Тип публикации: статья из журнала
Год издания: 2020
Идентификатор DOI: 10.1007/s00299-020-02561-9
Ключевые слова: mantling, epigenetics, whole-genome bisulfite sequencing, karma
Аннотация: Key message Several hypomethylated sites within theKarmaregion of EgDEF1and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling. One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the "mantled" phenotype that can lead to reduced yields. This clonal abnormality is an eПоказать полностьюpigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC(3)-poor genes) were increasingly methylated towards their 3 ' region, while GC(3)-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5 ' UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within theKarmaof EgDEF1and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.
Журнал: PLANT CELL REPORTS
Выпуск журнала: Vol. 39, Is. 9
Номера страниц: 1219-1233
ISSN журнала: 07217714
Место издания: NEW YORK
Издатель: SPRINGER