Cite this paper:
NIU Sufang, ZHAI Yun, WU Renxie, ZHANG Haoran, TIAN Letian, DENG Jiaxin, XIAO Yao. Isolation and characterization of 49 polymorphic microsatellite loci for Decapterus maruadsi using SLAF-seq, and cross-amplification to related species[J]. HaiyangYuHuZhao, 2019, 37(1): 245-255

Isolation and characterization of 49 polymorphic microsatellite loci for Decapterus maruadsi using SLAF-seq, and cross-amplification to related species

NIU Sufang, ZHAI Yun, WU Renxie, ZHANG Haoran, TIAN Letian, DENG Jiaxin, XIAO Yao
College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
Abstract:
Decapterus maruadsi is a commercially important species in China, but has been heavily exploited in some areas. There is a growing need to develop microsatellites promoting its genetic research for the adequate management of this fishery resources. The recently developed specific-locus amplified fragment sequencing (SLAF-seq) is an efficient and high-resolution method for genome-wide microsatellite markers discovery. In this study, 28 905 microsatellites (mono-to hexa-nucleotide repeats) were identified using SLAF-seq technology, of which di-nucleotide was the most frequent (13 590, 47.02%), followed by mono-nucleotide (8 138, 28.15%), tri-nucleotide (5 727, 19.81%), tetra-nucleotide (1 104, 3.82%), pentanucleotide (234, 0.81%), and hexa-nucleotide (112, 0.39%). One hundred and thirty-two microsatellite loci (di- and tri-nucleotide) were randomly selected for amplification and polymorphism, of which 49 were highly polymorphic and well-resolved. The average number of alleles per locus was 13.63, ranging from 4 to 25, and allele sizes varied between 110 bp and 309 bp. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.233 to 1.000 and from 0.374 to 0.959, with mean values of 0.738 and 0.836, respectively. The polymorphism information content (PIC) ranged from 0.341 to 0.941 (mean=0.806). However, 12 loci deviated from Hardy-Weinberg equilibrium. Furthermore, transferability tests were also successful in validating the utility of the developed markers in five phylogenetically related species of family Carangidae. A total of 48 microsatellite markers were successfully cross-amplified in Decapterus macarellus, Decapterus macrosoma, Decapterus kurroides, Trachurus japonicus, and Selaroides leptolepis. The present microsatellites provided the first known set of microsatellite DNA markers for D. maruadsi, D. macarellus, D. kurroides, and D. macrosoma, and would be useful for further population genetic and molecular phylogeny studies as well as help with the fisheries management formulation and implementation of the understudied species.
Key words:    Decapterus maruadsi|SLAF-seq|microsatellite markers|cross-amplification   
Received: 2017-10-28   Revised: 2017-12-06
Tools
PDF (240 KB) Free
Print this page
Add to favorites
Email this article to others
Authors
Articles by NIU Sufang
Articles by ZHAI Yun
Articles by WU Renxie
Articles by ZHANG Haoran
Articles by TIAN Letian
Articles by DENG Jiaxin
Articles by XIAO Yao
References:
Addamo A M, García-Jiménez R, Taviani M, Machordom A. 2015. Development of microsatellite markers in the deepsea cup coral Desmophyllum dianthus by 454 sequencing and cross-species amplifications in Scleractinia order.Journal of Heredity, 106(3):322-330, https://doi.org/10.1093/jhered/esv010.
Altshuler D, Pollara V J, Cowles C R, Van Etten W J, Baldwin J, Linton L, Lander E S. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 407(6803):513-516.
Babbucci M, Zane L, Andaloro F, Patarnello T. 2006. Isolation and characterization of microsatellite loci from yellowtail Seriola dumerilii (Perciformes:Carangidae). Molecular Ecology Notes, 6(4):1 126-1 128, https://doi.org/10.1111/j.1471-8286.2006.01459.x.
Botstein D, White R L, Skolnick M, Davis R W. 1980.Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3):314-331.
Carreras-Carbonell J, Macpherson E, Pascual M. 2008. Utility of pairwise mtDNA genetic distances for predicting crossspecies microsatellite amplification and polymorphism success in fishes. Conservation Genetics, 9(1):181-190, https://doi.org/10.1007/s10592-007-9322-2.
Castoe T A, Streicher J W, Meik J M, Ingrasci M J, Poole A W, De Koning A P J, Campbell J A, Parkinson C L, Smith E N, Pollock D D. 2012. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Molecular Ecology Resources, 12(6):1 105-1 113, https://doi.org/10.1111/1755-0998.12000.
Chapuis M P, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24(3):621-631, https://doi.org/10.1093/molbev/msl191.
Chen G B, Li Y Z, Zhao X Y, Chen Y Z, Jin X S. 2006. Acoustic assessment of five groups commercial fish in South China Sea. Acta Oceanologica Sinica, 28(2):128-134. (in Chinese with English abstract)
Chen S L, Xing S C, Xu G B, Liao X L, Yang J F. 2009.Isolation and characterization of 10 polymorphic microsatellite loci from small yellow croaker(Pseudosciaena polyactis). Conservation Genetics, 10(5):1 469-1 471, https://doi.org/10.1007/s10592-008-9762-3.
Gill P, Urquhart A, Millican E, Oldroyd N, Watson S, Sparkes R, Kimpton C P. 1996. A new method of STR interpretation using inferential logic-development of a criminal intelligence database. International Journal of Legal Medicine, 109(1):14-22, https://doi.org/10.1007/BF01369596.
Goudet J. 2002. FSTAT:a program to estimate and test gene diversities and fixation indices (Version 2.9.3.2). https://www2.unil.ch/popgen/softwares/fstat.htm. Accessed on 2017-07-27.
Henshaw M T, Toth A L, Young T J. 2011. Development of new microsatellite loci for the genus Polistes from publicly available expressed sequence tag sequences.Insectes Sociaux, 58(4):581-585, https://doi.org/10.1007/s00040-011-0164-z.
Heras S, Planella L, Caldarazzo I, Vera M, García-Marín J L, Roldán M I. 2016. Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus. PeerJ, 4(3):e2200, https://doi.org/10.7717/peerj.2200.
Kalinowski S T, Taper M L, Marshall T C. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16(5):1 099-1 106, https://doi.org/10.1111/j.1365-294X.2007.03089.x.
Khan G, Zhang F Q, Gao Q B, Jiao X J, Fu P C, Xing R, Zhang J H, Chen S L. 2014. Isolation of 16 microsatellite markers for Spiraea alpina and S. mongolica (Rosaceae) of the Qinghai-Tibet Plateau. Applications in Plant Sciences, 2(1):1 300 059, https://doi.org/10.3732/apps.1300059.
Li F Q, Xie Y J, Zhou Z C, Chen H P, Chu X L. 2017. The distribution types and characteristics of SSR loci based on SLAF-seq in Ormosia hosiei genome. Molecular Plant Breeding, 15(5):1 774-1 781. (in Chinese with English abstract)
Li M, Chen Z Z, Chen T, Xiong D, Fan J T, Liang P W. 2016.Whole mitogenome of the Japanese scad Decapterus maruadsi (Perciformes:Carangidae). Mitochondrial DNA Part A:DNA Mapping, Sequencing, and Analysis, 27(1):306-307, https://doi.org/10.3109/19401736.2014.892089.
Liu J, Wu R X, Kang B, Ma L. 2016. Fishes of Beibu Gulf.Science Press, Beijing, China. (in Chinese)
Lu Z B, Dai Q S, Yan Y M. 2000. An estimation of resources of chub mackerel, round scad and other pelagic fish stocks in the Taiwan Strait and the adjacent waters. Journal of Fishery Sciences of China, 7(1):41-45. (in Chinese with English abstract)
Luan M B, Yang Z M, Zhu J J, Deng X, Liu C C, Wang X F, Xu Y, Sun Z M, Chen J H. 2016. Identification, evaluation, and application of the genomic-SSR loci in ramie. Acta Societatis Botanicorum Poloniae, 85(3):3 510, https://doi.org/10.5586/asbp.3510.
Michael O, Jonathan M W. 1997. Microsatellite DNA in fishes.Reviews in Fish Biology and Fisheries, 7(3):331-363, https://doi.org/10.1023/A:1018443912945.
Ministry of Agriculture Fishery Administration. 1999-2017.China Fishery Statistical Yearbook:1999-2017. China Agricultural Press, Beijing, China. (in Chinese)
Ohara E, Nishimura T, Sakamoto T, Nagakura Y, Mushiake K, Okamoto N. 2003. Isolation and characterization of microsatellite loci from yellowtail Seriola quinqueradiata and cross-species amplification within the genus Seriola.Molecular Ecology Notes, 3(3):390-391, https://doi.org/10.1046/j.1471-8286.2003.00460.x.
Renshaw M A, Patton J C, Rexroad Ⅲ C E, Gold J R. 2007.Isolation and characterization of dinucleotide microsatellites in greater amberjack, Seriola dumerili.Conservation Genetics, 8(4):1 009-1 011, https://doi.org/10.1007/s10592-006-9221-y.
Restrepo A, Páez V P, Vásquez A, Daza J M. 2015. Rapid microsatellite marker development in the endangered neotropical freshwater turtle Podocnemis lewyana(Testudines:Podocnemididae) using 454 sequencing.Biochemical Systematics and Ecology, 59:220-225, https://doi.org/10.1016/j.bse.2015.01.017.
Rice W R. 1989. Analyzing tables of statistical tests. Evolution, 43(1):223-225, https://doi.org/10.1111/j.1558-5646.1989.tb04220.x.
Rousset F. 2008. GENEPOP'007:a complete reimplementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources, 8(1):103-106, https://doi.org/10.1111/j.1471-8286.2007.01931.x.
Sambrook J, Russell D W. 2002. Molecular Cloning:A Laboratory Manual. Huang P T, Trans. 3rd ed. Science Press, Beijing, China. (in Chinese)
Seyoum S, Denison S H, Tringali M D. 2007. Isolation and characterization of 13 polymorphic microsatellite loci for the Florida pompano, Trachinotus carolinus. Molecular Ecology Notes, 7(1):141-143, https://doi.org/10.1111/j.1471-8286.2006.01556.x.
Shan T F, Pang S J, Li J, Li X, Su L. 2015. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida(Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing.BMC Genomics, 16:902, https://doi.org/10.1186/s12864-015-2184-y.
Sousa-Santos C, Fonseca P J, Amorim M C P. 2015.Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus.PeerJ, 3:e731, https://doi.org/10.7717/peerj.731.
Stabile J, Lipus D, Maceda L, Maltz M, Roy N, Wirgin I. 2016.Microsatellite DNA analysis of spatial and temporal population structuring of Phragmites australis along the Hudson River Estuary. Biological Invasions, 18(9):2 517-2 529, https://doi.org/10.1007/s10530-016-1157-7.
Sun X W, Liu D Y, Zhang X F, Li W B, Liu H, Hong W G, Jiang C B, Guan N, Ma C X, Zeng H P, Xu C H, Song J, Huang L, Wang C M, Shi J J, Wang R, Zheng X H, Lu C Y, Wang X W, Zheng H K. 2013. SLAF-Seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One, 8(3):e58700, https://doi.org/10.1371/journal.pone.0058700.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013.MEGA6:molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12):2 725-2 729, https://doi.org/10.1093/molbev/mst197.
Tong Y H, Mai R L, Chen J M, Li X M. 2012. Survey and analysis of landings on Hainan Island. South China Fisheries Science, 8(6):85-91. (in Chinese with English abstract)
Umino T, Ueno K, Mihara T, Koike M, Watanabe M, AhmadSyazni K, Ishitani M, Ohara K. 2013. Isolation of eleven polymorphic microsatellite loci for the endangered Sillago parvisquamis and cross-species amplification with Sillago japonica. Conservation Genetics Resources, 5(3):771-773, https://doi.org/10.1007/s12686-013-9904-x.
Van Oosterhout C, Hutchinson W F, Wills D P M, Shipley P. 2004. MICRO-CHECKER:software for identifying and correcting genotyping errors in microsatellite data.Molecular Ecology Notes, 4(3):535-538, https://doi.org/10.1111/j.1471-8286.2004.00684.x.
Villanova G V, Vera M, Díaz J, Martinez P, Calcaterra N B, Arranz S E. 2015. Isolation and characterization of 20 polymorphic microsatellite loci in the migratory freshwater fish Leporinus obtusidens (Characiformes:Anostomidae) using 454 shotgun pyrosequencing.Journal of Fish Biology, 86(3):1 209-1 217, https://doi.org/10.1111/jfb.12632.
Wu R X, Zhang H R, Niu S F, Zhai Y, Liu X F. 2016.Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica. Genetics and Molecular Research, 15(4):gmr15049046, https://doi.org/10.4238/gmr15049046.
Zhang H R, Liang Z B, Wu R X, Niu S F, Ke Z Y, Su S, Wei H, Wang Q, Sun B. 2017b. Development of microsatellite loci for Hairtail (Trichiurus japonicus) by using SLAFseq technology and cross-species amplification test.Genomics and Applied Biology. http://kns.cnki.net/kcms/detail/45.1369.Q.20170705.1459.004.html. (in press) (in Chinese with English abstract)
Zhang H R, Liang Z B, Wu R X, Niu S F, Liang Y, Wang Q, Wei H, Xiao Y, Sun B. 2017a. Microsatellite loci isolation in the Savalai Hairtail (Lepturacanthus savala) based on SLAF-seq technology and transferability in the related species. Genomics and Applied Biology. http://kns.cnki.net/kcms/detail/45.1369.Q.20170926.1457.002.html. (in press) (in Chinese with English abstract)
Zhang H R, Niu S F, Wu R X, Zhai Y, Tian L T. 2016.Development and characterization of 26 polymorphic microsatellite markers in Lateolabrax maculatus and cross-species amplification for the phylogenetically related taxa. Biochemical Systematics and Ecology, 66:326-330.
Zhang Q H, Cheng J H, Xu H X, Shen X Q, Yu G P, Zheng Y J. 2007. The Fishery Resources and Sustainable Utilization of the East China Sea. Fudan University Press, Shanghai, China. (in Chinese)