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A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis)

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Abstract

To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.

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References

  • Anderson LK, Naser S, Bass HW, Harper LC, Cande WZ, Gerd W, Stack SM (2004) Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics 166(4):1923–1933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Budiman MA, Chang S, Lee S, Yang T, Zhang H, Jong H, Wing RA (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108(2):190–196

    Article  CAS  PubMed  Google Scholar 

  • Dong G, Shen J, Zhang Q, Wang J, Yu Q, Ming R, Wang K, Zhang J (2018) Development and applications of chromosome-specific cytogenetic BAC-FISH probes in S. spontaneum. Front Plant Sci 9:218–218

    Article  PubMed  PubMed Central  Google Scholar 

  • Feng L, Hu L, Fu X, Liao H, Li X, Zhan A, Zhang L, Wang S, Huang X, Bao Z (2014) An integrated genetic and cytogenetic map for Zhikong scallop, Chlamys farreri, based on microsatellite markers. PLoS One 9(4):e92567

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guo X, Luo Y (2016) Scallops and scallop aquaculture in China. In Shumway S E (ed) Scallops: Biology, Ecology, Aquaculture, and Fisheries, 3rd edn. Elsevier, Amsterdam

    Chapter  Google Scholar 

  • Guo X, Wang Y, Xu Z (2007) Genomic analyses using fluorescence in situ hybridization. Aquac Genome Technol 289:311

    Google Scholar 

  • Guyon R, Rakotomanga M, Azzouzi N, Coutanceau JP, Bonillo C, D’Cotta H, Pepey E, Soler L, Rodier-Goud M, D’Hont A (2012) A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics 13(1):222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hou R, Bao Z, Wang S, Su H, Li Y, Du H, Hu J, Wang S, Hu X (2011) Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One 6(6):e21560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang X, Hu J, Hu X, Zhang C, Zhang L, Wang S, Lu W, Bao Z (2007a) Cytogenetic characterization of the bay scallop, Argopecten irradians irradians, by multiple staining techniques and fluorescence in situ hybridization. Genes Genet Syst 82(3):257–263

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Hu X, Hu J, Zhang L, Shi W, Wei L, Bao Z (2007b) Mapping of ribosomal DNA and (TTAGGG)n telomeric sequence by FISH in the bivalve Patinopecten yessoensis (Jay, 1857). J Molluscan Stud 73(4):393–398

    Article  Google Scholar 

  • Islamfaridi MN, Childs KL, Klein PE, Hodnett G, Menz MA, Klein RR, Rooney WL, Mullet JE, Stelly DM, Price HJ (2002) A molecular cytogenetic map of sorghum chromosome 1. Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes. Genetics 161(1):345–353

    CAS  Google Scholar 

  • Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95

    Article  CAS  PubMed  Google Scholar 

  • Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H, Naruse K, Brenner S (2011) Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol Evol 3:424–442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim JS, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169(2):1169–1173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levan A, Fredga K, Sandberg AA (1964) Nomenclature for centromeric position on chromosomes. Hereditas 52(2):201–220

    Article  Google Scholar 

  • Lewin HA, Larkin DM, Pontius J, O’Brien SJ (2009) Every genome sequence needs a good map. Genome Res 19(11):1925–1928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Yang Z, Liao H, Zhang Z, Huang X, Bao Z (2016) Chromosomal mapping of tandem repeats in the Yesso scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization. Comp Cytogenet 10(1):157–169

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu W, Bao X, Song W, Zhou Z, He C, Yu X (2009) The construction of a preliminary genetic linkage map in the Japanese scallop Mizuhopecten yessoensis. Hereditas 31(6):629–637

    Article  CAS  PubMed  Google Scholar 

  • Phillips RB, Nichols KM, Dekoning JJ, Morasch MR, Keatley KA, Rexroad C, Gahr SA, Danzmann RG, Drew RE, Thorgaard GH (2007) Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 272(3):S299–S300

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1982) Molecular cloning: a laboratory manual. Anal Biochem 186:182–183

    Google Scholar 

  • Sun C, Zhan A, Hui M, Lu W, Hu X, Hu J, Bao Z (2007) Characterization of novel microsatellite markers from the Yesso scallop Mizuhopecten yessoensis. Mol Ecol Notes 7(1):106–108

    Article  CAS  Google Scholar 

  • Taboada X, Pansonato-Alves JC, Foresti F, Martínez P, Viñas A, Pardo BG, Bouza C (2014) Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 123(3):281–291

    Article  PubMed  Google Scholar 

  • Tang X, Boer JM, Eck HJ, Bachem C, Visser RG, Jong H (2009) Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosom Res 17(7):899–915

    Article  CAS  Google Scholar 

  • Wang Y, Guo X (2004) Chromosomal rearrangement in Pectinidae revealed by rRNA loci and implications for bivalve evolution. Biol Bull 207(3):247–256

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Xu Z, Pierce JC, Guo X (2005) Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones. Mar Biotechnol 7(3):207–214

    Article  CAS  Google Scholar 

  • Wang CJR, Harper L, Cande WZ (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18(3):529–544

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang R, Wang Z, Zhang J (2008) Science of marine shellfish culture. Ocean University of China Press, Qingdao

  • Wang X, Hu X, Li J, Li L, Hou R, Wang S, Zhang L, Bao Z (2012) Characterization of 38 EST-derived SNP markers in Zhikong scallop (Chlamys farreri) and their cross-species utility in Yesso scallop (Patinopecten yessoensis). Conserv Genet Resour 4(3):747–753

    Article  Google Scholar 

  • Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, Guo X, Huan P, Dong B, Zhang L (2017) Scallop genome provides insights into evolution of bilaterian karyotype and development. Nat Ecol Evol 1(5):0120

    Article  Google Scholar 

  • Wells DE, Gutierrez L, Xu Z, Krylov V, Macha J, Blankenburg KP, Hitchens M, Bellot LJ, Spivey M, Stemple DL (2011) A genetic map of Xenopus tropicalis. Dev Biol 354(1):1–8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiong Z, Kim JS, Pires JC (2010) Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Cytogenet Genome Res 129(1–3):190–198

    Article  CAS  PubMed  Google Scholar 

  • Xu K, Li Q, Kong L, Yu R (2010) A first-generation genetic map of the Japanese scallop Patinopecten yessoensis-based AFLP and microsatellite markers. Aquac Res 40(1):35–43

    Article  CAS  Google Scholar 

  • Yang Z, Li X, Liao H, Hu L, Zhang Z, Zhao B, Huang X, Bao Z (2016) Physical mapping of immune-related genes in Yesso scallop (Patinopecten yessoensis) using fluorescent in situ hybridization. Comp Cytogenet 10(4):529–541

    Article  PubMed  PubMed Central  Google Scholar 

  • Yoshido A, Bando H, Yasukochi Y, Sahara K (2005) The Bombyx mori karyotype and the assignment of linkage groups. Genetics 170(2):675–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Bao Z, Wang S, Huang X, Hu J (2007) Chromosome rearrangements in Pectinidae (Bivalvia: Pteriomorphia) implied based on chromosomal localization of histone H3 gene in four scallops. Genetica 130(2):193–198

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Bao Z, Wang S, Hu X, Hu J (2008) FISH mapping and identification of Zhikong scallop (Chlamys farreri) chromosomes. Mar Biotechnol 10(2):151–157

    Article  CAS  Google Scholar 

  • Zhang W, Pan J, He H, Zhang C, Li Z, Zhao J, Yuan X, Zhu L, Huang S, Cai R (2012) Construction of a high density integrated genetic map for cucumber (Cucumis sativus L). Theor Appl Genet 124(2):249–259

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Yan G, Yang X, Wong Y, Sun J, Zhang Y, He L, Xu Y, Qian P (2016) Characterization of arginine kinase in the barnacle Amphibalanus amphitrite and its role in the larval settlement. J Exp Zool B Mol Dev Evol 326(4):237–249

    Article  CAS  PubMed  Google Scholar 

  • Zhao L, Lv Y, Cai C, Tong X, Chen X, Zhang W, Du H, Guo X, Guo W (2012) Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. BMC Genomics 13(1):539

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao R, Miao H, Song W, Chen C, Zhang H (2017) Identification of Sesame (Sesamum indicum L) chromosomes using the BAC-FISH system. Plant Biol 20(1):85–92

    Article  PubMed  CAS  Google Scholar 

Download references

Funding

This research was funded by the National Key R&D Program of China (2018YFD0901402 and 2018YFD0900304), the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-49), and the Key Research and Development Program of Shandong Province (2016ZDJQ0208).

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Author notes

  1. Zujing Yang and Xuan Li contributed equally to this work.

Authors and Affiliations

  1. MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China

    Zujing Yang, Xuan Li, Huan Liao, Liping Hu, Cheng Peng, Shenhai Wang, Xiaoting Huang & Zhenmin Bao

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China

    Zujing Yang, Xiaoting Huang & Zhenmin Bao

  3. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands

    Xuan Li

  4. College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China

    Huan Liao

  5. Yantai Fisheries Research Institute, Yantai, China

    Liping Hu

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  1. Zujing Yang
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Correspondence to Xiaoting Huang.

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Fig. S1

SNP-anchored clones covering 9 LGs (LG1, LG2, LG3, LG4, LG5, LG6, LG7, LG8, LG9) mapped on the single pairs of chromosomes. The arrow indicated red signals of clones correspond to digoxigenin-labeled probes located on specific chromosomal pairs. Scale bar = 10um. (PNG 618 kb)

High Resolution Image (TIF 3968 kb)

Fig. S2

SNP-anchored clones covering 6 LGs (LG10, LG11, LG12, LG13, LG14, LG15) mapped on the single pairs of chromosomes. The arrow indicated red signals of clones correspond to digoxigenin-labeled probes located on specific chromosomal pairs. Scale bar = 10um. (PNG 335 kb)

High Resolution Image (TIF 2344 kb)

Fig. S3

SNP-anchored clones covering 4 LGs (LG16, LG17, LG18, LG19) mapped on the single pairs of chromosomes. The arrow indicated red signals of clones correspond to digoxigenin-labeled probes located on specific chromosomal pairs. Scale bar = 10um. (PNG 340 kb)

High Resolution Image (TIF 2575 kb)

Fig. S4

SNP-anchored clones did not produce any significant positive signals. a: the signals of clone distributed in multiple chromosomes. b: clones did not produce signals on chromosomes. c: the signals distributed in at least two pairs of chromosomes. Scale bar = 10um. (PNG 236 kb)

High Resolution Image (TIF 1237 kb)

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Yang, Z., Li, X., Liao, H. et al. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). Mar Biotechnol 21, 731–742 (2019). https://doi.org/10.1007/s10126-019-09918-6

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