Genetic Properties of the Maize Nested Association Mapping Population

Abstract

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.

Comparison of biometrical models for joint linkage association mapping

“…The bi-parental populations of a JLAM data set result in more balanced allele frequencies compared with association mapping populations, thus enhancing QTL detection power while reducing the potentially confounding effects of population structure (McMullen et al, 2009). Although the balanced experimental design should render the correction for population stratification in JLAM unnecessary, spurious associations may arise if the trait is associated with the population structure.…”

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

“…For example, the publicly available maize nested association mapping (NAM) population consists of 25 recombinant inbred line (RIL) families derived from crosses between the reference parent B73 and 25 diverse inbred lines (McMullen et al, 2009). Each mapping family is composed of 200 RILs; hence, evaluation of the entire population requires testing 5000 inbred lines, beyond the capability of many researchers to assay, particularly for phenotypes that are difficult to measure.…”

Maize early endosperm growth and development: From fertilization through cell type differentiation

“…Given the simplicity of controlled genetic crossings with maize (due to the physical separation of male and female fl owers) and the high productivity of seeds from a single pollinated ear, maize has become the most thoroughly researched genetic system among cereals ( Strable and Scanlon, 2009 ). The recently described maize reference genome (inbred line B73; Schnable et al, 2009 ) and the nested association mapping (NAM) population composed of 5000 recombinant inbred lines derived from crosses of B73 with each of 25 founder inbred lines that capture much of the genetic diversity of maize ( Yu et al, 2008 ;McMullen et al, 2009 ) is fostering dissection of complex genetic traits. Subpopulations represented by the NAM founders include temperate stiff stalk, temperate non-stiff stalk, tropical or semitropical, popcorn, and sweet corn ( Liu et al, 2003 ), and manifest the diversity of ear and plant morphology ( McMullen et al, 2009 ).…”

“…The recently described maize reference genome (inbred line B73; Schnable et al, 2009 ) and the nested association mapping (NAM) population composed of 5000 recombinant inbred lines derived from crosses of B73 with each of 25 founder inbred lines that capture much of the genetic diversity of maize ( Yu et al, 2008 ;McMullen et al, 2009 ) is fostering dissection of complex genetic traits. Subpopulations represented by the NAM founders include temperate stiff stalk, temperate non-stiff stalk, tropical or semitropical, popcorn, and sweet corn ( Liu et al, 2003 ), and manifest the diversity of ear and plant morphology ( McMullen et al, 2009 ). These genetic materials are ideal for comparisons of endosperm development across the diversity of maize germplasm.…”