PDR 2014, 36(06) 723-729 DOI:   10.7677/ynzwyj201414053  ISSN: 2095-0845 CN: 53-1217/Q

Current Issue | Archive | Search                                                            [Print]   [Close]
Information and Service
This Article
Supporting info
Service and feedback
Email this article to a colleague
Add to Bookshelf
Add to Citation Manager
Cite This Article
Email Alert
Null alleles
HardyWeinberg Equilibrium method
Progeny tests method
HOU Meng-1、2
DU Fang-1
Article by Hou, M. 1、2
Article by Du, F. 1

Null Allele Detection in Plant Microsatellite Studies: Comparisons and Applications

 HOU  Meng-1、2, DU  Fang-1

1 College of Forestry, Beijing Forestry Unversity, Beijing 100083, China; 2 School of Life Science, Lanzhou University, Lanzhou 730000, China


Microsatellites remain the most popular markers in the studies of population genetics, conservation biology and molecular ecology because of its ease to development, high mutation rate and lowcost. Nowadays, the improvement of new technologies, such as NextGeneration Sequencing (NGS), multiplexPCR and capillary electrophoresis system have greatly promoted the development and using of microsatellite markers. However, null alleles, one of the most primary defects of microsatellite markers, widely presented in the studies using microsatellite markers, may lead to biased results. Unfortunately, the detection of null alleles has not been paid enough attention. In this review, we attempted to construct an indepth and comprehensive understanding on null alleles detection, and then, applied a detailed comparison for the different methods used to detect the occurrence of null alleles. Finally, we propose a meaningful suggestion for null allele’s detection in plant.

Keywords Null alleles   Microsatellite   HardyWeinberg Equilibrium method   Progeny tests method  
Received 2014-03-28 Revised  Online: 2014-07-16 
DOI: 10.7677/ynzwyj201414053

国家自然基金青年项目 (41201051),中央高校基本业务经费 (TD201201),111引智计划 (B13007)和教育部创新团队发展计划 (IRT13047)

Corresponding Authors:
About author:


Brookeld JFY, 1996. A simple new method for estimating null allele frequency from heterozygote deciency[J]. Molecular Ecology, 5: 453—455
Carlsson J, 2008. Effect of microsatellite null alleles on assignment testing[J]. Journal of Heredity, 99: 616—623
Chakraborty R, De Andrade M, Daiger SP et al., 1992. Apparent heterozygote deciencies observed in DNA typing data and their implications in forensic applications[J]. Annals of Human Genetics, 56: 45—57
Chen XF (程晓凤), Huang FJ (黄福江), Liu MD (刘明典) et al., 2011. Development of microsatellite markers use 454 pyrosequencing[J].  Biotechnology Bulletin (生物技术通报), 8: 82—90
Dbrowski MJ, Pilot M, Kruczyk M et al., 2014. Reliability assessment of null allele detection: inconsistencies between and within different methods[J]. Molecular Ecology Resources, 14: 361—373
Dakin EE, Avise JC, 2004. Microsatellite null alleles in parentage analysis[J]. Heredity, 93: 504—509
Dempster AP, Laird NM, Rubin DB, 1977. Maximum likelihood from incomplete data via the EM algorithm[J]. Journal of the Royal Statistical Society Series B (Methodological), 39: 1—38
Du FK, Xu F, Qu H et al., 2013. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new ESTSSR markers and construct an ESTSSR database[J]. PloS One, 8: e61337
Edwards AL, Civitello A, Hammond HA et al., 1991. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats[J]. American Journal of Human Genetics, 49: 746—756
Ellegren H, 2004. Microsatellites: simple sequences with complex evolution[J]. Nature Reviews Genetics, 5: 435—445
Garcia de Leon FJ, Canonne M, Quillet E et al., 1998. The application of microsatellite markers to breeding programmes in the sea bass, Dicentrarchus labrax[J]. Aquaculture, 159: 303—316
Guichoux E, Lagache L, Wagner S et al., 2011a. Current trends in microsatellite genotyping[J]. Molecular Ecology Resources, 11: 591—611
Guichoux E, Lagache L, Wagner S et al., 2011b. Two highly validated multiplexes (12plex and 8plex) for species delimitation and parentage analysis in oaks (Quercus spp.) [J]. Molecular Ecology Resources, 11: 578—585
Hoban S, Anderson R, Mccleary T et al., 2008. Thirteen nuclear microsatellite loci for butternut (Juglans cinerea L.) [J]. Molecular Ecology Resources, 8: 643—646
Ishibashi Y, Saitoh T, Abe S et al., 1996. Null microsatellite alleles due to nucleotide sequence variation in the greysided vole Clethrion mys rufocanus[J]. Molecular Ecology, 5: 589—590
Jacob HJ, Lindpaintnesr K, Kusumir EL et al., 1991. Genetic mapping of a gene causing hypertension in the strokeprone spontaneously hypertensive rat[J]. Cell, 67: 213—224
Jarne P, Lagoda PJ, 1996. Microsatellites, from molecules to populations and back[J]. Trends in Ecology & Evolution, 11: 424—429
Jones AG, Small CM, Paczolt KA et al., 2010. A practical guide to methods of parentage analysis[J]. Molecular Ecology Resources, 10: 6—30
Kalia RK, Rai MK, Kalia S et al., 2011. Microsatellite markers: an overview of the recent progress in plants[J]. Euphytica, 177: 309—334
Kalinowski ST, Taper ML, 2006. Maximum likelihood estimation of the frequency of null alleles at microsatellite loci[J]. Conservation Genetics, 7: 991—995
Kelkar YD, Strubczewski N, Hile SE et al., 2010. What is a microsatellite: A computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats[J]. Genome Biology and Evolution, 2: 620—635
Kwok S, Kellogg DE, McKinney N et al., 1990. Effects of primertemplate mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies[J]. Nucleic Acids Research, 18: 999—1005
Marshall TC, Slate J, Kruuk LEB et al., 1998. Statistical condence for likelihoodbased paternity inference in natural populations[J]. Molecular Ecology, 7: 639—655
McCoy EE, Jones AG, Avise JC, 2001. The genetic mating system and tests for cuckoldry in a pipesh species in which males fertilize eggs and brood offspring externally[J]. Molecular Ecology, 10: 1793—1800
Mittal N, Dubey A, 2009. Microsatellite markers—A new practice of DNA based markers in molecular genetics[J]. Pharmacognosy Reviews, 3: 235—246
OddouMuratorio S, Vendramin GG, Buiteveld J et al., 2009. Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?[J]. Conservation Genetics, 10: 1343—1347
Paetkau D, Strobeck C, 1995. The molecular basis and evolutionary history of a microsatellite null allele in bears[J]. Molecular Ecology, 4: 519—520
Primmer CR, Moller AP, Ellegren H, 1995. Resolving genetic relationship with microsatellite markers: a parentage testing system for the swallow Hirundo rustica[J]. Molecular Ecology, 4: 493—498
Raymond M, Rousset F, 1995. GENEPOP Version 12: population genetics software for exact tests and ecumenicism[J]. Journal of Heredity, 86: 248—249
Rousset F, 2008. Genepop′007: a complete reimplementation of the genepop software for Windows and Linux[J]. Molecular Ecology Resources, 8: 103—106
Summers K, Amos W, 1997. Behavioral, ecological, and molecular genetic analyses of reproductive strategies in the Amazonian dartpoison frog, Dendrobatesven trimaculatus[J]. Behavioral Ecology, 8: 260—267
Szabo LJ, 2007. Development of simple sequence repeat markers for the plant pathogenic rust fungus, Puccinia graminis[J]. Molecular Ecology Notes, 7: 92—94
Tautz D, 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers[J]. Nucleic Acids Research, 17: 6463—6471
Tsui CKM, Feau N, Ritland CE et al., 2009. Characterization of microsatellite loci in the fungus, Grosmannia clavigera, a pine pathogen associated with the mountain pine beetle[J]. Molecular Ecology Resources, 9: 1500—1503
Van Oosterhout C, Hutchinson WF, Wills DMP et al., 2004. MICROCHECKER: software for identifying and correcting genotyping errors in microsatellite data[J]. Molecular Ecology Notes, 4: 535—538
Wagner AP, Creel S, Kalinowski ST, 2006. Estimating relatedness and relationships using microsatellite loci with null alleles[J]. Heredity, 97: 336—345
Wattier R, Engel CR, SaumitouLaprade P et al., 1998. Short allele dominance as a source of heterozygote deciency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta) [J]. Molecular Ecology, 7: 1569—1573
Wen YF (文亚峰), Kentaro Uchiyama, Han WJ (韩文军) et al., 2013. Null alleles in microsatellite markers[J]. Biodiversity Science (生物多样性), 21: 117—126
Xu F, Feng S, Wu R et al., 2013. Two highly validated SSR multiplexes (8plex) for Euphrates′ poplar, Populus euphratica (Salicaceae) [J]. Molecular Ecology Resources, 13: 144—153
Zane L, Bargelloni L, Patarnello T, 2002. Strategies for microsatellite isolation: a review[J]. Molecular Ecology, 11: 1—16

Similar articles
1. LIU Lin, LI Cheng-Yun.SSR Variation in the WD Repeats Domain Genes and It′s Effects on Protein Structure of Rice Blast Fungus, Magnaporthe oryzae[J]. PDR, 2011,33(4): 376-382
2. XIONG Min-1, WANG Jing-1, ZHANG Zhi-Rong-3, ZHANG Zhi-Yong-1、2.The Development of Nuclear Microsatellite Markers for an Endangered Plant, Sinomanglietia glauca (Magnoliaceae)[J]. PDR, 2011,33(5): 535-539
3. YAN Li-Jun, ZHANG Zhi-Rong, LI De-Zhu, GAO Lian-Ming.Isolation and Characterization of Microsatellite Markers for the Chinese Endemic Species Rhododendron spinuliferum (Ericaceae)[J]. PDR, 2014,36(01): 41-46
4. YE Lin-Jiang, WANG Jing, SUN Peng, DONG Shu-Peng, ZHANG Zhi-Yong.The Transferability of Nuclear Microsatellite Markers in Four Castanopsis Species to Castanopsis tibetana (Fagaceae)[J]. PDR, 2014,36(04): 443-448
5. LI Miao-Miao, MEEGAHAKUMBURA M. Kasun, YAN Li-Jun, LIU Jie, GAO Lian-Ming.Genetic Involvement of Camellia taliensis in the Domestication of C.sinensis var. assamica (Assimica Tea) Revealed by Nuclear Microsatellite Markers[J]. PDR, 2015,37(01): 29-37

Comment for this article:

Copyright by PDR