Data from: Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Plant architecture, phenology and yield components of cultivated plants
have repeatedly been shaped by selection to meet human needs and
adaptation to different environments. Here we assessed the genetic
architecture of 24 correlated maize traits that interact during plant
cycle. Overall, 336 lines were phenotyped in a network of 9 trials and
genotyped with 50K single-nucleotide polymorphisms. Phenology was the main
factor of differentiation between genetic groups. Then yield components
distinguished dents from lower yielding genetic groups. However, most of
trait variation occurred within group and we observed similar overall and
within group correlations, suggesting a major effect of pleiotropy and/or
linkage. We found 34 quantitative trait loci (QTLs) for individual traits
and six for trait combinations corresponding to PCA coordinates. Among
them, only five were pleiotropic. We found a cluster of QTLs in a 5 Mb
region around Tb1 associated with tiller number, ear row number and the
first PCA axis, the latter being positively correlated to flowering time
and negatively correlated to yield. Kn1 and ZmNIP1 were candidate genes
for tillering, ZCN8 for leaf number and Rubisco Activase 1 for kernel
weight. Experimental repeatabilities, numbers of QTLs and proportion of
explained variation were higher for traits related to plant development
such as tillering, leaf number and flowering time, than for traits
affected by growth such as yield components. This suggests a simpler
genetic determinism with larger individual QTL effects for the first
category.