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Production of triploid, doubled haploid (DH) and meiogynogenetic brook trout (Salvelinus fontinalis) – efficiency and development of body deformities. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
In the present research we produced triploid, mitogynogenetic (doubled haploid; DH) and meiogynogenetic brook trout (Salvelinus fontinalis) to examine efficiency of these technologies and potential susceptibility of chromosome set manipulated individuals for the spinal disorders. Triploidy was induced by shocking (High Hydrostatic Pressure – HHP) of fertilized eggs 30 min. after insemination. In turn, gynogenetic development was induced by activation of eggs with UV-irradiated sperm. Activated eggs were then exposed to HHP shock applied 30 and 420 minutes after insemination to provide meiogynogenotes and gynogenetic DHs, respectively. When compared to non-manipulated diploids, the highest survival rates were observed among triploid brook trout while DHs showed the highest mortality. Malformation rates in the diploid larvae from the control groups did not exceed 7.0% while percentage of malformed triploid individuals equaled 19.1%. Drastically increased number of deformed larvae (> 30%) was observed in both DH and meiogynogenetic individuals. Intensification of kyphosis and scoliosis was clearly demonstrated in the gynogenetic and triploid brook trout. Genetic factors such as increased number of sets of chromosomes in triploids and expression of lethal alleles in the gynogenetic fish plus side effects of HHP shock utilized for retention of the second polar body or inhibition of the first cell cleavage when induced triploid and gynogenetic development have been discussed to affect survival rates and prevalence for the skeletal deformities in the chromosome set manipulated brook trout.
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Tian L, Rahman SR, Ezray BD, Franzini L, Strange JP, Lhomme P, Hines HM. A homeotic shift late in development drives mimetic color variation in a bumble bee. Proc Natl Acad Sci U S A 2019; 116:11857-11865. [PMID: 31043564 PMCID: PMC6575597 DOI: 10.1073/pnas.1900365116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally nonmodel systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns through parallel shifts of midabdominal segments from red to black. Using genome-wide association, we establish that a cis-regulatory locus between the abdominal fate-determining Hox genes, abd-A and Abd-B, controls the red-black color switch in a western species, Bombus melanopygus Gene expression analysis reveals distinct shifts in Abd-B aligned with the duration of setal pigmentation at the pupal-adult transition. This results in atypical anterior Abd-B expression, a late developmental homeotic shift. Changing expression of Hox genes can have widespread effects, given their important role across segmental phenotypes; however, the late timing reduces this pleiotropy, making Hox genes suitable targets. Analysis of this locus across mimics and relatives reveals that other species follow independent genetic routes to obtain the same phenotypes.
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Affiliation(s)
- Li Tian
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Briana D Ezray
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - Luca Franzini
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - James P Strange
- United States Department of Agriculture-Agricultural Research Service Pollinating Insects Research Unit, Utah State University, Logan, UT 84322
| | - Patrick Lhomme
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Biodiversity and Crop Improvement Program, International Center of Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
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Yasuike M, Iwasaki Y, Nishiki I, Nakamura Y, Matsuura A, Yoshida K, Noda T, Andoh T, Fujiwara A. The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract. DNA Res 2018; 25:547-560. [PMID: 30329019 PMCID: PMC6191305 DOI: 10.1093/dnares/dsy024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93.3%) were functionally annotated. Given our lack of knowledge of the yellowtail digestive system, and using the annotated draft genome as a reference, we conducted an RNA-Seq analysis of its three digestive organs (stomach, intestine and rectum). The RNA-Seq results highlighted the importance of certain genes in encoding proteolytic enzymes necessary for digestion and absorption in the yellowtail gastrointestinal tract, and this finding will accelerate development of formulated feeds for this species. Since this study offers comprehensive annotation of predicted protein-coding genes, it has potential broad application to our understanding of yellowtail biology and aquaculture.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazunori Yoshida
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tsutomu Noda
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tadashi Andoh
- Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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Nomura K, Fujiwara A, Iwasaki Y, Nishiki I, Matsuura A, Ozaki A, Sudo R, Tanaka H. Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica). PLoS One 2018; 13:e0201784. [PMID: 30157280 PMCID: PMC6114518 DOI: 10.1371/journal.pone.0201784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 07/23/2018] [Indexed: 01/31/2023] Open
Abstract
The Japanese eel (Anguilla japonica) is among the most important aquaculture fish species in Eastern Asia. The present study aimed to identify the genetic parameters underlying body size and the timing at metamorphosis from leptocephali to glass eels in captive-bred Japanese eels, with the intent to foster sustainable development. Larvae from a partly factorial cross (14 sires × 11 dams) were reared until the point of metamorphosis into glass eels. In these organisms, we observed moderate heritability and mild genetic correlations among traits related to body size (h2 = 0.16–0.33) and timing at metamorphosis (h2 = 0.36–0.41). In an F1 full-sib family, quantitative trait loci (QTL) mapping for these traits identified one significant (genome-wide P < 0.05) and five suggestive QTLs (chromosome-wide P < 0.05). These results suggest that in the Japanese eel, metamorphic traits exhibit a polygenic genetic structure comprising many QTLs with small effects. In addition, we updated the genetic linkage map for the Japanese eel and integrated it with our newly constructed de novo genome assembly. The information and tools generated from this study will contribute to the development of freshwater eel genetics and genomics.
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Affiliation(s)
- Kazuharu Nomura
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
- * E-mail:
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Ryusuke Sudo
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Hideki Tanaka
- National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
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