[Show abstract][Hide abstract] ABSTRACT: Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement.
[Show abstract][Hide abstract] ABSTRACT: Landrace rice in Thailand consists of managed populations grown under traditional and long-standing agricultural practices. These populations evolve both in response to environmental conditions within the local agro-ecosystem and in response to human activities. Single landraces are grown across varying environments and recently have experienced temporal changes in local environments due to climate change. Here we assess the interplay between natural selection in a changing climate and human-mediated selection on the population genetic structure of Muey Nawng, a local landrace of Thai rice. Genetic diversity and population structure of landrace rice were assessed by a STRUCTURE analysis of 20 microsatellite loci. The first exon–intron junction of the waxy gene was sequenced to determine genotypes for glutinous or non-glutinous grain starch. Muey Nawng rice is genetically variable and is structured based on starch grain types and the level of resistance to gall midge pest. A strong positive correlation was found between genetic diversity and the percentage of gall midge infestation. Variation in the waxy locus is correlated with starch quality; selection for non-glutinous rice appears to involve additional genes. The dynamics of genetic diversity within Muey Nawng rice depends on three factors: (a) a genetic bottleneck caused by strong selection associated with gall midge infestation, (b) selection by local farmers for starch quality and (c) variation introduced by farmer practices for cultivation and seed exchange. These results, when taken in total, document the ability of landrace rice to quickly evolve in response to both natural and human-mediated selection.
Full-text · Article · Jun 2014 · Annals of Applied Biology
[Show abstract][Hide abstract] ABSTRACT: The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011; Cusimano et al., 2012; Nauheimer et al., 2012). However, phylogenetic ambiguity near the root of the tree precludes answering questions about the early evolution of the family. We use Illumina sequencing technology and reference based assembly to resolve the remaining questions in the deep phylogeny of Araceae. We sampled 32 genera and obtained 7 from GenBank (including an outgroup), representing 42 of 44 major clades described in Cusimano et al. (2011). A subsequent phylogenomic analysis based on mitochondrial data was performed to test congruence between plastid and mitochondrial data for phylogenetic inference. Plastid sequences produced strongly supported phylogenies. In contrast, mitochondrial phylogenies were weakly supported and incongruent with chloroplast data (Templeton test, p=<0.0001), although several smaller clades were recovered. New strongly-supported clades seen here are: (1) Anubias and Montrichardia, excluding Calla, form a clade that is sister to the Zantedeschia clade; (2) the South African genus Zantedeschia is sister to the Old World Anchomanes clade; and (3) within the Zantedeschia clade, Philodendron is sister to the rest. Calla and Schismatoglottis form a clade at the base of one of two major clades in Aroideae based on complete chloroplast sequences. Morphological and cytological features support this topology, although statistical support is weak.
Full-text · Article · Mar 2014 · Molecular Phylogenetics and Evolution
[Show abstract][Hide abstract] ABSTRACT: The gene pool of cultivated Asian rice consists of wild rice (Oryza rufipogon Griff.), cultivated rice (O. sativa L.) and a weedy form (O. sativa f. spontanea). All three components are widespread in Thailand, frequently co-occurring within fields and providing the opportunity for gene flow and introgres-sion. The purpose to this study is to understand the on-going evolutionary processes that affect the gene pool of rice by analysis of microsatellite variation. Results indicate that O. rufipogon, the wild ancestor of rice, has high levels of genetic variation both within and among populations. Moreover, the variation is structured pre-dominantly by annual and perennial life history. High levels of variation are detected among cultivars indicating Thai cultivated rice has a broad genetic base with only a 20 % reduction in diversity from its wild ancestor. The weedy rice populations reveal varying levels of genetic variation, from nearly as high as wild rice to near zero. Weedy rice is genetically structured into 2 groups. Some populations of invasive weedy rice are the result of hybridization and gene flow between local wild rice and local cultivated rice in the regions of co-occurrence. Other populations of weedy rice are genetically nearly identical to the local cultivated rice. The diversity analysis indicates that the rice gene pool in Thailand is a dynamic genetic system. Gene flow is ongoing among its three main components, first between cultivated and wild rice resulting in weedy rice. Weedy rice in turn crosses with both cultivated varieties and wild rice.
Full-text · Article · Jan 2013 · Genetic Resources and Crop Evolution
[Show abstract][Hide abstract] ABSTRACT: Premise of the study:
The combination of traditional population genetic studies and species distribution modeling (SDM) provides many new insights in detecting phylogeographic signals. In Asian wild rice (Oryza rufipogon), the progenitor of cultivated Asian rice, geographical subdivision has been documented in many genetic studies although the root cause of this subdivision remains unknown. Surprisingly, environmental factors associated with the spatial and temporal distribution of O. rufipogon have rarely been examined. The aim of this study is to understand the historical distribution of O. rufipogon and its relationship to the current geographical pattern of genetic variation.
We used SDM to examine the present, past, and future distribution of O. rufipogon. The estimated distribution during the Last Glacial Maximum was then compared with genetic data from our previous work.
The predicted paleodistribution of O. rufipogon at the Last Glacial Maximum was separated into disconnected east and west ranges. This past distribution is consistent with the current geographic pattern of genetic variation, with two genetic groups that intergrade. Annual precipitation is the single factor that contributes most to SDM estimates. SDM predictions for 2080 indicate a general trend of increasing probability of presence and range expansion.
(1) The historically disjunct distribution potentially contributes to the current genetic subdivision of O. rufipogon. (2) Water availability is an important factor that limits the distribution of O. rufipogon. (3) Global warming is a lesser threat than other human-mediated factors to the conservation of this endangered species.
Full-text · Article · Nov 2012 · American Journal of Botany
[Show abstract][Hide abstract] ABSTRACT: Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed.
No preview · Article · May 2012 · Molecular Ecology
[Show abstract][Hide abstract] ABSTRACT: • Premise of the study: We developed and characterized microsatellite markers for Byrsonima crassifolia (Malpighiaceae), a widely distributed neotropical fruit tree. • Methods and Results: Eight polymorphic and two monomorphic microsatellite loci were identified and screened in 60 samples from four geographically disparate populations (Bolivia, Brazil, Mexico, and Panama). Each locus exhibited between two and 11 alleles. Expected heterozygosity ranged from 0 to 0.839. All loci amplify in the congeners B. variabilis and B. basiloba, four amplify in B. bucidaefolia, and seven amplify in B. variabilis, although levels of polymorphism have not been assessed. • Conclusions: These loci will provide novel tools for comparing genetic diversity present in cultivated and noncultivated populations of B. crassifolia throughout its range, and may prove valuable in related species.
Preview · Article · Mar 2012 · American Journal of Botany
[Show abstract][Hide abstract] ABSTRACT: Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
Full-text · Article · Jan 2012 · The Plant Journal
[Show abstract][Hide abstract] ABSTRACT: The widespread use of genetically modified crops has precipitated acrimonious debate on the health effects, environmental safety, and ethics of genetically modified agricultural species. The debate is contentious, often with unsubstantiated claims of both potentially harmful and beneficial effects. Here we examine the possible effects of GM agriculture on issues of the environment and biodiversity. Possible negative aspects of GM agriculture include unanticipated effects on non-target organisms, gene flow between GM crop or animal and closely related wild species, and hybridization resulting in new weedy taxa. Positive effects include reduction in agrochemical use, reduction in harvest pressure on native species, and new methods for bioremediation, among others. The demand for GM crops in developing countries is expected to be high, due to their potential for greatly enhancing yields. But, the widespread application of GM agriculture to the tropics presents new challenges. In the tropics, systems of agriculture are both variable and different than in developed countries. Tropical regions contain high levels of native biodiversity, and many wild relatives of agricultural species are often growing within the vicinity of their derived domesticated plants and animals. Assessment of the environmental consequences of GM agriculture is essential. In some cases environmental benefits may accrue, in other cases GM agriculture may negatively effect both the environment and biodiversity. Only by carefully applying science-based knowledge can the effects of GM agriculture, both positive and negative, be accurately determined.
[Show abstract][Hide abstract] ABSTRACT: Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill-Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species.
[Show abstract][Hide abstract] ABSTRACT: Cowpea (Vigna unguiculata spp unguiculata) is adapted to the drier agro-ecological zones of West Africa where it is a major source of dietary protein and widely used as a fodder crop. Improving the productivity of cowpea can enhance food availability and security in West Africa. Insect predation--predominately from the legume pod borer (Maruca vitrata), flower thrips (Megalurothrips sjostedti) and a complex of pod-sucking bugs (e.g., Clavigralla spp)--is a major yield-limiting factor in West African cowpea production. Dramatic increases in yield are shown when M. vitrata is controlled with insecticides. However, availability, costs, and safety considerations limit pesticides as a viable option for boosting cowpea production. Development of Bt-cowpea through genetic modification (GM) to control the legume pod borer is a promising approach to cowpea improvement. Cowpea expressing the lepidopteran-active Cry1Ab protein from Bacillus thuringiensis is being developed as a first generation Bt-cowpea crop for West Africa. Appropriate stewardship of Bt-cowpea to assure its sustainability under West African conditions is critical to its successful development. A first step in this process is an environmental risk assessment to determine the likelihood and magnitude of adverse effects of the Cry1Ab protein on key environmental protection goals in West Africa. Here we describe the results of an expert panel convened in 2009 to develop the problem formulation phase for Bt-cowpea and to address specific issues around gene flow, non-target arthropods, and insect resistance management.
[Show abstract][Hide abstract] ABSTRACT: Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200-13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.
Full-text · Article · May 2011 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Anthropogenic climate change may threaten many species with extinction. However, species at risk today survived global climate change in recent geological history. Describing how habitat tracking and adaptation allowed species to survive warming since the end of the Pleistocene can indicate the relative importance of dispersal and natural selection during climate change. By taking this historical perspective, we can identify how contemporary climate change could interfere with these mechanisms and threaten the most vulnerable species. We focused on a group of closely related plant species in the genus Dodecatheon (Primulaceae) in eastern North America. Two rare species (Dodecatheon amethystinum and Dodecatheon frenchii) that are endemic to patchy cool cliffs may be glacial relicts whose ranges constricted following the last glacial maximum. Alternatively, these species may be extreme ecotypes of a single widespread species (Dodecatheon meadia) that quickly adapted to microclimatic differences among habitats. We test support for these alternative scenarios by combining ecophysiological and population genetic data at a regional scale. An important ecophysiological trait distinguishes rare species from D. meadia, but only a few northern populations of D. amethystinum are genetically distinctive. These relict populations indicate that habitat tracking did occur with historical climate change. However, relatively stronger evidence for isolation by distance and admixture suggests that local adaptation and genetic introgression have been at least as important. The complex response of Dodecatheon to historical climate change suggests that contemporary conservation efforts should accommodate evolutionary processes, in some cases by restoring genetic connectivity between ecologically differentiated populations.
Preview · Article · Mar 2011 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Pinustorreyana Parry ex Carrière has only two extant populations, containing less than 10 000 individuals in total. The two populations are in California, in San Diego County and on the island Santa Rosa. They are separated by 280 km and have been isolated for more than 8000 years. Random genetic drift over this period of time should have resulted in genetic differentiation between the two populations. We surveyed the chloroplast DNA of 24 individuals of P. torreyana for both restriction site and length polymorphisms with 26 restriction enzymes. The San Diego and Santa Rosa populations were monomorphic at over 150 restriction sites. Moreover, there was no detectable length variation. The results of this study suggest that P. torreyana has been monomorphic at these sites since before the two populations were isolated.
No preview · Article · Feb 2011 · Canadian Journal of Forest Research
[Show abstract][Hide abstract] ABSTRACT: The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.
Full-text · Article · Jan 2011 · Molecular Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase lla (Sslla) is a major candidate gene for starch quality variation. Within Sslla, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in Sslla that is responsible for starch quality variation in rice, we sequenced the Sslla exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in Sslla enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.
[Show abstract][Hide abstract] ABSTRACT: Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.
[Show abstract][Hide abstract] ABSTRACT: Ludwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of the Ludwigia sect. Isnardia, which is a polyploid complex (x = 8) of five species distributed in North America. The phylogeny of L. sect. Isnardia was reconstructed based on sequences of cpDNA atpB-rbcL intergenic spacer and nrITS (internal transcribed spacer). Most L. sect. Isnardia species are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted at L. sect. Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploid L. spathulata are nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. Allopolyploid L. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggesting L. palustris as the paternal genome donor. Ludwigia brevipes may have arisen via bi-directional hybridization between L. palustris and L. arcuata followed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species of L. sect. Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution in L. sect. Isnardia.