Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers

Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts.Extensive studies have shown genetic,transcriptomic,and epigenetic dynamics upon polyploidization in multiple plant species.However,few studies have unveiled those alternations imposed only by ploidy level,without any interference from heterozygosity.Cultivated potato is highly heterozygous.Thus,in this study,we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato.We confirmed their ploidy levels using chloroplast counting and karyotyping.Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous.We investigated variations in phenotypes,transcription,and histone modifications between two ploidies.Both autotetraploid lines produced larger but fewer tubers than the diploid line.Interestingly,each autotetraploid line displayed ploidy-related differential expression for various genes.We also discovered a genomewide enrichment of H3K27ac in genic regions upon whole-genome doubling(WGD).However,such enrichment was not associated with the differential gene expression between two ploidies.The tetraploid lines may exhibit better resistance to cold-induced sweetening(CIS)than the diploid line in tubers,potentially regulated through the expression of CIS-related key genes,which seems to be associated with the levels of H3K4me3 in cold-stored tubers.These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes,transcription,and histone modifications,as well as on CIS-related genes in response to cold storage.

Chromatin architectural alterations due to null mutation of a major CG methylase in rice

Associations between 3D chromatin architectures and epigenetic modifications have been characterized in animals.However,any impact of DNA methylation on chromatin architecture in plants is understudied,which is confined to Arabidopsis thaliana.Because plant species differ in genome size,composition,and overall chromatin packing,it is unclear to what extent findings from A.thaliana hold in other species.Moreover,the incomplete chromatin architectural profiles and the low-resolution high-throughput chromosome conformation capture(Hi-C)data from A.thaliana have hampered characterizing its subtle chromatin structures and their associations with DNA methylation.We constructed a high-resolution Hi-C interaction map for the null OsMET1-2(the major CG methyltransferase in rice)mutant(osmet1-2)and isogenic wild-type rice(WT).Chromatin structural changes occurred in osmetl-2,including intra-/inter-chromosomal interactions,compartment transition,and topologically associated domains(TAD)variations.Our findings provide novel insights into the potential function of DNA methylation in TAD formation in rice and confirmed DNA methylation plays similar essential roles in chromatin packing in A,thaliana and rice.