Genetics, Vol. 165, 2117-2128, December 2003, Copyright © 2003

Genetic Structure and Diversity Among Maize Inbred Lines as Inferred From DNA Microsatellites

Kejun Liua, Major Goodmanb, Spencer Musea, J. Stephen Smithc, Ed Bucklerd, and John Doebleye
a Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695,
b Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695,
c Crop Genetics Research and Development, DuPont Agriculture and Nutrition, Pioneer Hi-Bred International, Johnston, Iowa 50131,
d United States Department of Agriculture-Agricultural Research Service and Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
e Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706

Corresponding author: John Doebley, University of Wisconsin, 445 Henry Mall, Madison, WI 53705., jdoebley{at}wisc.edu (E-mail)

Communicating editor: J. A. BIRCHLER

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.




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