Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the genetic linkage map and growth-related molecular markers are still lacking, hindering marker assisted selection (MAS) for genetic improvement of R. esculentum. Therefore, we firstly used 2b-restriction site-associated DNA (2b-RAD) method to sequence 152 R. esculentum specimens and obtained 9100 single nucleotide polymorphism (SNP) markers. A 1456.34 cM linkage map was constructed using 2508 SNP markers with an average interval of 0.58 cM. Then, six quantitative trait loci (QTLs) for umbrella diameter and body weight were detected by QTL analysis based on the new linkage map. The six QTLs are located on four linkage groups (LGs), LG4, LG13, LG14 and LG15, explaining 9.4% to 13.4% of the phenotypic variation. Finally, 27 candidate genes in QTLs regions of LG 14 and 15 were found associated with growth and one gene named RE13670 (sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1-like) may play an important role in controlling the growth of R. esculentum. This study provides valuable information for investigating the growth mechanism and MAS breeding in R. esculentum.

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

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>