Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome

Abstract

Background: The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The objective of our study was to contribute to the knowledge of these genes and gene networks by transcription profiling with microarrays.

Results: We assessed the grain yield and grain dry matter content (an indicator for early maturity) of 98 maize hybrids in multi-environment field trials. The gene expression in seedlings of the parental inbred lines, which have four different genetic backgrounds, was assessed with genome-scale oligonucleotide arrays. We identified genes associated with grain yield and grain dry matter content using a newly developed two-step correlation approach and found overlapping gene networks for both traits. The underlying metabolic pathways and biological processes were elucidated. Genes involved in sucrose degradation and glycolysis, as well as genes involved in cell expansion and endocycle were found to be associated with grain yield.

Conclusions: Our results indicate that the capability of providing energy and substrates, as well as expanding the cell at the seedling stage, highly influences the grain yield of hybrids. Knowledge of these genes underlying grain yield in maize can contribute to the development of new high yielding varieties.

Figure 1

Schematic representation of a two-step correlation approach. L, average expression level of a gene in the parents of a hybrid; g*, gene not included in set S in a previous repetition of Step 2; r, correlation coefficient; p, p-value for statistical significance; PY, hybrid performance for grain yield; HY, mid-parent heterosis for grain yield.

Figure 2

Representation of grain yield-involved genes in sucrose degradation and glycolysis pathways. The rectangular boxes with the colored scales show the fold-changes (FD) of mid-parent expression for each gene. The mean mid-parent expression (log2 scale) is represented by the numbers in the boxes. Positively (P) and negatively (N) associated genes are shown in brown and blue, respectively. The boxes with two frames show genes with interactions to grain dry matter content (GDMC).

Figure 3

Schematic representation of grain yield-involved genes in cell expansion and endocycle processes. The rectangular boxes with the colored scales show the fold-changes (FD) of mid-parent expression for each gene. The mean mid-parent expression (log2 scale) is represented by the numbers in the boxes. Positively (P) and negatively (N) associated genes are shown in brown and blue, respectively. The boxes with two frames show genes with interactions to grain dry matter content (GDMC). The representation of the cell cycle genes regulating endocycle were taken from a previous review [25].