Mapped genomic locations for developmental functions and QTLs reflect concerted groups in maize (Zea mays L.)

For maize, we have analyzed conjointly the map locations reported to-date of genes for growth, development, and stress response. We find that these genes associate into functional clusters, 10-30 cM long, distributed non-randomly along all ten chromosomes. These clusters comprise the loci for environmental and hormonal sensors, the growth machinery genes (e.g., genes for the enzymes of hormone synthesis, mutations disturbing sporophyte and gametophyte development, or genes for programmed cell death) and the master genes presiding over the spatial and temporal transitions in cell growth and differentiation (e.g., genes expressing transcription factors). Taking into consideration mapping accuracy, the putative associations of developmental genes generally coincide with the location of homeotic genes mapped with cDNA probes. The majority of over 800 quantitative trait loci (QTLs) for plant architecture, growth and development in vivo and in vitro, the grain yield as the integer of growth, and ABA accumulation and effects, also map within these clusters. Several physiologically different quantitative traits of plant development and yield are often mapped by one and the same molecular probe. The clusters are redundant, apparently due to several duplication events in the course of maize evolution. We presume that these clusters are the functional units of genes expressed in concert to contribute toward regulating plant development and, apparently, some of the plant responses to abiotic stress. The major QTLs for plant height, earliness and grain yield are visible manifestations of the developmental clusters. The evolutionary and cytogenetic evidence seems to support the adaptive significance of functional gene networks for development. The physiological advantage of the close association of functionally related genes in the clusters may rely on compartmentation and tunneling of signal molecules, which helps to cooperatively recruit the transcription factors into multicomponent regulatory modules of high specificity.