilizing effects indicate that these carboxylic acid molecules were selectively associated with the branched side chains of schizophyllan to stabilize the ordered state. The composition dependencies of T
and ΔH
were analyzed by the linear cooperative transition theory to estimate the association parameters between the side chains and carboxylic acid. The theoretical parameters obtained were compared with those for the other active substances for the transition to discuss the molecular interactions between the triple helix and carboxylic acid.
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In 45,X/46,XY DSDs, the proportion of the two cell lineages is uneven in different organs and tissues, and 45,X and 46,XY cells can be found throughout the body. The gonadal development of 45,X/46,XY ...patients depends on the population of 46,XY cells in the gonads and the clinical features are variable. We had a 45,X/46,XY DSD patient whose 46,XY population in peripheral blood was extremely low, less than 0.2%, and was not detected by FISH analysis. However, the patient showed bilateral testicular development and more than 50% of the cells in the gonads had the 46,XY karyotype. This case suggests that a drastically imbalanced distribution could occur in 45,X/46,XY DSD cases.
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