skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Deleterious variants in Asian rice and the potential cost of domestication
Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a “cost of domestication”. Here, we investigated the numbers and frequencies of deleterious variants in Asian rice (Oryza sativa), focusing on two varieties (japonica and indica) and their wild relative (O. rufipogon). We investigated three signals of a potential cost of domestication in Asian rice relative to O. rufipogon: an increase in the frequency of deleterious SNPs (dSNPs), an enrichment of dSNPs compared with synonymous SNPs (sSNPs), and an increased number of deleterious variants. We found evidence for all three signals, and domesticated individuals con- tained 􏰚3–4% more deleterious alleles than wild individuals. Deleterious variants were enriched within low recombin- ation regions of the genome and experienced frequency increases similar to sSNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping both deleterious and neutral diversity in rice.  more » « less
Award ID(s):
1339393
PAR ID:
10065382
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Molecular Biology and Evolution
Volume:
34
Issue:
4
ISSN:
0737-4038
Page Range / eLocation ID:
msw296
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; (, Molecular Biology and Evolution)
    Purugganan, Michael (Ed.)
    Abstract Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type—which included inversions, duplications, deletions, translocations, and mobile element insertions—was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest. 
    more » « less
  2. ; ; ; ; (, Weed Science)
    Abstract There are two species of cultivated rice in the world— Oryza sativa L. from Asia and Oryza glaberrima Steud. from Africa. The former was domesticated from the wild progenitor Oryza rufipogon Griff. and the latter from the African wild rice species Oryza barthii A. Shiv. The first known center of rice cultivation in China generated the O. sativa subspecies japonica . The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded or dry-drill-seeded rice. Weedy rice ( Oryza spp.) is the most difficult weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop de-domestication, and regionalized adaptation have resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice— Oryza sativa L. and Oryza sativa f. spontanea . Genomic data show that O. sativa L. applies to weedy rice populations derived from cultivated O. sativa , whereas O. sativa f. spontanea applies only to weedy types that primarily descended from O. rufipogon . Neither of these names applies to African weedy rice, which is of African wild rice or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, Proceedings of the National Academy of Sciences)
    Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis viniferassp.sylvestris) and cultivated (V. viniferassp.vinifera) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources. 
    more » « less
  4. ; ; ; ; ; ; ; (, The Plant Journal)
    SUMMARY We examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within the genusOryza. These included three varieties from subspecies within domesticated Asian riceO. sativaas well as their closely related wild relativesO. rufipogonandO. meridionalis. We used the high‐resolution chromosome conformation capture technique Micro‐C, which we modified for use in rice. Our analysis of rice TADs shows that TAD boundaries have high transcriptional activity, low methylation levels, low transposable element (TE) content, and increased gene density. We also find a significant correlation of expression levels for genes within TADs, suggesting that they do function as genomic domains with shared regulatory features. Our findings indicate that animal and plant TADs may share more commonalities than were initially thought, as evidenced by similar genetic and epigenetic signatures associated with TADs and boundaries. To examine 3D genome divergence, we employed a computer vision‐based algorithm for the comparison of chromatin contact maps and complemented this analysis by assessing the evolutionary conservation of individual TADs and their boundaries. We conclude that overall chromatin organization is conserved in rice, and 3D structural divergence correlates with evolutionary distance between genomes. We also note that individual TADs are not well conserved, even at short evolutionary timescales. 
    more » « less
  5. ; ; ; ; (, Journal of Experimental Botany)
    Abstract The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email