Zhongming Huo

Heavy Metal Concentrations in Surface Sediments and Manila Clams (Ruditapes philippinarum) from the Dalian Coast, China after the Dalian Port Oil Spill

We conducted an investigation of heavy metal concentrations in Manila clams (Ruditapes philippinarum) and surface sediments after the Dalian Port oil spill. Samples were collected from three mariculture zones (Jinshitan, Dalijia, and Pikou) along the Dalian coast. Heavy metal concentrations in R. philippinarum were consistent and ranked in decreasing order of Zn > Cu > As > Cr > Pb > Cd > Hg, while concentrations in surface sediments were ranked as Zn > Cr > Cu > Pb > As > Cd > Hg, respectively. Bioaccumulation of Zn, Cd, and Hg had obviously occurred in R. philippinarum. Statistically significant correlations (p < 0.05) between concentrations of Pb, Cd, and Hg in R. philippinarum and in surface sediments were observed. Except for Cr and As, heavy metal concentrations in R. philippinarum were well within the legal limits for human consumption.

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.

Larval and juvenile growth performance of Manila clam hybrids of two full-sib families

In order to determine whether growth performance could be improved by hybridizing full-sib families of Manila clam (Ruditapes philippinarum), crosses between two full-sib families including self and reciprocal crosses were carried out. The effects of heterosis, combining ability and interaction on the growth of shell length were estimated. The results showed that the growth of hybrid larvae was intermediate between parents on days 6 and 9. Heterosis on shell length was observed, which varied at juvenile stage. The cross of ♂A × ♀B (Hp varied between 10.41% and 68.27%) displayed larger heterosis than ♂B × ♀A (Hp varied between 1.89% and 32.33%) did, suggesting that ♂A × ♀B was an ideal hatchery method of improving the growth performance of Manila clam. The variances of general combining ability (GCA), special combining ability (SCA) and interaction (I) were significant in shell length (P < 0.05), indicating that both additive and non-additive genetic factors were important contributors to the growth of larvae and juveniles. The GCA for shell length of ♂A × ♀B was higher than that of ♂B × ♀A at both larval and juvenile stages. This confirmed that the cross between ♂A and ♀B showed great growth in shell length. In summary, the growth of Manila clam seeds could be improved by hybridizing selected parents from large numbers of full-sib families.

High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response

Ruditapes philippinarum, is an economically important marine bivalve species. The ability to cope with low salinity stress is quite important for the survival of aquatic species under natural conditions. In this study, the transcriptional response of the Manila clam to low salinity stress was characterized using RNA sequencing. The transcriptomes of a low salinity-treatment group (FRp1, FRp2), which survived under low salinity stress, and control group (SRp1, SRp2), which was not subjected to low salinity stress, were sequenced with the Illumina HiSeq platform. A total of 196,578 unigenes were generated. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under low salinity stress. All these pathways could be assigned to the following biological functions in the low salinity tolerant Manila clam: signal response to low salinity stress, antioxidant response, intracellular free amino acid transport and metabolism, energy production and conversion, cell signaling pathways, and regulation of ionic content and cell volume. In summary, this is the first study using high-throughput sequencing to identify gene targets that could explain osmotic regulation mechanisms under salinity stress in R. philippinarum.

Genetic Variation and Differentiation in Wild and Selected Manila Clam Inferred from Microsatellite Loci

ABSTRACT Manila clam is widely distributed and cultured along the coasts of China. To assess genetic variation in selected strains cultured in China, four selected strains or populations, zebra (Z), white (W), orange (O), and white zebra (WZ), along with one wild population from Lvshun were analyzed with 10 microsatellite loci. The observed heterozygosity ranged from 0.335–0.538 across populations. The highest expected heterozygosity value was detected in the Z strain (0.716), whereas the lowest value was found in the WZ strain (0.578). FST revealed significant differentiation between all pairs of populations. The differentiation between the W strain and the O strain is the lowest (FST = 0.086). whereas the differentiation between Z and WZ strains was the highest (FST = 0.337). There was no significant reduction in heterozygosity in all four selected strains; however, the number of alleles per locus was considerably lower in the selected strains than in the wild population. These results provide valuable genetic information for the preservation, management, and further selective breeding of the Manila clam.

Publisher Correction: Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

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Inbreeding depression on growth and survival of full-sib family of Manila clam (Ruditapes philippinarum)

In present study, the inbreeding depression (ID) of growth and survival of Manila clam (Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families (A2, B2, C2, D2, E2, F2, G2, H2 and I2) were established by mating within nine full-sib families with expected inbreeding coefficient of 0.25. Inbred families showed significant differences in shell length and hatching rate of D-larvae (straight-hinged larvae). The larvae of the nine inbred families grew slower than those of control group (CG), and their ID value ranged from 0.81% ± 6.09% to 16.10% ± 1.49%. The ID value of larval survival rate varied between 27.47% ± 9.36% and 70.50% ± 13.66%. The ID was also detected for juvenile growth in A2, B2, C2, and D2, which ranged from 4.60 ± 2.21 to 17.71 ± 7.73. The A2 family maintained the highest juvenile survival rate, whereas the other inbred families exhibited ID values varying between 62.79% ± 4.54% and 96.14% ± 0.87%. The linear relationship of estimated ID between growth and survival was negatively correlated (R = −0.434, P < 0.05). The results of this study suggested that the ID of growth was common at the larval stage but was less prevalent at juvenile stage. In contrast, the ID of survival increased from larval to juvenile stage. A better understanding of the effect of inbreeding may aid to selective breeding of Manila clam.

Effect of substrate component on the growth and survival of juvenile sunray surf clam (Mactra chinensis Philippi)

Substrate is a critical environmental factor affecting the activity of bivalves. To examine the effect of the substrate component on the growth and survival of juvenile sunray surf clam (Mactra chinensis Philippi), a series of short-term experiments were conducted using a variety of substrates with different ratios of sand to mud. The experimental group cultured without substrate showed poor survival, with all juveniles died after day 20. The juveniles cultured in mud without sand showed a lower survival rate (25.54% ± 0.40% on day 45) than those in other groups. The juveniles cultured in sand without mud, or the mixtures of sand and mud with a ratio of 1:1 and 2:1, respectively, exhibited modest survival at day 45. Maximal weight gain rate (WGR), shell length growth rate (LGR), and specific growth rate (SGR) were observed when the sand concentration was 61.97%, 77.69%, and 64.64%, respectively. As the fast growth and high survival were observed when the sand to mud ratio was 1:1 (50% sand) and 2:1 (67% sand), a sand concentration of more than 50% is optimal. The optimal concentration of sand in the substrate for rearing juvenile sunray surf clams was 67% which resulted in the fastest growth and highest survival. These results can be used to developing a nursery/farming technique of improving the yield of sunray surf clams.

Growth performance of larval and juvenile manila clam (Ruditapes philippinarum) from divergently selected individuals of a full-sib family

In this study, the method of divergent selection was employed to test the larval and juvenile growth performance within a full-sib family of Manila clam Ruditapes philippinarum. The 10% largest and 10% smallest clam individuals (on the basis of shell length) of a full-sib family were selected as parents for the fast and slow growing lines, respectively. The difference in shell length was significant among the three lines (fast, control, and slow) tested. The sequence of shell length were fast line > control line > slow line. The responses to selection, realized heritability, and genetic gain were 0.06%–0.81%, 0.04%–0.47% and 0.58%–18.89% in the fast direction, respectively; and were 0.14%–1.27%, 0.08%–0.73%, and 0.31%–49.03% in the slow direction, respectively. The results suggested that there was a large portion of additive genetic variance affecting the growth in the full-sib family. Selection in the fast direction within the full-sib family would greatly improve the growth of R. philippinarum.