Abstract:
KEY MESSAGE:Several hypomethylated sites within the Karma region of EgDEF1 and 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 epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. 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 (GC3-poor genes) were increasingly methylated towards their 3' region, while GC3-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 the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.
journal_name
Plant Cell Repjournal_title
Plant cell reportsauthors
Sarpan N,Taranenko E,Ooi SE,Low EL,Espinoza A,Tatarinova TV,Ong-Abdullah Mdoi
10.1007/s00299-020-02561-9subject
Has Abstractpub_date
2020-09-01 00:00:00pages
1219-1233issue
9eissn
0721-7714issn
1432-203Xpii
10.1007/s00299-020-02561-9journal_volume
39pub_type
杂志文章abstract:KEY MESSAGE:Wheat MAPK gene TaMPK14 is N starvation response and is crucial in modulating plant low-N stress tolerance. Improving plant N use efficiency (NUE) contributes largely to the sustainable crop production worldwide. In this study, TaMPK14, a mitogen-activated protein kinase (MAPK) family gene in T. aestivum, w...
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journal_title:Plant cell reports
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