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This article in CS

  1. Vol. 51 No. 4, p. 1470-1480
     
    Received: Dec 21, 2010


    * Corresponding author(s): liz.jones@pioneer.com
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doi:10.2135/cropsci2010.07.0401

Evaluation of the Numbers of Single Nucleotide Polymorphisms Required to Measure Genetic Distance in Maize (Zea mays L.)

  1. Barry K. Nelsona,
  2. Alex L. Kahlerb,
  3. Jonathan L. Kahlerb,
  4. Mark A. Mikelc,
  5. Steven A. Thompsond,
  6. Ronald S. Ferrisse,
  7. Stephen Smitha and
  8. Elizabeth S. Jones *a
  1. a Pioneer Hi-Bred, 7300 NW 62nd Ave., Johnston, IA 50131
    b Biogenetic Services, Inc., 801 32nd Ave., Brookings, SD 57006
    c Dep. of Crop Sciences and Roy J. Carver Biotechnology Center, 2608 Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Dr., Urbana, IL 61801
    d Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268-1054
    e 7500 Olson Memorial Highway, Golden Valley, MN 55427

Abstract

We examined the number, genomic coverage, and discrimination abilities of single nucleotide polymorphism (SNP) markers required to provide equivalent measures of genetic distance compared to previously assayed simple sequence repeat (SSR) loci among inbred lines of maize (Zea mays L). A diverse set of public inbred lines was profiled with 768 public SNP markers and subsets of 601, 446, 305, 204, 165, 83, and 42 SNP markers were selected based on maintenance of expected heterozygosity (He) and/or even genomic coverage. The effectiveness of each SNP marker set was evaluated by comparison with standard SSR marker sets and pedigree distance values. Each marker set was evaluated using the full set of data for 80 diverse public inbred lines, a subset of inbred lines selected to represent the diversity of the full range of inbreds, and a subset of more closely related Stiff Stalk Synthetic (SSS) inbreds. A set of 305 SNP markers with mean He of greater than 0.4 had comparable or lower genetic distance sampling variance compared with SSR markers and resulted in r values comparable to larger SNP sets when pair-wise Roger's distances were correlated with distance estimates generated from pedigree or SSR data. We found that, where SNP markers are selected to maintain high He and even genome coverage, then data from only 2 to 3 times the number of SNP markers are needed to reveal associations among lines compared with SSR markers.

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