Karyotyping for phenotype paper
Phenotypic consequences of aneuploidy in Arabidopsis thaliana
Whole-genome sequencing was performed on 6 A. thaliana individual in order to obtain a detailed karyotype of each of them.  Col-0 A (normalization control)  Col-0 B: diploid Col-0 control  Ap2x*4#10 and Ap2x*4#20 are two Aneuploid-parented diploid individuals that exhibit meristematic abnormalities  Col.Tr3 is a trisomic of chromosome 3  Aneuploid1 is an aneuploid of unknown karyotype, hybrid between the Col-0 and the Wa-1 genotypes.  Genomic libraries were created from each of these six individuals, barcoded and pooled before sequencing.  After sequencing, reads were divided according to their barcodes and binned according to their mapping position in order to derive coverage across the length oft he five A. thaliana chromosomes.
Because of their tolerance to aneuploidy, plants provide a powerful system for a genome-wide investigation of aneuploid syndromes. We phenotyped a population of Arabidopsis thaliana aneuploid individuals containing 25 different karyotypes. Even in this highly heterogeneous population, we demonstrate that certain traits are strongly associated with the dosage of specific chromosome types and that chromosomal effects can be additive. Further, we identified subtle developmental phenotypes expressed in the diploid progeny of aneuploid parent(s) but not in euploid controls from diploid lineages. These results indicate long-term phenotypic consequences of aneuploidy that can persist after chromosomal balance has been restored. We verified the diploid nature of these individuals by whole-genome sequencing and discuss the possibility that trans-generational phenotypic effects stem from epigenetic modifications passed from aneuploid parents to their diploid progeny.