Running head : Development of a maize B 73 - Mo 17 NIL

Recombinant inbred lines developed from the maize (Zea mays ssp mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci (QTL) controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for discovery and validation of QTL was assessed through analysis of plant height variation. www.plantphysiol.org on July 19, 2017 Published by Downloaded from Copyright © 2011 American Society of Plant Biologists. All rights reserved.