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Originally published as Genetics Published Articles Ahead of Print on February 16, 2005.
Genetics, Vol. 169, 2267-2275, April 2005, Copyright © 2005
doi:10.1534/genetics.104.033217
Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.)
Yuan-Ming Zhang*,
Yongcai Mao*,
Chongqing Xie
,
Howie Smith,
Lang Luo and
Shizhong Xu*,1
* Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124
Pioneer Hi-Bred International, Johnston, Iowa 50131-1004
1 Corresponding author: Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521-0124.
E-mail: xu{at}genetics.ucr.edu
Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.
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