Four Parent Maize (FPM) Population: Effects of Mating Designs on Linkage Disequilibrium and Mapping Quantitative Traits

Multiparent advanced generation inter-cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; Zea mays L.) population implemented five different mating designs used in MAGIC and bi-parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years. Linkage disequilibrium (LD) analysis of subpopulations indicated MAGIC population designs should incorporate generations of intermating to overcome initial LD increase caused by population admixture in a non-intermated four parent population (4way0sib). A 3- to 4-fold increase in genetic resolution (r(2) < 0.8) and a 2.5-fold decrease in the extent of LD decay (r(2) < 0.2) compared to the biparental populations was found for the four parent cross at the third generation of intermating (4way3sib). Power of QTL detection was affected to a greater extent by sample size rather than by mating designs. The FPM power simulations indicated that MAGIC populations have the ability to meet or exceed the mapping power of nested association panels with fewer individuals and diversity inputs. Using association mapping software we identified 2, 5, 7, and 6 QTL for PH, EH, DTA, and DTS, respectively. The FPM population is a valuable resource for quantifying empirical improvements of parent number, intermating, and the number of progeny for QTL linkage mapping.