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Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties.
ABSTRACT: Transcriptomic responses of plants to weed presence gives insight on the physiological and molecular mechanisms involved in the stress response. This study evaluated transcriptomic and morphological responses of two teosinte (Zea mays ssp parviglumis) (an ancestor of domesticated maize) lines (Ames 21812 and Ames 21789) to weed presence and absence during two growing seasons. Responses were compared after 6 weeks of growth in Aurora, South Dakota, USA. Plant heights between treatments were similar in Ames 21812, whereas branch number decreased when weeds were present. Ames 21789 was 45% shorter in weedy vs weed-free plots, but branch numbers were similar between treatments. Season-long biomass was reduced in response to weed stress in both lines. Common down-regulated subnetworks in weed-stressed plants were related to light, photosynthesis, and carbon cycles. Several unique response networks (e.g. aging, response to chitin) and gene sets were present in each line. Comparing transcriptomic responses of maize (determined in an adjacent study) and teosinte lines indicated three common gene ontologies up-regulated when weed-stressed: jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase (3-O and 7-O). Overall, morphologic and transcriptomic differences suggest a greater varietal (rather than a conserved) response to weed stress, and implies multiple responses are possible. These findings offer insights into opportunities to define and manipulate gene expression of several different pathways of modern maize varieties to improve performance under weedy conditions.
Project description:Weed presence early in the life cycle of maize (typically, from emergence through the 8 to 12 leaf growth stage) can reduce crop growth and yield and is known as the critical weed-free period (CWFP). Even if weeds are removed during or just after the CWFP, crop growth and yield often are not recoverable. We compared transcriptome responses of field-grown hybrid maize at V8 in two consecutive years among plants grown under weed-free and two weed-stressed conditions (weeds removed at V4 or present through V8) using RNAseq analysis techniques. Compared with weed-free plant responses, physiological differences at V8 were identified in all weed-stressed plants and were most often associated with altered photosynthetic processes, hormone signaling, nitrogen use and transport, and biotic stress responses. Even when weeds were removed at V4 and tissues sampled at V8, carbon: nitrogen supply imbalance, salicylic acid signals, and growth responses differed between the weed-stressed and weed-free plants. These underlying processes and a small number of developmentally important genes are potential targets for decreasing the maize response to weed pressure. Expression differences of several novel, long noncoding RNAs resulting from exposure of maize to weeds during the CWFP were also observed and could open new avenues for investigation into the function of these transcription units.
Project description:A novel weed has recently emerged, causing serious agronomic damage in one of the most important maize-growing regions of Western Europe, the Northern Provinces of Spain. The weed has morphological similarities to a wild relative of maize and has generally been referred to as teosinte. However, the identity, origin or genetic composition of 'Spanish teosinte' was unknown. Here, we present a genome-wide analysis of single-nucleotide polymorphism (SNP) data for Spanish teosinte, sympatric populations of cultivated maize and samples of reference teosinte taxa. Our data are complemented with previously published SNP datasets of cultivated maize and two Mexican teosinte subspecies. Our analyses reveal that Spanish teosinte does not group with any of the currently recognized teosinte taxa. Based on Bayesian clustering analysis and hybridization simulations, we infer that Spanish teosinte is of admixed origin, most likely involving Zea mays ssp. mexicana as one parental taxon, and an unidentified cultivated maize variety as the other. Analyses of plants grown from seeds collected in Spanish maize fields and experimental crosses under controlled conditions reveal that hybridization does occur between Spanish teosinte and cultivated maize in Spain, and that current hybridization is asymmetric, favouring the introgression of Spanish teosinte into cultivated maize, rather than vice versa.
Project description:Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean. Samples were collected from two treatments ("Control" and "Weedy") with six biological replicates (2008, 2009, and twop each for 2010 and 2011) for each treatment.
Project description:Microarray analysis was used to identify changes in gene expression in maize leaves collected from plants at the 11-14 leaf stage that resulted from competition with velvetleaf. Genes involved in carbon and nitrogen utilization, photosynthesis, growth and development, oxidative stress, signal transduction, responses to auxin and ethylene, and zinc transport are repressed in maize growing in competition with velvetleaf. Very few genes are induced due to competition with velvetleaf, and those that are provide little indication of the physiological response of maize. No significant differences were observed in multiple genes responsive to water stress or sequestering/transporting most micronutrients indicating that these stresses are not a major component of velvetleaf competition with maize at the developmental stage tested. Keywords: Stress response (weed competition) Overall design: Maize plants were grown in 8 separate plots. Four of the plots were seeded with velvetleaf (1W-4W) and four were hand cultivated periodically to remove most weeds throughout the growing season (1-4). Samples of leaf material was collected from four plants in each plot and pooled. A balanced labeling comparison (R vs B) of weedy verses control was done with 10 independent hybridizations. Thus, experiment 1R4WB represents the comparison of control sample 1 labeled with Cy3 (R) to weedy sample 4 labeled with Cy5(B).
Project description:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement.In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 retained introns with transposable element (TE) sequences were detected in maize, which is far more than 9 retained introns with TEs detected in teosinte. This indicates that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3864 genes were significantly different between maize and teosinte. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes.We suggest that both maize and teosinte share similar AS mechanisms, but more genes have increased AS complexity during domestication from teosinte to maize. Importantly, a subset of AS level-increased genes that encode transcription factors and stress-responsive proteins may have been selected during maize improvement.
Project description:Weedy rice is a representative of the extensive group of feral weeds that derive from crops, but has returned to the lifestyle of a wild species. These weeds develop either from a hybridization of crops with wild relatives (exoferality), or by mutation of crops to weedy forms (endoferality). Due to the close relation of weed and crop, the methods for weed-targeted containment are limited to date. A deeper understanding of the development of such weeds might help to design more efficient and sustainable approaches for weed management. Weedy rice poses a serious threat to rice yields worldwide. It is widely accepted that weedy rice has originated independently in different regions all over the world. However, details of its evolution have remained elusive. In the current study, we investigated the history of weedy rice in northern Italy, the most important rice-growing area in Europe. Our approach was to analyze genes related to weedy traits (SD1, sh4, Rc) in weedy rice accessions compared to cultivars, and to integrate these results with phenotypic and physiological data, as well as historical information about rice farming in Italy. We arrive at a working model for the timeline of evolution of weedy rice in Italy indicating that both exoferality and endoferality acted as forces driving the development of the diverse weedy rice populations found in the region today. Models of weed evolution can help to predict the direction which weed development might take and to develop new, sustainable methods to control feral weeds.
Project description:Weedy rice (Oryza spp.) is a problematic weed of cultivated rice (O. sativa) around the world. Recent studies have established multiple independent evolutionary origins of weedy rice, raising questions about the traits and genes that are essential for the evolution of this weed. Among world regions, South Asia stands out due to the heterogeneity of its weedy rice populations, which can be traced to at least three origins: two through de-domestication from distinct cultivated rice varieties, and one from local wild rice (O. rufipogon/O. nivara). Here we examine five traits considered typical of or advantageous to weedy rice in weedy, cultivated and wild rice samples from South Asia. We establish that convergence among all three weed groups occurs for easy seed shattering, red pericarp color, and compact plant architecture, suggesting that these traits are essential for weed success in the South Asian agricultural environment. A high degree of convergence for black hull color is also seen among weeds with wild ancestors and weeds evolved from the aus cultivated rice group. We also examine polymorphism in five known domestication candidate genes, and find that Rc and Bh4 are associated with weed seed pericarp color and hull color, respectively, and weedy alleles segregate in the ancestral populations, as do alleles for the seed dormancy-linked gene Sdr4 The presence of a domestication related allele at the seed shattering locus, sh4, in weedy rice populations with cultivated ancestry supports a de-domestication origin for these weedy groups, and raises questions about the reacquisition of the shattering trait in these weedy populations. Our characterization of weedy rice phenotypes in South Asia and their associated candidate genes contribute to the emerging understanding of the mechanisms by which weedy rice evolves worldwide, suggesting that standing ancestral variation is often the source of weedy traits in independently evolved groups, and highlighting the reservoir of genetic variation that is present in cultivated varieties as well as in wild rice, and its potential for phenotypic evolution.
Project description:Transgene introgression into crop weedy/wild relatives can provide natural selective advantages, probably causing undesirable environmental impact. The advantages are likely associated with factors such as transgenes, selective pressure, and genetic background of transgene recipients. To explore the role of the environment and background of transgene recipients in affecting the advantages, we estimated the fitness of crop-weed hybrid lineages derived from crosses between marker-free insect-resistant transgenic (Bt/CpTI) rice with five weedy rice populations under varied insect pressure. Multiway anova indicated the significant effect of both transgenes and weedy rice genotypes on the performance of crop-weed hybrid lineages in the high-insect environment. Increased fecundity was detected in most transgene-present F1 and F2 hybrid lineages under high-insect pressure, but varied among crop-weed hybrid lineages with different weedy rice parents. Increased fecundity of transgenic crop-weed hybrid lineages was associated with the environmental insect pressure and genotypes of their weedy rice parents. The findings suggest that the fitness effects of an insect-resistant transgene introgressed into weedy populations are not uniform across different environments and genotypes of the recipient plants that have acquired the transgene. Therefore, these factors should be considered when assessing the environmental impact of transgene flow to weedy or wild rice relatives.
Project description:Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.
Project description:Increased infestation of weedy rice-a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (He?=?0.62) and limited among-population differentiation (Fst?=?0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.