Skip to main content
Download PDF

Analysis of protein kinase C (HcPKC) gene expression and single-nucleotide polymorphisms related to inner shell color traits in Hyriopsis cumingii

BMC Genomic Data volume 23, Article number: 71 (2022) Cite this article

Abstract

Background

Protein kinase C (PKC) is a multifunctional serine and PKC can phosphorylate serine residues in the cytoplasmic domain of tyrosinase, thereby regulating the activity of tyrosinase. Activated PKC is bound to the melanosome membrane, and unactivated PKC is free in the cytoplasm of melanocytes. In this study, we study the role of PKC gene in the melanin synthesis pathway and its effect on the color of the nacre of H. cumingii.

Results

In this study, a HcPKC gene in H. cumingii was cloned and its effects on melanin synthesis and nacre color were studied. HcPKC was expressed in both purple and white mussels, and the level of mRNA expression was higher in the purple mussels than in white mussels. Strong and specific mRNA signals were detected in the dorsal epithelial cells of the mantle pallial layer, indicating that HcPKC may be involved in nacre formation. After SNP association with inner shell color related traits, according to the principle that 0.25 < PIC < 0.5 is medium polymorphism and PIC < 0.25 is low polymorphism, the A + 332G site on the HcPKC gene was a site of moderate polymorphism, and the other four sites were low polymorphism sex sites. There was strong linkage disequilibrium among the five loci. A haplotype was constructed and it was found that the frequency of T1 (AGGAA)in the white population was significantly higher than that in the purple population (P < 0.05).

Conclusion

The study found that HcPKC of H. cumingii can be used as a candidate gene related to inner shell color, and some of the SNP sites can be used for molecular-assisted breeding in the spinnaker mussel, providing a reference for cultivating high-quality freshwater pearls.

Peer Review reports

Background

Hyriopsis cumingii is a unique freshwater mussel in China, which can cultivate high-quality pearls [1]. Mussels of this species produce pearls of high quality in terms of color, luster, and shape [2]. The freshwater pearls produced by purple H. cumingii have a very high economic value [3]. Recently, due to overexploitation, habitat loss, and environmental pollution, wild populations have declined significantly and are facing local extinction [2]. Therefore, the need to harvest high-quality freshwater pearls artificially is imminent. However, there are few relevant studies on the mechanisms involved in the formation of shell nacre color, but it is still in its infancy. Studies have shown that in addition to environmental factors, the color of pearls is also affected by the donor and recipient mussels [4]. Some studies suggest that some metal ions can also affect the formation of pearl color [5, 6], and other studies show that pearl color is related to organic pigments, such as porphyrin [7], carotenoids [8], and melanin [9,10,11], which produce pearls of different colors.

Protein kinase C (PKC) is a lipid- and Ca2+-dependent serine/threonine kinase consisting of a single polypeptide chain [12]. Because the structure of each subtype has a certain conservation and specificity, the functions of the subtypes are also diverse [13]. PKC widely exists in animal tissues and cells, is the main mediator of signal transduction pathway, and also plays a role that cannot be underestimated in physiological processes such as cell proliferation and differentiation [14]. In the melanin metabolism pathway, PKC activates the tyrosinase by phosphorylation of its two serine residues [15]. Activated PKC is bound to the melanosome membrane, and unactivated PKC is free in the cytoplasm of melanocytes [16]. The physiological activation of PKC reportedly stimulates melanin production [17], whereas the inhibition of PKC activity or depletion of cellular PKC has been shown to inhibit melanin synthesis [18]. Park et al. [19] paired cultures of primary human melanocytes treated with PKC inhibitors, found that the PKC inhibitor bisindolylmaleimide can reduce skin pigmentation, and demonstrated that the inhibition of PKC-β activity can reduce pigmentation. Jung et al. [20] found that syndecan- 2 overexpression increased the membrane localization of PKCbΙΙ, and that activated PKCbΙΙ associates with the melanosome through RACK1 to regulate melanogenesis.

In this study, a PKC gene (HcPKC) was identified in H. cumingii, and its full length was cloned. The expression level of the HcPKC gene was detected in different tissues. In situ hybridization was used to detect the distribution of mRNA expression in the mantle. Single-nucleotide polymorphism (SNP) mutation sites were detected in H. cumingii using HcPKC as a candidate gene and correlation analysis was performed with color traits. The molecular markers related to the color traits of the shell nacre were screened and then H. cumingii were selected. This selection and breeding process provides basic data for further research.

Results

Full-length and sequence analysis of HcPKC gene

The full length of the HcPKC (GenBank accession MW241548) gene was obtained by 3′ and 5′ RACE cloning. The HcPKC gene sequence is 2134 bp in total, of which the 5′-UTR was 12 bp, the 3′-UTR was 1246 bp, and the ORF was 876 bp long, encoding a total of 291 amino acidsThe molecular weight of the mature protein corresponding to the amino acid sequence was 117.04 kDa, and the isoelectric point was calculated as 4.73. S_TKc and S_TK_X domains typical of serine- and threonine-specific kinase families were found. No signal peptide was found (Fig. 1).

Fig. 1
figure 1

cDNA sequence analysis of the HcPKC gene in H. cumingii. The shaded part is the domain. The start codon, stop codon, and the poly-A tail are underlined. The shaded part of yellow represents S_TKc domains typical of serine- and threonine-specific kinase families. The green shaded part represents S_TK_X domains typical of serine- and threonine-specific kinase families

Full size image

Quantitative gene expression analysis

The relative expression of the HcPKC gene in purple and white mussels was detected by qPCR. As shown in Fig. 2, the expression of HcPKC in purple mussels was higher than that in white mussels, with an extremely significant difference in the marginal membrane (P < 0.01), and no significant difference in other tissues. In purple mussels, the highest expression was in the marginal membrane, and it was significantly different from other tissues (P < 0.05). In the white mussel, the highest expression was in the adductor muscle, but there was no significant difference between the tissues.

Fig. 2
figure 2

Relative expression level of HcPKC. The relative expression level of PKC in various tissues of purple (A) and white (B) mussels. Comparison of PKC expression in white and purple mussels (C). H: hepatopancreas, G: gill, AM: adductor muscle, F: foot. PM: marginal membrane, MC: central membrane. Data from the qPCR experiments are expressed as the means ± SD (n = 6). Bars with different letters indicate significant differences (p < 0.05). ** represents a highly significant difference at P < 0.01

Full size image

In situ hybridization results

The location of the specific expression of the HcPKC gene in the mantle tissue was determined by in situ hybridization. The results are shown in Fig. 3, The positive hybridization signal mainly appeared in the dorsal membrane epithelial cells of the outer fold of the mantle (arrow in Fig. 3 A), and no obvious signal was seen in other parts. No positive signal was detected in the negative control group.

Fig. 3
figure 3

In situ hybridization analysis of HcPKC in the mantle (A), the arrow indicates the position of the hybridization signal. B is a higher magnification of A, C is background. IF, inner fold; MF, middle fold; OF, outer fold

Full size image

SNP site screening

The samples were amplified with the designed primers, and a total of five SNP sites were found in the amplified fragments. Starting from the ATG start codon, each SNP site is named by the number of bases from the mutation site to the start codon.

Polymorphism analysis

The HcPKC gene was amplified and sequenced from 70 purple mussels and 70 white mussels to screen for the SNP loci. The polymorphic genetic parameters of the five SNP loci of the HcPKC gene obtained after the sequencing results were analyzed by software (Table 1). Their observed heterozygosity was in the range of 0.0143–0.0929, the expected heterozygosity was in the range of 0.0624–0.3254, the polymorphic information content(PIC) was in the range of 0.060–0.272, and the effective number of alleles was in the range of 1.0663–1.4799. A 0.25 < PIC < 0.5 was considered moderate polymorphism and PIC < 0.25 was considered low polymorphism, the A + 332G site on the HcPKC gene was a site of moderate polymorphism, and the other four sites were low polymorphism locus.

Table 1 The polymorphic parameters of five SNP sites in the HcPKC gene
Full size table

Association analysis between the SNP loci of the HcPKC gene and inner shell color traits

The genotypes of the SNPs found on the HcPKC gene were correlated with the inner shell color traits (L, a, b, and dE) of 140 mussels (Table 2). The results showed that among the five SNPs in the HcPKC gene, there was no significant difference between the genotypes of the three loci A + 87 T, G + 145 T, and A + 328G, and the parameters of the four inner shell color traits. The genotypes of the G + 217 T locus had significant differences in b and dE parameters (P < 0.05) and the genotypes of the A + 332G loci had significant differences in L, b and a, dE parameters (P < 0.05).

Table 2 Association of the five SNP sites of HcPKC polymorphisms with nacre color
Full size table

Linkage disequilibrium and haplotype analysis of the SNP loci in the HcPKC gene

Linkage disequilibrium analysis was performed on the five SNP loci (Table 3), and it was found that there was a strong linkage disequilibrium between all the loci (D' > 0.75, r2 > 0.33). After haplotype construction (Table 4), it was found that T1 appeared more frequently in the white population than in the purple cultivar.

Table 3 Linkage disequilibrium analysis of the five SNP sites of the HcPKC gene
Full size table
Table 4 Haplotype analysis of the five SNP sites of the HcPKC gene
Full size table

Discussion

In this study, a HcPKC gene was fully cloned in H. cumingii and investigated for the first time. The tissue quantification results showed that the expression level of HcPKC in the marginal membrane of purple mussels was significantly higher than that of other tissues (p < 0.05). Relevant studies have shown that the outer fold of the mantle is directly involved in the formation of shell nacre [21, 22]. Protein kinase C not only plays a role in the process of melanin synthesis, but also plays a role in other physiological activities, such as nerve and immunity [23], the specific location of HcPKC expression in the mantle tissue was determined by in situ hybridization, and a positive hybridization signal mainly appeared in the mantle. The results from the dorsal membrane epithelial cells at the outer fold suggest that HcPKC may be involved in the formation of the nacre in H. cumingii [24]. Further comparative analysis found a higher expression of HcPKC in the tissues of purple mussels than in those of white mussels, and there was a very significant difference in the marginal membrane (p < 0.01). Luo et al. [25] found similar results in the phenotypic difference of the HcCUBDC gene in white and purple H. cumingii, this indicates that the HcPKC gene may have a positive effect on the formation of purple nacre.

Studies have shown that the color of shells is heritable [26], and the inner shell color is a breeding target that can improve breeding efficiency [27]. The addition of small pieces of mantle with different inner shell colors will have a significant impact on the color of the pearls produced [28, 29]. Compared with traditional breeding methods, molecular marker-assisted breeding as an emerging breeding method can greatly improve breeding efficiency [30] and has been studied in a variety of aquatic animals [31,32,33]. In this experiment, primers were designed using the known full-length cDNA sequence of PKC in the H. cumingii. After primer amplification and sequencing, five SNP sites were found in the exons of the HcPKC gene, which was significantly higher than the 1SNP/1000 bp in the previous study [34]. This indicates that there are relatively abundant single nucleotide polymorphisms in the HcPKC gene. According to the polymorphism analysis, it was found that in the HcPKC gene, the A + 332G site is a moderate polymorphism site, and the other four sites are low polymorphism sites, but no high polymorphism was found in this gene. This is because SNP markers are DNA sequence polymorphisms caused by single nucleotide variation, and it is difficult to show higher polymorphisms such as in Simple Sequence Repeat (SSR) markers [35]. Preliminary analysis of the SNP correlation between the purple and white inner shell color of the spinnaker mussels and the HcPKC gene showed that the genotypes of the G + 217 T locus had significant differences in b and dE parameters (P < 0.05), A + 332G. The genotypes of the loci were significantly different in L, b and a, dE parameters (P < 0.05). It is speculated that this gene may play a certain role in the formation of nacre color in the H. cumingii [36, 37]. Due to the limitation of the number of samples, this experiment can explain the problem to a certain extent, and subsequent experiments need to further expand the sample size to verify the results of this study.

To further investigate whether the polymorphism of the HcPKC gene is associated with nacre color traits, we analyzed linkage disequilibrium [38] and haplotype analysis [39]. The results showed that among the haplotypes constructed by the HcPKC gene, therefore, the dominant type can be selected according to demand to speed up breeding efficiency and provide a reference for the rapid selection of the target shell color [40].

Conclusions

In this study, a HcPKC gene was fully cloned in H. cumingii and investigated for the first time. Validation of the effect of HcPKC gene on shell nacre by fluorescence quantification, in situ hybridization experiments, and discovery of single-nucleotide polymorphisms (SNPs) associated with inner shell color-related traits that HcPKC of H. cumingii can be used as a candidate gene related to inner shell color, and some of the SNP sites can be used for molecular-assisted breeding in the spinnaker mussel, providing a reference for cultivating high-quality freshwater pearls.

Methods

Ethical approval statement

H. cumingii were treated according to animal care and use guidelines for scientific purposes established by the Institutional Animal Care and Use Committee of Shanghai Ocean University, Shanghai, China.

Experimental materials

Two-year-old healthy H. cumingii mussels (average shell length of 10 cm) with purple and white inner-shell colors were obtained from Weimin Aquaculture Base, Jinhua City, Zhejiang Province, China (Fig. 4). Before the experiment, the mussels were placed in a laboratory water tank for oxygenation for about a week, and then fresh mantle samples were stored at − 80 °C for later use.

Fig. 4
figure 4

Purple (left) and white (right) H.cumingii mussels used in the experiment

Full size image

Experimental method

Total RNA extraction and cloning of the full-length HcPKC

The TRIzol method was used to extract total RNA from healthy mantle tissue samples. The SMARTer RACE 5′/3′ kit was used to synthesize RACE-Ready cDNA as a gene cloning template. Specific primers (Table 5) were designed based on the HcPKC (HcPKC-F and HcPKC-R) expressed sequence tags (ESTs) of H. cumingii which were obtained from the H. cumingii mantle transcriptome library [41]. The PKC gene fragment was obtained from a mantle transcriptome library of H. cumingii (Table 5), and the specific primers were designed by Primer 5.0 to perform PCR amplification and verify the sequence. According to the SMARTer RACE 5′/3′ kit instructions, 5′-RACE and 3′-RACE specific primers were designed, RACE cloning was performed, and the DNA was sequenced by Sangon (Shanghai, China) to obtain the full-length PKC gene.

Table 5 Primers used in the study
Full size table

Gene sequence analysis

ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) was used to predict the ORF (open reading frame) of the HcPKC gene sequence and the encoded amino acid sequence [42]. Smart Blast was used to predict amino acid sequence homology analysis [43]. The amino acid inclusion domains were analyzed by Simple Modular Architecture Research Tool SMART (http://smart.embl-heidelberg.de/). The Protparam online tool (https://www.expasy.org/) was used to obtain information on physical parameters such as amino acid sequence composition, molecular weight, isoelectric point, etc. [44]. ClustalX software was used for multiple sequence alignment analysis [45] and MEGA 5.2 (Arizona State University, USA) was used to construct a phylogenetic tree [46].

Tissue-specific expression analysis of the HcPKC gene

Hepatopancreas, gill, adductor muscle, foot, marginal membrane, central membrane samples were taken from six healthy H. cumingii individuals and were used for RNA extraction. The RNA was then reverse-transcribed to cDNA by using SYBR®Premix Ex Taq II (TliRNaseH Plus, TaKaRa). Bio-Rad-CFX-96 (Bio-Rad, USA) was used for fluorescence quantitative PCR. The PCR reaction mixture was as follows: SYBR®Premix Ex Taq II (TliRNaseH Plus), 10 μL; upstream and downstream primers, 0.8 μL; ddH2O, 6.8 μL and cDNA template 1.6 µL. Each reaction was performed in three replicates. The reaction parameters were: pre-denaturation at 95 °C for 30 s; followed by 40 cycles of 95 °C for 5 s; 56 °C for 35 s; and 72 °C for 30 s. Referring to the previous research results of our laboratory, EF1α was used as an internal reference gene [47] (Table 5).

In situ hybridization

Specific primers were designed and the T7 promoter sequence TAATACGACTCACTATAGGG (Table 5) was added at the 5′ end. The target fragment was obtained after PCR amplification and product purification, and in vitro transcription was performed using a Complete Gold in vitro transcription kit. The fresh mantle tissue of the mussel was placed in 4% paraformaldehyde to fix and dehydrate for 4 h (in a 4 °C refrigerator), then placed in 25% sucrose solution at 4 °C overnight. The tissue was cut into ~ 10 μm sections. They were marked and stored on glass slides at − 80 °C for later use. Follow-up in situ hybridization experiments were performed later.

Extraction of genomic DNA

For SNP experiments, 70 white mussels and 70 purple mussels were selected randomly. The genomic DNA of the experimental samples was extracted using a TIANamp Marine Animals DNA Kit and coagulated with 1% agarose. The quality of DNA was detected by gel electrophoresis and a NanoDrop 2000C spectrophotometer, and the samples were placed in a − 20 °C refrigerator for later use.

Data measurement

Using a Lovibond-RT200 surface colorimeter to measure the inner shell color of purple and white experimental mussels, and according to the uniform color space determined by the International Commission on Illumination (CIE), L* represents the brightness. L* > 0 indicated that the color was bright, L* < 0, darker color; a* > 0, redder color, a* < 0, greener color; b* > 0, yellowish color, and b* < 0, bluer color [48]. The anterior, middle, and posterior margins of the right shell of 140 mussels were measured, and the difference in the color parameter was calculated as follows: dE = (L2 + a2 + b2)½, L = Lx-L0, a = ax-a0, b = bx-b0. Lx, ax, and bx are the color parameter values of different shells. L0, a0, and b0 are the color parameters of standard white inner shell mussels and ML, Ma, Mb, and MdE represent the average value of L, a, b, and dE.

Screening of SNP loci in the HcPKC gene of H. cumingii

The HcPKC gene was compared with the PKC gene in the genome of the H. cumingii to determine the exon and intron regions. Primers specific to exonic regions were designed (Table 6). The DNA samples of 10 white mussels and 10 purple mussels were selected randomly for sequence amplification, and the amplified products were sent to MAP BIOTECH (Shanghai) for sequencing. Sequence 5.4.6 was used to obtain the SNP site from the compared sequencing results.

Table 6 The primers of SNP in the HcPKC gene of H. cumingii
Full size table

Data analysis

Genetic parameters such as observed heterozygosity, expected heterozygosity, and polymorphism content were analyzed using Popgene software [49]. The chi-square test was performed using SPSS software to analyze the correlation between the genotypes of different SNPs in the HcPKC gene fragment and the inner shell color of the mussels [50]. Analysis of linkage disequilibrium and haplotype construction with SHEsis online software (http://analysis.bio-x.cn/) [51, 52].

Statistical analysis

Data are shown as the mean ± SD and was analysed using SPSS 17.0 software. Differences were recognized as significant when p < 0.05 and highly significant when p < 0.01.

Availability of data and materials

All data generated during this study are included in this published article.

Abbreviations

PKC:

Protein kinase C

SNP:

Single-nucleotide polymorphisms

H. cumingii:

Hyriopsis cumingii

HcPKC:

A PKC gene in Hyriopsis cumingii

References

  1. Li J, Li Y: Aquaculture in China--freshwater pearl culture. World Aquaculture 2009, 41(60).

  2. Bai Z, Luo M, Zhu W, Lin J, Wang G, Li J. Multiple paternity in the freshwater pearl mussel Hyriopsis cumingii (Lea, 1852). J Molluscan Stud. 2011;78(1):142–6.

    Article  Google Scholar 

  3. Hu H, Sun C, Bai Z, Li J. Genotype by environment interactions for inner shell color and growth traits in the purple freshwater pearl mussel, Hyriopsis cumingii, reared with different water depths and mud substrates. Aquaculture. 2021;531: 735942.

    Article  CAS  Google Scholar 

  4. Jiale L, Yue L. The main influencing factors on the quality of cultured pearls. J Fish China. 2011;35(11):1753–60.

    Google Scholar 

  5. Xueying L, Haizeng W, Shengli S, Jibiao Z. Analysis on Fourier Transform Infrared and Graphite Furnace Atomic Absorption Spectrometry of Pearls with Different Colours. J Gem Gemmol. 2007;01:15–8.

    Google Scholar 

  6. Genfang Z, Ronghui Y, Aiping F. Research Progress about the Color of Pearl and Shell Nacre. Chin J Zool. 2014;49(01):137–44.

    Google Scholar 

  7. Yuntao Z: The contribution of porphyrin and metalloporphyrin to the color of Pearl and its mechanism. China University of Geosciences 2006.

  8. Jinpan Z, Zhiyi B, Mengying Z, Ling Y, Fenghui L, He W. Functional analysis and SNP screening of lysophosphaticly lcholine acyltransferase 1 HcLPCAT1 gene and its association analysis with shell color traits in Hyriopsis cumingii. J Fish Sci China. 2021;28(11):1373–84.

    Google Scholar 

  9. Zhang M, Chen X, Zhang J, Li J, Bai Z. Cloning of a HcCreb gene and analysis of its effects on nacre color and melanin synthesis in Hyriopsis cumingii. PLoS ONE. 2021;16(5): e0251452.

    Article  CAS  Google Scholar 

  10. Chen X, Liu X, Bai Z, Zhao L, Li J. HcTyr and HcTyp-1 of Hyriopsis cumingii, novel tyrosinase and tyrosinase-related protein genes involved in nacre color formation. Comp Biochem Physiol B: Biochem Mol Biol. 2017;204:1–8.

    Article  CAS  Google Scholar 

  11. Shen J, Huang D, Sun C, Li J, Bai Z. Cloning of a microphthalmia-associated transcription factor gene and its functional analysis in nacre formation and melanin synthesis in Hyriopsis cumingii. Aquaculture and Fisheries. 2018;3(6):217–24.

    Article  Google Scholar 

  12. Azzi A, Boscoboinik D, Hensey C. The protein kinase C family. Eur J Biochem. 1992;208(3):547–57.

    Article  CAS  Google Scholar 

  13. Olive MF, Messing RO. Protein kinase C isozymes and addiction. Mol Neurobiol. 2004;29(2):139–53.

    Article  CAS  Google Scholar 

  14. Qiang D, Dingxin L: Research progress of protein kinase C. 1013488/jsmhx20180314 2018, 38(03).

  15. Lee DW, Kim HJ, Choi CH, Shin JH, Kim EK. Development of a Protein Chip to Measure PKC beta Activity. Applied Biochemistry And Biotechnology. 2011;163(6):803–12.

    Article  CAS  Google Scholar 

  16. Zhang J. Advances in the research of melanogenesis-related proteins. Henan Medical Research. 2009;18(3):257–61.

    Google Scholar 

  17. Allan AE, Archambault M, Messana E, Gilchrest BA. Topically Applied Diacylglycerols Increase Pigmentation in Guinea Pig Skin. J Investig Dermatol. 1995;105(5):687–92.

    Article  CAS  Google Scholar 

  18. Ando H, Oka M, Ichihashi M, Mishima Y. Protein kinase C activators inhibit melanogenesis in B16 melanoma cells. J Dermatol Sci. 1990;1(3):228.

    Article  Google Scholar 

  19. Park H-Y, Lee J, Kapasi S, Peterson S, Gilchrest BA, González S, Middelkamp-Hup MA. Topical Application of a Protein Kinase C Inhibitor Reduces Skin and Hair Pigmentation. J Investig Dermatol. 2004;122(1):159–66.

    Article  CAS  Google Scholar 

  20. Jung H, Chung H, Chang SE, Choi S, Oh ES: Syndecan‐2 regulates melanin synthesis via protein kinase C βII‐mediated tyrosinase activation. Pigment Cell Melanoma Res 2014, 27(3).

  21. Liu X, Dong S, Jin C, Bai Z, Wang G: Silkmapin of Hyriopsis cumingii, a novel silk-like shell matrix protein involved in nacre formation. Gene 2014, 555.

  22. Zhang C, Xie L, Huang J, Chen L, Zhang R. A novel putative tyrosinase involved in periostracum formation from the pearl oyster (Pinctada fucata). Biochem Biophys Res Commun. 2006;342(2):632–9.

    Article  CAS  Google Scholar 

  23. Oka M, Kikkawa U. Protein kinase C in melanoma. Cancer And Metastasis Reviews. 2005;24(2):287–300.

    Article  CAS  Google Scholar 

  24. Chen X, Liu X, Bai Z, Zhao L, Li J: HcTyr and HcTyp-1 of Hyriopsis cumingii , novel tyrosinase and tyrosinase-related protein genes involved in nacre color formation. Comparative Biochemistry and Physiology, Part B 2017, 204.

  25. Hongrui L, Zhiyi B, Xiaojun L, Qingqing L, Shaojian D, Shimei Z, Jiale L. Full-length c DNA cloning and expression analysis of Hc CUBDC gene from Hyriopsis cumingii. J  Fish China. 2015;39(09):1313–23.

    Google Scholar 

  26. Jerry D, Kvingedal R, Lind C, Evans B, Taylor J, Safari A. Donor-oyster derived heritability estimates and the effect of genotype × environment interaction on the production of pearl quality traits in the silver-lip pearl oyster. Pinctada maxima Aquaculture. 2012;338–341:66–71.

    Article  Google Scholar 

  27. Zhaoqi W, Xuekai H, Zhiyi B, Jiale L. Estimates of genetic parameters for inner shell color and growth straits during one year old stage in the purple strain of Hyriopsis cumingii using microsatellite based parentage assignment. J Fish China. 2014;38(05):644–50.

    Google Scholar 

  28. Jebelli A, Khalaj-Kondori M, Bonyadi M, Feizi MAH, Rahmati-Yamchi M. Beta-Boswellic Acid and Ethanolic Extract of Olibanum Regulating the Expression Levels of CREB-1 and CREB-2 Genes. Iran J Pharm Res. 2019;18(2):877–86.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Qingqing L, Zhiyi B, Xiaojun L, Xuekai H, Hongrui L, Shaojian D, Jiale L. Correlation analysis of non-nucleated pearl quality parameters with growth traits and inner shell color of Hyriopsis cumingii. J Fish China. 2015;39(11):1631–9.

    Google Scholar 

  30. Cuiyun L, Youyi K, Xianhu Z, Chao L, Xiaowen S. Advances of molecular marker-assisted breeding for aquatic species. J Fish China. 2019;43(01):36–53.

    Google Scholar 

  31. Xuekai H, Xiajun C, Zhiyi B, Xiaojun L, Jiale L. Detection of shell nacre colour-related SNP and gene mapping of HcTyr gene in Hyriopsis cumingii. J Fish China. 2017;41(07):1044–53.

    Google Scholar 

  32. Xiajun C, Xuekai H, Zhiyi B, Jiale L. Detection of nacre colour-related SNPs and genetic mapping of HcTyp-1 gene in Hyriopsis cumingii. J Fish China. 2019;43(02):467–73.

    Google Scholar 

  33. Chao L: Screening and SNP analysis on carotenoid metabolism related genes in Pinctada fucata martensii. Guangdong Ocean University; 2018.

  34. Vignal A, Milan D, SanCristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol. 2002;34(3):275–305.

    Article  CAS  Google Scholar 

  35. Hubert S, Bussey JT, Higgins B, Curtis BA, Bowman S. Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences. Aquaculture. 2009;296(1–2):7–14.

    Article  CAS  Google Scholar 

  36. Mengying Z, Xiajun C, Jinpan Z, Jiale L, Zhiyi B. Cloning of a HcCreb gene and analysis of its effects on nacre color and melanin synthesis in Hyriopsis cumingii. PloS One. 2021;16(5):e0251452.

    Article  Google Scholar 

  37. Li X, Bai Z, Luo H, Liu Y, Wang G, Li J. Cloning, differential tissue expression of a novel hcApo gene, and its correlation with total carotenoid content in purple and white inner-shell color pearl mussel Hyriopsis cumingii. Gene. 2014;538(2):258–65.

    Article  CAS  Google Scholar 

  38. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001;29(2):229–32.

    Article  CAS  Google Scholar 

  39. Clark AG. The role of haplotypes in candidate gene studies. Genet Epidemiol. 2004;27(4):321–33.

    Article  Google Scholar 

  40. Fuping L, Junjie B. Single nucleotide polymorphisms and its application in genetic breeding of aquatic animals. J Fish Sci China. 2008;04:704–12.

    Google Scholar 

  41. Bai ZY, Zheng HF, Lin JY, Wang GL, Li J. Comparative Analysis of the Transcriptome in Tissues Secreting Purple and White Nacre in the Pearl Mussel Hyriopsis cumingii. PLOS ONE. 2013;8(1):e53617.

    Article  CAS  Google Scholar 

  42. Rong OU: A New PubMed Search Tool——NCBI Search Toolbar and Its Applications. Researches in Medical Education 2006.

  43. Ivica L, Tobias D, Peer B. SMART: recent updates, new developments and status in 2015. Nuclc Acids Research. 2015;D1:257–60.

    Google Scholar 

  44. Gasteiger E, Hoogland C, Gattiker A, Duvaud SE, Wilkins MR, Appel RD, Bairoch A: Protein Identification and Analysis Tools on the ExPASy Server. 1999.

  45. J D T: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research 1997, 24(25).

  46. Kumar S, Nei M, Dudley J, Tamura K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9(4):299–306.

    Article  CAS  Google Scholar 

  47. Zhiyi, Bai, Jingyun, Lin, Keyi, Ma, Guiling, Wang, Donghong, Niu: Identification of housekeeping genes suitable for gene expression analysis in the pearl mussel, Hyriopsis cumingii, during biomineralization. Molecular Genetics & Genomics 2014.

  48. Hunt R: The Specification of Colour Appearance. II. Effects of Changes in Viewing Conditions. Color Research & Application 2007, 2:109–120.

  49. Francis CY, Rong CY, Boyle T: POPGENE, Microsoft Window-based freeware for population genetic analysis. University of Alberta 1999:1–31.

  50. Shanzhao Y: SPSS statistical software application basis: SPSS statistical software application basis; 2001.

  51. YonYon Sh, n H: SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Research 2006.

  52. Li ZQ, Zhang Z, He ZD, Tang W, Li T, Zeng Z, He L, Shi YY: A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis (http://analysis.bio-x.cn). Cell Research 2009, 19(4):519–523.

Download references

Acknowledgements

We thank International Science Editing (http://www.internationalscienceediting.com) for editing this manuscript.

Funding

This study was supported by the National Natural Science Foundation of China (31872565), the China Agriculture Research System of MOF and MARA, the National Key R&D Program of China (2018YFD0901406), and the Sponsored by Program of Shanghai Academic Research Leader (19XD1421500). The above funds are all provided by Zhiyi Bai.

Author information

Author notes

  1. Mengying Zhang and Xiajun Chen contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China

    Mengying Zhang, Xiajun Chen, Jinpan Zhang, Baiying Guo, Jiale Li & Zhiyi Bai

  2. Shanghai Collaborative Innovation Center of Aquatic Animal Breeding and Green Aquaculture, Shanghai Ocean University, Shanghai 201306, China

    Mengying Zhang, Xiajun Chen, Jinpan Zhang, Baiying Guo, Jiale Li & Zhiyi Bai

  3. Fisher Institute of Anhui Academy of Agricultural Sciences, Hefei, China

    Xiajun Chen

  4. Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China

    Jiale Li & Zhiyi Bai

Authors
  1. Mengying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiajun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jinpan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Baiying Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jiale Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhiyi Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MYZ, ZYB designed the experiments. MYZ, JPZ, XJC and BYG carried out the experiments. XJC, JLL and ZYB conducted the statistical analysis and discussion. MYZ and ZYB organized and wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Zhiyi Bai.

Ethics declarations

Ethics approval and consent to participate

H. cumingii were treated according to animal care and use guidelines for scientific purposes established by the Institutional Animal Care and Use Committee of Shanghai Ocean University, Shanghai, China.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, M., Chen, X., Zhang, J. et al. Analysis of protein kinase C (HcPKC) gene expression and single-nucleotide polymorphisms related to inner shell color traits in Hyriopsis cumingii. BMC Genom Data 23, 71 (2022). https://doi.org/10.1186/s12863-022-01085-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12863-022-01085-3

Keywords

BMC Genomic Data

ISSN: 2730-6844

Contact us