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Title: Experimental studies of adaptation in Clarkia xantiana . III. Phenotypic selection across a subspecies border: SPATIALLY VARIABLE SELECTION ACROSS A SUBSPECIES BORDER
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Author(s) / Creator(s):
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Page Range / eLocation ID:
2249 to 2261
Medium: X
Sponsoring Org:
National Science Foundation
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  1. Abstract

    The origins of geographic races in wide‐ranging species are poorly understood. In Texas, thetexanussubspecies ofHelianthusannuushas long been thought to have acquired its defining phenotypic traits via introgression from a local congener,H. debilis, but previous tests of this hypothesis were inconclusive. Here, we explore the origins ofH. a. texanususing whole genome sequencing data from across the entire range ofH. annuusand possible donor species, as well as phenotypic data from a common garden study. We found that although it is morphologically convergent withH. debilis,H. a. texanushas conflicting signals of introgression. Genome wide tests (Patterson'sDandTreeMix) only found evidence of introgression fromH. argophyllus(sister species toH. annuusand also sympatric), but notH. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression usingPCAdmixand found minimal but nonzero introgression fromH. debilisand significant introgression fromH. argophyllusin some populations. Given the paucity of introgression fromH. debilis, we argue that the morphological convergence observed in Texas is probably from standing genetic variation. We also found that genomic differentiation inH. a. texanusis mostly driven by large segregating inversions, several of which have signatures of natural selection based on haplotype frequencies.

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  2. Summary

    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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