Combined linkage and association mapping revealsCYCD5;1as a quantitative trait gene for endoreduplication inArabidopsis

Abstract

Endoreduplication is the process where a cell replicates its genome without mitosis and cytokinesis, often followed by cell differentiation. This alternative cell cycle results in various levels of endoploidy, reaching 4× or higher one haploid set of chromosomes. Endoreduplication is found in animals and is widespread in plants, where it plays a major role in cellular differentiation and plant development. Here, we show that variation in endoreduplication between Arabidopsis thaliana accessions Columbia-0 and Kashmir is controlled by two major quantitative trait loci, ENDO-1 and ENDO-2. A local candidate gene association analysis in a set of 87 accessions, combined with expression analysis, identified CYCD5;1 as the most likely candidate gene underlying ENDO-2, operating as a rate-determining factor of endoreduplication. In accordance, both the overexpression and silencing of CYCD5;1 were effective in changing DNA ploidy levels, confirming CYCD5;1 to be a previously undescribed quantitative trait gene underlying endoreduplication in Arabidopsis.change-of-function allele | endopolyploidy | regulatory haplotype

Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis

“…The currently available large populations, dense genotyping, and the advantage of homozygous lines in the mainly self-fertilizing species Arabidopsis, ought to greatly enhance the power of such studies. Indeed, GWA studies confirmed many of the previously identified genes in experimental mapping populations and mutant studies and detected a number of, to our knowledge, novel candidate genes, although this is limited for quantitative traits (Atwell et al, 2010;Brachi et al, 2010;Li et al, 2010;Todesco et al, 2010;Chan et al, 2011;Chao et al, 2012;Filiault and Maloof, 2012;Sterken et al, 2012;Yano et al, 2013;Chao et al, 2014;Meijón et al, 2014;Bac-Molenaar et al, 2015). Similar to the problem of missing heritability in human GWA studies, where individual variants cannot explain the phenotypic variation despite high heritabilities (Yang et al, 2010;Gibson, 2011;Makowsky et al, 2011), genetic variants cannot fully explain the high heritabilities in plant studies (Brachi et al, 2010;Sasaki et al, 2015).…”

The ATM-Dependent DNA Damage Response Acts as an Upstream Trigger for Compensation in thefas1Mutation during Arabidopsis Leaf Development

“…Given that the DNA-damaging chemical, zeocin, phenocopies these phenotypes, it is thought that the DNA damage promotes the endocycle and accompanied cell expansion. To examine whether the high-ploidy phenotypes of fas1 are induced through the ATM-dependent DNA damage response, we performed flow cytometry analysis using fully mature leaves and calculated the endoreduplication index (Sterken et al, 2012). The nuclear ploidy levels of cells in first leaves of 21-d-old wildtype plants range from 2C to 32C, indicating that many cells in wild-type leaves have undergone several rounds of endocycles (Fig.…”

“…At least 7,000 nuclei isolated from the first pair of leaves were used for each ploidy measurement. Endoreduplication index (EI) was calculated as EI = (0 3 %2C) + (1 3 %4C) + (2 3 %8C) + (3 3 %16C) + (4 3 %32C) (Sterken et al, 2012) and averaged over at least three technical replicates.…”

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

“…Although length, width, and the dimensions of leaves are important, natural variation in leaf morphology is immense, and methods to quantify the entirety of shape variance are required to determine the full complement of genes regulating differences in populations (Langlade et al, 2005;Chitwood et al, 2012bChitwood et al, , 2012cChitwood et al, , 2012d. Ultimately, the morphology of leaves is determined at the cellular level, and the genetics underlying natural variation in cellular traits are only now beginning to be examined (Massonnet et al, 2011;Sterken et al, 2012).…”