Agronomy and Horticulture Department


Date of this Version



De la Rosa-Santamaria, Roberto. 2012. Organellar Signaling Expands Plant Phenotypic Variation and Increases the Potential for Breeding the Epigenome. PhD Dissertation, University of Nebraska, 104 pp.


A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Agronomy (Plant Breeding and Genetics), Under the Supervision of Professor Sally A. Mackenzie. Lincoln, Nebraska: October, 2012

Copyright (c) 2012 Roberto De la Rosa Santamaria

RNAi down regulation of the nuclear gene MSH1 allowed to derive heritable epigenetic variation in sorghum and Arabidopsis as a result of physiological changes in the chloroplast. Additional information can be read in:

The Chloroplast Triggers Developmental Reprogramming When MUTS HOMOLOG1 Is Suppressed in Plants. Ying-Zhi Xu, Roberto de la Rosa Santamaria, et al. Plant Physiology, June 2012, Vol. 159, pp. 710–720,


MUTS HOMOLOGUE 1 (MSH1) is a nuclear gene unique to plants that functions in mitochondria and plastids, where it confers genome stability. Phenotypic effects of MSH1 down- regulation were studied in sorghum inbreed line Tx430 and Arabidopsis ecotype Columbia-0, with the hypothesis that RNAi suppression of MSH1 triggers retrograde signaling from organelles to the nucleus, alters the epigenome, and derives heritable phenotypic variation suitable for artificial selection. An array of morphological traits and metabolic pathways was detected, including leaf variegation, male sterility and dwarfism, associated with altered gibberellic acid metabolism, higher levels of reactive oxygen species (ROS), and decreased synthesis of ATP. A phenotype that combines dwarf, increased branching, reduced stomatal density and delayed flowering was identified, and designated developmental reprogrammed (MSH1-dr). Reproducible in additional plant species, this phenotypic variation is partially reversed by exogenous GA. In sorghum, the phenotype displays complete penetrance under self-pollination, even after segregation of the transgene, whereas progeny of MSH1-dr transgene null plants x wildtype Tx430 display enhanced growth. Significant differences for agronomic traits and response to selection were observed in the tested F2 to F4 generations, with mean values that surpass the wildtype up to 70% for grain yield/panicle and plant height, and 100% for biomass yield/plant. SSR marker analyses among the parental phenotypes Tx430 and MSH1-dr transgene null, and their derived lines, show no polymorphism, suggesting that the observed changes are non-genetic. In Arabidopsis, this enhanced growth is accompanied by genome methylation changes, whereas genetic hemi-complementation indicates that the novel phenotype results from chloroplast disruption.

Adviser: Sally A. Mackenzie