Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

Soliman, Taha; Fernández-Silva, Iria; Reimer, James Davis

doi:10.1007/s10592-016-0823-8

Cited by 24 publications

(22 citation statements)

References 33 publications

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“…Also in horticultural crops, the deployment of haplotype-based approaches holds a great potential for a genetic improvement of future varieties. In cucumber ( Holothuria edulis L.) for example, Soliman et al (2016) used PCR-based markers to study sequence diversity in a mitochondrial cytochrome oxidase subunit I (COI), 16S ribosomal RNA, and a nuclear histone. Applying marker-based haplotype analyses they were able to gain insights into population structure, providing valuable information for the management of sea cucumber populations in Okinawa.…”

Section: Haplotype-based Improvement Of Molecular Breeding Approachesmentioning

confidence: 99%

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

Qian¹,

Hickey²,

Stahl³

et al. 2017

Front. Plant Sci.

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In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP–trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

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Section: Haplotype-based Improvement Of Molecular Breeding Approachesmentioning

confidence: 99%

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

Qian¹,

Hickey²,

Stahl³

et al. 2017

Front. Plant Sci.

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“…In the present study, we assess the genetic diversity and population structure among eight S. chloronotus locations in southern Japan (Okinawa and Okinoerabu Islands) using sequences of mitochondrial DNA (16S ribosomal DNA) and nuclear DNA (histone H3), in order to provide genetic connectivity. We examine whether S. chloronotus on the east and west coasts of Okinawa are genetically differentiated as has been observed in a number of recent studies on other sea cucumber ( Soliman, Fernandez-Silva & Reimer, 2016 ) and other invertebrate species ( White, Reimer & Lorion, 2016 ). This information will be useful for future conservation and fisheries management.…”

Section: Introductionmentioning

confidence: 92%

“…In Okinawa, Japan, similar to many other regions of the world, sea cucumbers have been under increasing commercial pressure due to high demand. A recent study showed that some populations of Holothuria edulis Lesson, 1830 around Okinawa Island had lower than expected genetic diversity, indicating potential overharvesting and/or ecosystem degradation ( Soliman, Fernandez-Silva & Reimer, 2016 ). Prefectural regulations have been put in place to try and limit further damage to sea cucumber populations, but basic genetic and abundance data are lacking for all other sea cucumber species for the entire Ryukyu Archipelago, and for Okinawa Island in particular.…”

Section: Introductionmentioning

confidence: 99%

Extremely low genetic variability within and among locations of the greenfish holothurianStichopus chloronotusBrandt, 1835 in Okinawa, Japan

Soliman

Takama

Fernández-Silva

et al. 2016

PeerJ

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The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

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“…Both sexual reproduction and asexual reproduction of H. edulis were observed in nature (Uthicke 1997). So far, there are only a few DNA sequences such as COX1 and 16S rRNA of H. edulis were reported (Soliman et al 2016). Lack of genetic resources has hindered conservation and utilization of H. edulis.…”

Section: Holothuria Edulis; Mitochondrial Genome; Phylogenymentioning

confidence: 99%

The complete mitochondrial genome of Holothuria edulis (Lesson, 1830) (Aspidochirotida, Holothriidae)

Ling

Wen

Lin

et al. 2020

Mitochondrial DNA Part B

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The complete mitochondrial genome of Holothuria edulis was obtained and described in this study. This complete mitochondrial genome is 15,743 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Except ND6 and 5 tRNAs, the others were encoded by the heavy strand. The overall base composition of the heavy-strand was 32.29% A, 15.25% G, 25.88% C, and 26.57% T, with a high A þ T content of 58.86%. The phylogenetic analysis suggested that H. edulis was closest to H. pervicax. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Holothuroidea. ARTICLE HISTORY

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Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

Cited by 24 publications

References 33 publications

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops

Extremely low genetic variability within and among locations of the greenfish holothurianStichopus chloronotusBrandt, 1835 in Okinawa, Japan

The complete mitochondrial genome of Holothuria edulis (Lesson, 1830) (Aspidochirotida, Holothriidae)

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