Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)

Pikeperch (Sander lucioperca) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size (Ne), and assessed relatedness among parental individuals. A mean of 2,235 ± 526 and 1,841 ± 363 ROH segments per individual, resulting in a mean inbreeding coefficient of 0.33 ± 0.06 and 0.25 ± 0.06 were estimated for the progeny and parents, respectively. Ne was about 12 until four generations ago and at most 106 for 63 generations in the past, with varying genetic relatedness amongst the parents. This study shows the importance of genomic information when family relationships are unknown and the need of selective breeding programs for reproductive management decisions in the aquaculture industry.

Closure times of neurocranial sutures and synchondroses in Persian compared to Domestic Shorthair cats

Human-directed selective breeding has modified the phenotype of the modern Persian cat towards an extreme brachycephalic phenotype (‘peke-face’ Persian), which originates from a spontaneous mutation that first appeared in the 1950s in traditional Persian types. It was suggested that the peke-face phenotype results from pathologic skull development and might represent a craniosynostosis of the coronal sutures. We followed this hypothesis and investigated the time dependent status of the neurocranial sutures and synchondroses in an ontogenetic series of doll-faced and peke-faced Persian cats compared to Domestic Shorthair cats (DSHs). Cranial suture closure was assessed by examining an ontogenetic series of formalin-fixed head specimens (n = 55) and dry skulls (n = 32) using micro-computed tomography. Sagittal, metopic, coronal and lambdoid sutures as well as intersphenoidal, spheno-occipital and spheno-ethmoid synchondroses were examined. Logistic regression analysis was performed to test the global effect of age on suture closure within a group of peke-face Persians, doll-face Persians and DSHs and the 50% probability of having a closed suture was calculated and compared between groups. Age was a perfect predictor for the condition of the coronal sutures in peke-face Persians. Coronal sutures were found to be closed at 0–0.3 months. In doll-face and DSHs, coronal sutures were open throughout the lifetime with the exception of a few very old cats. Results of this study confirmed a coronal craniosynostosis that likely causes the extreme brachycephalic skull morphology in the peke-face Persian.

Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan

There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 linked to pgrn2, 2 linked to pgrn1, and 1 linked to piscidin 4 (TP4) genes were established for tilapia strains farmed in Taiwan after challenge with Streptococcus inae. The correlation analysis of genotypes and survival revealed a total of 55 genotypes related to survival by the chi-square and Z-test. Although fewer markers were found in B and N2 strains compared with A strain, they performed well in terms of disease resistance. It suggested that this may be due to the low potency of some genotypes and the combinatorial arrangement between them. Therefore, a predictive model was built by the genotypes of the parental generation and the mortality rate of different combinations was calculated. The results show the same trend of predicted mortality in the offspring of three new disease-resistant strains as in the challenge experiment. The present findings is a nonkilling method without requiring the selection by challenge with bacteria or viruses and might increase the possibility of utilization of selective breeding using SSR markers in farms.

The genomics of growth and blue spots in a cultured population of Australasian snapper Chrysophrys auratus

<p>Characterizing the genome and understanding how it influences phenotypic variation is a central goal for studies on evolution. The findings of genomic research are applicable to a wide range of human endeavours, including predicting disease risk, supporting selective breeding programmes, and understanding adaptive variation in natural populations. One industry that could particularly benefit from this knowledge is Aquaculture. In recent years, aquaculture production has been increasing to offset the production limits of wild fisheries. Genomics can be used in aquaculture to quantify variation of captive populations, reconstruct pedigrees, and improve the gains from selective breeding programs. The overall goal of this thesis research was to generate a genome-wide genotyping dataset and investigated several key traits for Australasian snapper (Chrysophrys auratus or Pagrus auratus). The findings will be used to establish one of the first genomics-informed New Zealand aquaculture programmes and provide a better understanding of the genotype-phenotype relationships in this teleost species. The first two chapters of this thesis provide a review of the literature and establish the background information and context for the research in subsequent data chapters. A brief overview of genomics, fisheries and aquaculture, and the intersection of these two fields are provided in the Chapter 1. An in-depth quantitative review of 146 Quantitative Trait Loci (QTL) studies in teleost fish was then carried out in Chapter 2. Chapter 3 provides details about the study population and the collection of genotyping data. Genotyping-By-Sequencing (GBS) was used to generate 11K Single Nucleotide Polymorphism (SNP) markers for individuals in the three generation pedigree. Together with phenotypic data the genotyping was used to reconstruct the pedigree, measure inbreeding, and estimate heritability for a range of traits. Parents were identified for 93% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent to the subsequent generations. The average inbreeding level did not change between generations, but significantly different inbreeding levels were observed between offspring from the two founding cohorts and as a result full and half sibling crosses within the group spawning teleost species. Heritability was estimated for a range of traits using both a pedigree relatedness matrix and a genomic relatedness matrix. Chapter 4, uses the genotyping and phenotyping data to generate a linkage map and carry out a scan for quantitative trait loci (QTLs) associated with growth rate. The linkage map reported in this thesis is one of the highest density maps for any Sparidae species at the time of writing. It contained 24 linkage groups, which represent the 24 snapper chromosomes. Growth QTLs were found on three linkage groups and a scan of available genome data identified three candidate growth genes nearby on the linkage groups. Chapter 5, uses the genotyping data and images collected during the study to characterize snappers blue spots and search for QTLs associated with spot numbers. QTLs were found on 12 of the 24 linkage groups, of which one was consistent between two QTL methods applied. A scan of available genome data identified the tyrosinase gene in the middle of the putative QTL region, which is a causal gene for iridophore cell numbers that form blue spots in other fish species. Chapter 6, discuss the implications, future directions, and application of this research to the snapper breeding programme.</p>

Among-individual variation of risk-taking behaviour in group and solitary context is uncorrelated but independently repeatable in a juvenile Arctic charr (Salvelinus alpinus) aquaculture strain

Behavioural traits have been shown to have implications in fish welfare and growth performances in aquaculture. If several studies have demonstrated the existence of repeatable and heritable behavioural traits (i.e., animal personality), the methodology to assess personality in fishes is often carried out in solitary context, which appears to somewhat limit their use from a selective breeding perspective because these tests are too time consuming. To address this drawback, group-based tests have been developed. In Nordic country, Arctic charr (Salvelinus alpinus) is widely used in aquaculture, but no selection effort on behavioural traits has yet been carried out. Specifically, in this study we examined if risk-taking behaviour was repeatable and correlated in group and solitary context and if the early influences of physical environment affect the among-individual variation of behavioural trait across time in order to verify whether a group risk-taking test could be used as a selective breeding tool. Here, we found that in both contexts and treatments, the risk-taking behaviour was repeatable across a short period of 6 days. However, no cross-context consistency was found between group and solitary, which indicates that Arctic charr express different behavioural trait in group and solitary.

The genomics of growth and blue spots in a cultured population of Australasian snapper Chrysophrys auratus

<p>Characterizing the genome and understanding how it influences phenotypic variation is a central goal for studies on evolution. The findings of genomic research are applicable to a wide range of human endeavours, including predicting disease risk, supporting selective breeding programmes, and understanding adaptive variation in natural populations. One industry that could particularly benefit from this knowledge is Aquaculture. In recent years, aquaculture production has been increasing to offset the production limits of wild fisheries. Genomics can be used in aquaculture to quantify variation of captive populations, reconstruct pedigrees, and improve the gains from selective breeding programs. The overall goal of this thesis research was to generate a genome-wide genotyping dataset and investigated several key traits for Australasian snapper (Chrysophrys auratus or Pagrus auratus). The findings will be used to establish one of the first genomics-informed New Zealand aquaculture programmes and provide a better understanding of the genotype-phenotype relationships in this teleost species. The first two chapters of this thesis provide a review of the literature and establish the background information and context for the research in subsequent data chapters. A brief overview of genomics, fisheries and aquaculture, and the intersection of these two fields are provided in the Chapter 1. An in-depth quantitative review of 146 Quantitative Trait Loci (QTL) studies in teleost fish was then carried out in Chapter 2. Chapter 3 provides details about the study population and the collection of genotyping data. Genotyping-By-Sequencing (GBS) was used to generate 11K Single Nucleotide Polymorphism (SNP) markers for individuals in the three generation pedigree. Together with phenotypic data the genotyping was used to reconstruct the pedigree, measure inbreeding, and estimate heritability for a range of traits. Parents were identified for 93% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent to the subsequent generations. The average inbreeding level did not change between generations, but significantly different inbreeding levels were observed between offspring from the two founding cohorts and as a result full and half sibling crosses within the group spawning teleost species. Heritability was estimated for a range of traits using both a pedigree relatedness matrix and a genomic relatedness matrix. Chapter 4, uses the genotyping and phenotyping data to generate a linkage map and carry out a scan for quantitative trait loci (QTLs) associated with growth rate. The linkage map reported in this thesis is one of the highest density maps for any Sparidae species at the time of writing. It contained 24 linkage groups, which represent the 24 snapper chromosomes. Growth QTLs were found on three linkage groups and a scan of available genome data identified three candidate growth genes nearby on the linkage groups. Chapter 5, uses the genotyping data and images collected during the study to characterize snappers blue spots and search for QTLs associated with spot numbers. QTLs were found on 12 of the 24 linkage groups, of which one was consistent between two QTL methods applied. A scan of available genome data identified the tyrosinase gene in the middle of the putative QTL region, which is a causal gene for iridophore cell numbers that form blue spots in other fish species. Chapter 6, discuss the implications, future directions, and application of this research to the snapper breeding programme.</p>

Strain-, Sex-, and Time-Dependent Antidepressant-like Effects of Cannabidiol

Cannabidiol (CBD) is a non-intoxicating compound extracted from Cannabis sativa, showing antidepressant-like effects in different rodent models. However, inconsistent results have been described depending on the species and the strain used to assess depressive-like behavior. Moreover, only a few studies investigated the effect of CBD in female rodents. Therefore, we aimed to (i) investigate the effects of CBD in two different strains of mice (Swiss and C57BL/6) and a rat model of depression based on selective breeding (Flinders Sensitive and Resistant Lines, FSL and FRL) subjected to tests predictive of antidepressant-like effects and (ii) investigate the influence of sex in the effects of CBD in both mice and rats. CBD induced an antidepressant-like effect in male Swiss but not in female Swiss or C57BL/6 mice in the tail suspension test (TST). In male FSL rats, CBD produced an antidepressant-like effect 1 h post injection. However, in female FSL, CBD induced a bimodal effect, increasing the immobility time at 1 h and decreasing it at 2 h. In conclusion, strain, sex, and administration time affect CBD’s behavioral response to rodents exposed to tests predictive of antidepressant effects.

ĐA HÌNH MICROSATELLITE LIÊN KẾT VỚI GEN HEPCIDIN/HAMP TIỀM NĂNG TRONG CHỌN GIỐNG CÁ RÔ PHI VẰN KHÁNG BỆNH DO Streptococcus iniae

Bệnh xuất huyết do vi khuẩn Streptococcus sp là mầm bệnh truyền nhiễm chính gây thiệt hại đáng kể đến sản lượng cá rô phi toàn cầu. Hepcidin/HAMP ở cá đã được báo cáo có liên quan đến miễn dịch bẩm sinh chống lại các mầm bệnh vi khuẩn. Trong nghiên cứu này, chúng tôi tiến hành phân tích mối quan hệ giữa tính đa hình microsatellites/SSRs liên kết với gen hepcidin/HAMP và khả năng kháng bệnh do Streptococcus iniae trên cá rô phi vằn dòng NT1 (Đài Loan). 17 chỉ thị SSRs và cặp mồi đặc hiệu đã được thiết kế dựa trên WebSat. Kết quả đánh giá trên 95 cá thể cho thấy 9/17 chỉ thị SSRs có tính đa hình cao và tuân theo định luật Hardy-Weinberg. Các chỉ thị này sẽ được sử dụng để đánh giá khả năng kháng vi khuẩn S. iniae. 29 cá rô phi NT1 thế hệ thứ nhất (khối lượng 23,59 ± 5,388 g/con) đã được cảm nhiễm với vi khuẩn S. iniae 89353 bằng phương pháp tiêm, với liều tiêm LD50 là 1,3x105 cfu/mL. Kết quả phân tích cho thấy, có sự sai khác có ý nghĩa thống kê về kiểu gen và tần số alen giữa nhóm sống và nhóm chết sau cảm nhiễm vi khuẩn ở 3 chỉ thị SSRs (SSR7, SSR9 và SSR16) (p<0,05). Đây là marker có tiềm năng cho chọn giống cá rô phi Đài Loan kháng bệnh do S. iniae. ABSTRACT Streptococcus has been recognized as a major infectious disease-causing significant economic loss in tilapia aquaculture in many countries. The hepatic antimicrobial peptide hepcidin/HAMP was reported to be associated with innate immunity which defends against various bacterial pathogens and viruses. In this study, we analyzed the corelation between the microsatellites/SSRs polymorphism in the hepcidin/HAMP genes and the resistance to Streptococcus iniae in the NT1strain (tilapia strain in Taiwan). Seventeen of hepcidin/HAMP-related SSRs and 17 SSR-specific PCR primer were designed using WebSat. The result showed that 9/17 hepcidin/HAMP-related SSRs were polymorphic markers and there is significant deviation from Hardy-Weinberg Equilibrium (HWE) (p<0,05). These SSRs were examined for disease resistance to S. iniae. Twenty-nine the First generation (G1) tilapia of NT1 strain (average weight of 23,59 ± 5,388g/fish) were challenged with virulent S. iniae 89353 through intraperioneal injection at dose of LD50 (1,3x105 cfu/ml). In this study, the genotype and the allele frequency in three SSRs (SSR7, SSR9 và SSR16) were significantly different between two groups (death fish with infected signals of S. iniae and alive fish infected with S. iniae) (p<0,05). Three SSRs (SSR7, SSR9 và SSR16) are considered as potential molecular markers for selective breeding of Taiwanese tilapia which resists to S. iniae.