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RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

Authors

  • Chuanxiao Xie
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
  • Marilyn Warburton
    • Applied Biotechnology Center CIMMYT Apdo
  • Mingshun Li
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
  • Xinhai Li
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
  • Muji Xiao
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
  • Zhuanfang Hao
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
  • Qi Zhao
    • Life SchoolBeijing Capital Normal University
    • National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural Sciences
Article

DOI: 10.1007/s11032-007-9140-8

Cite this article as:
Xie, C., Warburton, M., Li, M. et al. Mol Breeding (2008) 21: 407. doi:10.1007/s11032-007-9140-8

Abstract

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.

Keywords

Association mappingLinkage disequilibriumMaize (Zea mays L.)Population structure

Abbreviations

CTAB

Cetyltrimethylammonium bromide

LD

Linkage disequilibrium

PCR

Polymerase chain reaction

PIC

Polymorphic information content

QTL

Quantitative trait locus

SSR

Simple sequence repeat

TASSEL

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

Copyright information

© Springer Science+Business Media B.V. 2007