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Title: Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Alternative polyadenylation (APA) is a widespread post‐transcriptional mechanism that regulates gene expression throughmRNAmetabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativaL.). However, little is known about theAPA‐mediated regulation underlying the distinct characteristics between two major rice subspecies,indicaandjaponica. Using a poly(A)‐tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage betweenindicaandjaponica, and extensive differentiation inAPAprofiles was detected genome‐wide. Genes with subspecies‐specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance ofindicaand cold‐stress tolerance ofjaponica. In most tissues, differential usage ofAPAsites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000‐seed weight. In leaves of the booting stage,APAsite‐switching genes displayed global shortening of 3′ untranslated regions with increased expression inindicacompared withjaponica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis inindicathan injaponica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest thatAPAmay be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post‐transcriptional genetic basis underlying the divergence of rice traits.

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Author(s) / Creator(s):
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Publisher / Repository:
Date Published:
Journal Name:
The Plant Journal
Page Range / eLocation ID:
p. 260-276
Medium: X
Sponsoring Org:
National Science Foundation
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