title: Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population.
abstract: Quantitative trait locus (QTL) mapping has been used to dissect the genetic architecture of complex traits and predict phenotypes for marker-assisted selection. Many QTL mapping studies in plants have been limited to one biparental family population. Joint analysis of multiple biparental families offers an alternative approach to QTL mapping with a wider scope of inference. Joint-multiple population analysis should have higher power to detect QTL shared among multiple families, but may have lower power to detect rare QTL. We compared prediction ability of single-family and joint-family QTL analysis methods with fivefold cross-validation for 6 diverse traits using the maize nested association mapping population, which comprises 25 biparental recombinant inbred families. Joint-family QTL analysis had higher mean prediction abilities than single-family QTL analysis for all traits at most significance thresholds, and was always better at more stringent significance thresholds. Most robust QTL (detected in >50% of data samples) were restricted to one family and were often not detected at high frequency by joint-family analysis, implying substantial genetic heterogeneity among families for complex traits in maize. The superior predictive ability of joint-family QTL models despite important genetic differences among families suggests that joint-family models capture sufficient smaller effect QTL that are shared across families to compensate for missing some rare large-effect QTL.
authors.affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, USA.
authors.forename: F
authors.initials: F
authors.lastname: Ogut
authors.affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Bian
authors.affiliation: US Department of Agriculture, Agricultural Research Service, Plant, Soil, and Nutrition Research Unit, Ithaca, NY, USA.
authors.forename: P J
authors.initials: PJ
authors.lastname: Bradbury
authors.affiliation: 1] Department of Crop Science, North Carolina State University, Raleigh, NC, USA [2] US Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Raleigh, NC, USA.
authors.forename: J B
authors.initials: JB
authors.lastname: Holland
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D008040:Genetic Linkage; D005819:Genetic Markers; D005828:Genetics, Population; D008957:Models, Genetic; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
chemical_list: D005819:Genetic Markers