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Kanapeckas KL, Tseng TM, Vigueira CC, Ortiz A, Bridges WC, Burgos NR, Fischer AJ, Lawton-Rauh A. Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (Oryza sativa sp.) in Arkansas and California. PEST MANAGEMENT SCIENCE 2018; 74:1404-1415. [PMID: 29205860 DOI: 10.1002/ps.4820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/29/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations. RESULTS Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas. CONCLUSION Recent de-domestication of weedy species - such as in California weedy rice - can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Kimberly L Kanapeckas
- South Carolina Department of Natural Resources Marine Resources Research Institute and College of Charleston, Hollings Marine Laboratory, Charleston, SC, USA
| | - Te-Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, MS, USA
| | | | - Aida Ortiz
- Facultad de Agronomía, Universidad Central de Venezuela Maracay, Aragua, Venezuela
| | - William C Bridges
- Department of Mathematical Sciences, Clemson University, Clemson, SC, USA
| | - Nilda R Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Albert J Fischer
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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Mattila TM, Tyrmi J, Pyhäjärvi T, Savolainen O. Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata. Mol Biol Evol 2017; 34:2665-2677. [PMID: 28957505 DOI: 10.1093/molbev/msx193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaakko Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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Mattila TM, Aalto EA, Toivainen T, Niittyvuopio A, Piltonen S, Kuittinen H, Savolainen O. Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization. Mol Ecol 2016; 25:581-97. [PMID: 26600237 DOI: 10.1111/mec.13489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022]
Abstract
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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Affiliation(s)
- Tiina M Mattila
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Esa A Aalto
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Tuomas Toivainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Susanna Piltonen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Outi Savolainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
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Falahati-Anbaran M, Lundemo S, Ansell SW, Stenøien HK. Contrasting patterns of genetic structuring in natural populations of Arabidopsis lyrata Subsp. petraea across different regions in northern Europe. PLoS One 2014; 9:e107479. [PMID: 25226024 PMCID: PMC4166467 DOI: 10.1371/journal.pone.0107479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/11/2014] [Indexed: 01/08/2023] Open
Abstract
Level and partitioning of genetic diversity is expected to vary between contrasting habitats, reflecting differences in strength of ecological and evolutionary processes. Therefore, it is necessary to consider processes acting on different time scales when trying to explain diversity patterns in different parts of species' distributions. To explore how historical and contemporary factors jointly may influence patterns of genetic diversity and population differentiation, we compared genetic composition in the perennial herb Arabidopsis lyrata ssp. petraea from the northernmost parts of its distribution range on Iceland to that previously documented in Scandinavia. Leaf tissue and soil were sampled from ten Icelandic populations of A. lyrata. Seedlings were grown from soil samples, and tissue from above-ground and seed bank individuals were genotyped with 21 microsatellite markers. Seed bank density in Icelandic populations was low but not significantly different from that observed in Norwegian populations. While within-population genetic diversity was relatively high on Iceland (H(E) = 0.35), among-population differentiation was low (F(ST) = 0.10) compared to Norwegian and Swedish populations. Population differentiation was positively associated with geographical distance in both Iceland and Scandinavia, but the strength of this relationship varied between regions. Although topography and a larger distribution range may explain the higher differentiation between mountainous Norwegian relative to lowland populations in Sweden, these factors cannot explain the lower differentiation in Icelandic compared to Swedish populations. We propose that low genetic differentiation among Icelandic populations is not caused by differences in connectivity, but is rather due to large historical effective population sizes. Thus, rather than contemporary processes, historical factors such as survival of Icelandic lineages in northern refugia during the last glacial period may have contributed to the observed pattern.
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Affiliation(s)
- Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; School of Biology and Center of Excellence in Phylogeny of Living Organisms, University of Tehran, Tehran, Iran
| | - Sverre Lundemo
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Stephen W Ansell
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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Toivainen T, Pyhäjärvi T, Niittyvuopio A, Savolainen O. A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata. Mol Ecol 2014; 23:1040-52. [PMID: 24471518 DOI: 10.1111/mec.12682] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/14/2013] [Accepted: 01/08/2014] [Indexed: 11/29/2022]
Abstract
Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57-kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4-kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
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Affiliation(s)
- Tuomas Toivainen
- Department of Biology, University of Oulu, Oulu, 90014, Finland; Biocenter Oulu, University of Oulu, Oulu, 90014, Finland
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