Quantitative Trait Loci (QTL) Associated with Resistance to a Monogenean Parasite (Benedenia seriolae) in Yellowtail (Seriola quinqueradiata) through Genome Wide Analysis

Yoshida, Kazunori; Fuji, Kanako; Kubota, Shin; Wang, Kai; Aoki, Junya; Kawabata, Yoshinori; Suzuki, Jun; Akita, Kazuki; Koyama, Takashi; Nakagawa, Masahiro; Hotta, Tomomitsu; Tsuzaki, Tatsuo; Okamoto, Nobuaki; Araki, Kazuo; Sakamoto, Takashi

doi:10.1371/journal.pone.0064987

Cited by 38 publications

(17 citation statements)

References 34 publications

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“…Permutation tests were performed (1000 replicates) to determine the LOD threshold by type one error. The significant thresholds derived from the permutation tests was estimated by dividing the nominal P value by the total number of chromosomes (Churchill and Doerge 1994;Ozaki et al 2013). A graphical representation of the significant QTLs was constructed using MAPCHART version 2.1 and MapQTL 5.…”

Section: Qtl Analysismentioning

confidence: 99%

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

et al. 2016

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To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F 1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using nonparametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1 % of the genomewide significance and accounted for 14.6-18.9 and 14.7-18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.

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Section: Qtl Analysismentioning

confidence: 99%

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

et al. 2016

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“…In addition, shortening of the generation period is an important requirement to precede breeding programs of YT. Recently, genetic tools for the establishment of efficient breeding by marker-assisted selection (MAS) have been exploited in YT (Ohara et al 2005;Ozaki et al 2013;Aoki et al 2014). Establishment of MAS in YT would make it possible to select the individuals with desirable economic traits before the fish reaches maturity.…”

Section: Discussionmentioning

confidence: 99%

Functional Sperm of the Yellowtail (Seriola quinqueradiata) Were Produced in the Small-Bodied Surrogate, Jack Mackerel (Trachurus japonicus)

et al. 2015

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Production of xenogeneic gametes from large-bodied, commercially important marine species in closely related smaller surrogates with short generation times may enable rapid domestication of the targeted species. In this study, we aimed to produce gametes of Japanese yellowtail (Seriola quinqueradiata) using jack mackerel (Trachurus japonicus) as a surrogate with a smaller body size and shorter maturation period. Donor spermatogonia were collected from the testes of yellowtail males and transferred into the peritoneal cavity of 10- and 12-day-old jack mackerel larvae. Twenty days later, 59.5% of the recipients survived of which 88.2% had donor-derived germ cells in their gonads. One year later, genomic DNA templates were prepared from the semen of 96 male recipients and subjected to polymerase chain reaction (PCR) analyses using primers specific for the yellowtail vasa sequence, resulting in the detection of positive signals in semen from two recipients. The milt collected from the recipients was used for fertilization with yellowtail eggs. Of eight hatchlings obtained from the crosses, two were confirmed to be derived from donor yellowtail by DNA markers, although the others were gynogenetic diploids. These findings indicate that it is possible to produce donor-derived sperm in xenogeneic recipients with a smaller body size and shorter generation time by transplanting spermatogonia. Thus, the xenogeneic transplantation of spermatogonia might be a potential tool to produce gametes of large-bodied, commercially important fish, although the efficiency of the method requires further improvement. This is the first report demonstrating that donor-derived sperm could be produced in xenogeneic recipient via spermatogonial transplantation in carangid fishes.

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“…Bacteria disease for which QTL resistance traits have been identiied include coldwater disease in rainbow trout [187], Aeromonas hydrophila in rohu (Labeo rohita) [188], Vibrio anguillarum in Japanese lounder [189], Flavobacterium psychrophilum in rainbow trout [190] and pastuerellosis in Gilhead seabream [191]. As for parasitic diseases, QTL resistance traits have been identiied for Gyrodactylus salaris in Atlantic salmon [192] and Monohenean parasite (Benedenia seriolae) in Yellow tail (Seriola quinqueradiata) [193].…”

Section: Applications Of Rna-seq and Omics Strategies -From Microorgamentioning

confidence: 99%

Current Advances in Functional Genomics in Aquaculture

Munang’andu¹,

Evensen²

2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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Gene expression studies in aquaculture have slowly evolved from the traditional reductionist approach of single gene sequencing to high throughput sequencing (HTS) techniques able to sequence entire genomes of living organisms. The upcoming of HTS techniques has led to emergence of metagenomics, nutrigenomics, epigenetics and other omics technologies in aquaculture in the last decade. Metagenomics analyses have accelerated the speed at which emerging pathogens are being discovered, thereby contributing to the design of timely disease control strategies in aquaculture. Using metagenomics, it is easy to identify and monitor microbial communities found in diferent ecosystems. In vaccine production, genomic studies are being used to identify cross neutralizing antigens against variant strains of the same pathogens. In genetics and epigenetics, genomics traits have been identiied that are beginning to gain commercial applications in aquaculture. Nutrigenomics have not only enhanced our understanding of the biological markers for nutrition-related diseases, but they have also enhanced our ability to formulate diets able to maintain a stable immune homeostasis in the gut. Overall, herein, we have shown that functional genomics provide multifaceted applications ranging from monitoring microbial communities in aquatic environments to optimizing production systems in aquaculture.

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Quantitative Trait Loci (QTL) Associated with Resistance to a Monogenean Parasite (Benedenia seriolae) in Yellowtail (Seriola quinqueradiata) through Genome Wide Analysis

Cited by 38 publications

References 34 publications

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

Functional Sperm of the Yellowtail (Seriola quinqueradiata) Were Produced in the Small-Bodied Surrogate, Jack Mackerel (Trachurus japonicus)

Current Advances in Functional Genomics in Aquaculture

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