Molecular Breeding

, Volume 21, Issue 4, pp 407–418

RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

  • Chuanxiao Xie
  • Marilyn Warburton
  • Mingshun Li
  • Xinhai Li
  • Muji Xiao
  • Zhuanfang Hao
  • Qi Zhao
  • Shihuang Zhang


This study analyzes population structure and linkage disequilibrium (LD) among 187 commonly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Relationship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder’s decisions regarding crosses. Extensive inter- and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D′  > 0.1 and 93 out of them at P < 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping.


Association mapping Linkage disequilibrium Maize (Zea mays L.) Population structure 



Cetyltrimethylammonium bromide


Linkage disequilibrium


Polymerase chain reaction


Polymorphic information content


Quantitative trait locus


Simple sequence repeat


Trait analysis by Association, Evolution & Linkage.

Supplementary material

11032_2007_9140_MOESM1_ESM.xls (38 kb)
Supplementary material
11032_2007_9140_MOESM2_ESM.xls (32 kb)
Supplementary material
11032_2007_9140_MOESM3_ESM.xls (46 kb)
Supplementary material


  1. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111:206–217PubMedCrossRefGoogle Scholar
  2. Camus-Kulandaivelu L, Veyrieras J, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449–2463PubMedCrossRefGoogle Scholar
  3. Chao SM, Zhang WJ, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47(3):1018–1030CrossRefGoogle Scholar
  4. Charcosset A, Essioux L (1994) The effect of population structure on the relationship between heterosis and heterozygosity at marker loci. Theor Appl Genet 89:336–343CrossRefGoogle Scholar
  5. Doebley J, Wendel JF, Smith JSC, Stuber CW, Goodman MM (1988) The origin of corn belt maize: the isozyme evidence. Econ Bot 42:120–131CrossRefGoogle Scholar
  6. Excoffier L (2001) Analysis of population subdivision. In: Balding D, Bishop M, Cannings C (eds) Handbook of Statistical Genetics. John Wiley & Sons, New York, pp 271–307Google Scholar
  7. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  8. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374PubMedCrossRefGoogle Scholar
  9. Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44(6):1054–64PubMedCrossRefGoogle Scholar
  10. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCrossRefGoogle Scholar
  11. Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446PubMedCrossRefGoogle Scholar
  12. Li XH, Fu JH, Zhang SH, Yuan LX, Li MS (2000) Genetic variation of inbred lines of maize detected by SSR markers. Sci Agric Sin 33:1–9Google Scholar
  13. Li Y (1998) Development and germplasm base of maize hybrids in China. Maydica 43:259–269Google Scholar
  14. Li Y, Du J, Wang T, Shi Y, Song Y, Jia J (2002) Genetic diversity and relationships among Chinese maize inbred lines revealed by SSR markers. Maydica 47:93–101Google Scholar
  15. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128PubMedGoogle Scholar
  16. Lu H, Bernardo R (2001) Molecular marker diversity among current and historical maize inbreds. Theor Appl Genet 103:613–617CrossRefGoogle Scholar
  17. Lu H, Redus, MA, Coburn JR, Rutger JN, McCouch SR, Tai TH (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45(1):66–76CrossRefGoogle Scholar
  18. Malysheva-Otto LV, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.) BMC. Genetics 7:6PubMedGoogle Scholar
  19. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193PubMedCrossRefGoogle Scholar
  20. Palaisa K, Morgante M, Tingey S, Rafalski A. (2004) Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101: 9885–9890Google Scholar
  21. Pejic I, Ajmore-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255CrossRefGoogle Scholar
  22. Pritchard JK (2001) Deconstructing maize population structure. Nat Genet 28(3):286–289CrossRefGoogle Scholar
  23. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  24. Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds), Non-mammalian genomic analysis. A practical guide. Academic Press, San Diego, pp 75–134Google Scholar
  25. Reif JC, Warburton ML, Xia XC, Hoisington DA, Crossa J, Taba S, Muminović J, Bohn M, Frisch M, Melchinger AE (2006) Grouping of accessions of Mexican races of maize revisited with SSR markers. Theor Appl Genet 113:177–185PubMedCrossRefGoogle Scholar
  26. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484Google Scholar
  27. Saghai-Maroof MA, Soliman K, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018Google Scholar
  28. Senior ML, Murphy JP, Goodman MM, Stuber CW (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci 38:1088–1098CrossRefGoogle Scholar
  29. Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L): comparisons with data from RFLPS and pedigree. Theor Appl Genet 95:163–173CrossRefGoogle Scholar
  30. Smith OS, Smith JSC (1992) Measurement of genetic diversity among maize hybrids - a comparison of isozymic, RFLP, pedigree, and heterosis data. Maydica 37:53–60Google Scholar
  31. Stich B, Melchinger AE, Frisch M, Maurer HP, Hecknberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723–730PubMedCrossRefGoogle Scholar
  32. Szalma SJ, Buckler ES, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333PubMedCrossRefGoogle Scholar
  33. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) Proc Natl Acad Sci USA 98:9161–9166Google Scholar
  34. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–89PubMedCrossRefGoogle Scholar
  35. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617–1630PubMedCrossRefGoogle Scholar
  36. Warburton ML, Ribaut JM, Franco J, Crossa J, Dubreuil P, Betrán FJ (2005) Genetic characterization of 218 elite CIMMYT inbred maize lines using RFLP markers. Euphytica 142:97–106CrossRefGoogle Scholar
  37. Wilson LM, Whitt SR, Ibáñez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association. Plant Cell 16:2719–2733PubMedCrossRefGoogle Scholar
  38. Wright S (1951) The genetical structure of population. Ann Eugen 15:323–354Google Scholar
  39. Xia XC, Reif JC, Melchinger AE, Frisch M , Hoisington DA, Beck D, Warburton ML (2005) Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: II. Subtropical, tropical mid-altitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci 45(6):2573–2582CrossRefGoogle Scholar
  40. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160PubMedGoogle Scholar
  41. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208PubMedCrossRefGoogle Scholar
  42. Yuan LX, Fu JH, Warburton LM, Li XH, Zhang SH, Khairallah M, Liu Z X, Peng ZB, Li LC (2000) Comparison of gentic diversity in maize inbreds based on RFLP, SSR, AFLP and RAPD markers. Acta Genet Sin 27:725–733PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Chuanxiao Xie
    • 1
  • Marilyn Warburton
    • 2
  • Mingshun Li
    • 1
  • Xinhai Li
    • 1
  • Muji Xiao
    • 1
  • Zhuanfang Hao
    • 1
  • Qi Zhao
    • 3
  • Shihuang Zhang
    • 1
  1. 1.National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingP.R. China
  2. 2.Applied Biotechnology Center CIMMYT ApdoMexicoMexico
  3. 3.Life SchoolBeijing Capital Normal UniversityBeijingP.R. China

Personalised recommendations