Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network

Abstract

Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement

Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

“…The phenotypes of the stacked transgenics containing UBIL:GA20ox-1 and GA2ox:PLA1 were additive compared with the single transgenes, suggesting that in certain situations, LER and LED can be decoupled and that PLA1 is mainly regulating LED. A similar conclusion was reached when natural variation for LER and LED was studied in the B73xH99 recombinant inbred line (RIL) population, as both processes were highly correlated with final leaf length but not with each other3031.…”

Genetics of barley tiller and leaf development

“…For example, leaf length depends on leaf elongation duration (LED) and leaf elongation rate (LER), which is closely connected to the size of the division zone (reviewed in Nelissen et al ). Interestingly, studies in maize and barley suggest that LER and LED are under (at least partially) distinct control mechanisms (Baute et al ; Digel et al ).…”

Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture

“…Moreover, the large genetic variation in the set of accessions adds complexity to the task of identifying a clear gene expression-phenotype relation. Recently, a similar approach in maize RIL populations identified genes whose expression in young, dividing leaf tissue correlated to phenotypes of mature leaves such as length, width, and leaf area (Baute et al, 2015(Baute et al, , 2016. It is likely that the lack of gene expression-phenotype correlation in natural accessions is due to higher genetic variation present in this population compared with a RIL population.…”