Genetic Design and Statistical Power of Nested Association Mapping in Maize

Abstract

We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes) to dissect the genetic basis of complex quantitative traits. The NAM design simultaneously exploits the advantages of both linkage analysis and association mapping. We demonstrated the power of NAM for highpower cost-effective genome scans through computer simulations based on empirical marker data and simulated traits with different complexities. With common-parent-specific (CPS) markers genotyped for the founders and the progenies, the inheritance of chromosome segments nested within two adjacent CPS markers was inferred through linkage. Genotyping the founders with additional high-density markers enabled the projection of genetic information, capturing linkage disequilibrium information, from founders to progenies. With 5000 genotypes, 30-79% of the simulated quantitative trait loci (QTL) were precisely identified. By integrating genetic design, natural diversity, and genomics technologies, this new complex trait dissection strategy should greatly facilitate endeavors to link molecular variation with phenotypic variation for various complex traits.

Comparison of biometrical models for joint linkage association mapping

“…The power of QTL detection in JLAM is determined by different factors, including the population size, the population structure, the mating design, the extent of LD in the parental population, as well as the genetic architecture and the heritability of the trait under consideration (Yu et al, 2008). The present study was based on experimental data of 441 testcross progenies from 12 segregating populations, and a population structure typical for JLAM populations appeared to be present in this population.…”

“…Joint linkage association mapping (JLAM) holds great potential for the evaluation of quantitative traits, as it potentially combines the high power of linkage mapping with the good mapping resolution of association mapping (Yu et al, 2008;Lu et al, 2010). The combination of the advantages of both approaches in JLAM is especially promising in applied plant breeding, where many segregating bi-parental populations are routinely generated in the course of the breeding program.…”

“…Several statistical approaches for JLAM have been suggested based on linear (Yu et al, 2008;Liu et al, 2011) or linear mixed models (Stich et al, 2008). In addition, the QIPDT approach has been suggested (Stich et al, 2006), but the relationship between parents can better be exploited by using linear mixed models including a kinship matrix.…”

“…In addition, the QIPDT approach has been suggested (Stich et al, 2006), but the relationship between parents can better be exploited by using linear mixed models including a kinship matrix. In analogy to composite interval mapping, Yu et al (2008) used cofactors to correct for the genetic background, and compared this approach in a simulation study with a model including a general population effect. A lower QTL detection power was observed for the latter model, indicating that incorporating cofactors might be advantageous as they control both population structure and genetic background within populations.…”

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 ).…”