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Browsing by Subject "legume"

Now showing 1 - 8 of 8
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    Data and analysis scripts for the paper: Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts
    (2018-10-15) Muller, Katherine E; Denison, R Ford; mulle374@umn.edu; Muller, Katherine E; University of Minnesota Department of Ecology Evolution and Behavior; University of Minnesota Graduate Program in Plant and Microbial Biology; Denison Lab, University of Minnesota
    This repository contains all analysis scripts and data files for Katherine Muller's first dissertation chapter: Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts. The data are being released to meet a publisher's data sharing requirements. The paper addresses two gaps in knowledge needed to understand how polyhydroxybutyrate (PHB), a storage compound accumulated by many nitrogen-fixing rhizobia during interactions with legume hosts, contributes to the in the evolution of the legume rhizobia mutualism. Part 1 provides evidence for wide-ranging, heritable phenotypic variation within natural rhizobia populations in the amount of PHB stored during symbiosis. The conclusions are based on observations of phenotypic variation in rhizobial PHB per cell measured in the field (soybean and Chamaecrista fasciulata) and in greenhouse plants inoculated with field soil, plus experiments with rhizobia isolates showing high heritability in PHB per cell within soybean nodules. Part 2 explores the implications of heritable PHB variation for variation in fitness during the free-living stage using modeling and laboratory experiments. The model shows that the levels of PHB accumulated in nodules could potentially support survival functions for many years after symbiosis, based on published metabolic parameters and soil temperature measurements. The experiments compared survival and PHB use among rhizobia isolates with heritable variation in initial PHB supply, incubated in starvation cultures for over a year. The results on survival were inconclusive (partially due to contamination), but the results on PHB use suggest that variation in PHB accumulation in nodules could contribute to fitness of individual rhizobia long after they are released into the cell.
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    Defense-related gene families in the model legume, Medicago truncatula: computational analysis, pan-genome characterization, and structural variation
    (2015-06) Zhou, Peng
    Medicago truncatula is a model for investigating legume genetics and the evolution of legume-rhizobia symbiosis. Over the past two decades, two large gene families in M. truncatula, the nucleotide-binding site leucine-rich repeat (NBS-LRR) family and the nodule-specific, cysteine-rich (NCR) gene family, have received considerable attention due to their involvement in disease resistance and nodulation, large family size, and high nucleotide and copy number diversity. While NBS-LRRs have been found in all plant species and therefore relatively well characterized at the sequence level, members of the cysteine-rich protein (CRP) families, including NCRs, have generally been overlooked by popular similarity search tools and gene prediction techniques due to their (a) small size, (b) high sequence divergence among family members and (c) limited availability of expression evidence. In this thesis, I first developed a homology-based gene prediction program (Small Peptide Alignment Detection Algorithm, i.e., SPADA) to accurately predict small peptides including CRPs at the genome level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed. Numerous mis-annotations in the current Arabidopsis and Medicago genome databases were found by SPADA, most supported by RNA-Seq data. As a homology-based gene prediction tool, SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologues) as well as non-secreted peptides outside the plant kingdom. I then comprehensively annotated the NBS-LRR and NCR gene families in the Medicago reference genome (version 4.0), and set out to characterize natural variation of these genes in diverse M. truncatula accessions. Previous studies using whole-genome sequence data to identify sequence polymorphisms (SNPs and short Insertion / Deletions) relied on mapping short reads to a single reference genome. However, limitations of read-mapping approaches have hindered variant detection, especially characterization of repeat-rich and highly divergent regions. As a result, studies of these large gene families are also hindered due to high sequence similarity among family members along with high divergence among accessions. In this work I constructed high-quality de novo assemblies for 15 M. truncatula accessions. This allowed me to detect novel genetic variation that would not have been found by mapping reads to a single reference. This analysis led to a within-species diversity estimate 70% higher than previous mapping-based resequencing efforts, even using a smaller sample size. These results clearly demonstrate that de novo assembly-based comparison is both more accurate and precise than mapping-based variant calling in exploring variation in repetitive and highly divergent regions. For the first time in plants, my results enable systematically identification and characterization of different types of structural variants (SVs) using a synteny-based approach. This analysis suggests that, depending on the divergence from the reference accession, 7% to 21% of the entire genome is involved in large structural changes, affecting 10% to 28% of all gene models. The results identify 64 Mbp of unique sequence segments absent in the reference, including 30 Mbp shared by at least 2 accessions and 34 Mbp of accessions-specific sequences, thus expanding the Medicago reference space (389-Mbp) by 16%. Evidence-based annotation of the 15 de novo assemblies revealed that more than half of reference gene models were structurally diverse (lower than 60% sequence similarity) in at least one other accession. Not surprisingly, the NBS-LRR gene family harbors by far the highest level of nucleotide diversity, large effect single nucleotide changes, mean pairwise protein distance and copy number variation (levels comparable with transposable elements), consistent with the rapidly-evolving dynamics of disease resistance phenotypes. Characterization of deletion and tandem duplication events in the NBS-LRR and NCR gene families suggests accession-specific subfamily expansion / contraction patterns. This work illustrates the value of multiple de novo assemblies and the strength of comparative genomics in exploring and characterizing novel genetic variation within a population, and provides insights in understanding the impact of SVs on genome architecture and large gene families underlying important traits.
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    Effect of variation in nitrogen environment and legume and rhizobia genetics on the outcome of the legume-rhizobium mutualism.
    (2017-09) Nedveck, Derek
    The legume-rhizobium mutualism has been studied for its agricultural importance from the nitrogen that the rhizobia fix in exchange for carbon from the plant, and additionally used as a model to understand the evolution of mutualisms. The objective of this research was to further understand the variation present in natural populations of legumes and rhizobia, and to use a population perspective to build upon the work done with inbred plant lines and single strains of rhizobia. I applied a gradient of nitrogen (N) to a single cultivar of Lotus corniculatus inoculated with a population of rhizobia to develop expectations of how L. corniculatus responds to N addition. I then used a full-factorial greenhouse experiment with natural populations of L. corniculatus and their associated rhizobia to assess the amount of variation present in natural populations, and how they respond to N addition. From this, I found that plant populations did not show variation in nodule traits that could affect rhizobial fitness, whereas rhizobial populations showed variation in all traits measured. The effect of N addition on L. corniculatus in general causes a decrease in nodule size, although when tested in the context of natural populations, there was a plant population-dependent effect, as some populations increased, decreased, or did not alter the size of their nodules. This work underscores the importance to incorporate population scale information in how this mutualism responds to varying environmental conditions. Furthermore, considering the amount of variation found in rhizobial populations, future work should focus on sampling legumes and their associated rhizobia in order to have a more accurate measure of the amount of variation present in the mutualism.
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    Evolution of energy storage traits in symbiotic rhizobia
    (2018-01) Muller, Katherine
    The mutually-beneficial symbiosis between legume plants and nitrogen-fixing rhizobia involves an inherent conflict-of-interest over how rhizobia allocate the resources they receive from the host plant. In theory, rhizobia could enhance their future fitness by diverting resources from nitrogen-fixation into storage compounds like polyhydroxybutyrate (PHB). Although the conflict-of-interest between PHB accumulation and nitrogen-fixation has been discussed as a driving factor in the evolution of legume-rhizobia interactions, its role in natural populations is unclear. Therefore, this dissertation fills in key empirical gaps between what we know about the functional role of PHB and hypotheses about how natural selection might act on continuous variation in the amount of PHB that rhizobia acquire during symbiosis. The first chapter assesses the extent of heritable phenotypic variation within natural rhizobia populations interacting with soybean (Glycine max) and partridge pea (Chamaecrista fasciculata) and evaluates implications for fitness in the free-living stage after rhizobia are released from nodules. The results from my first chapter show that 1) natural populations of rhizobia contain heritable, quantitative variation in the amount of PHB they accumulate during symbiosis (a prerequisite for evolution by natural selection) and, 2) natural selection on PHB accumulation may be mediated by how rhizobia allocate PHB over time and among life functions, which could vary independently from traits underlying the amount of PHB acquired during symbiosis. The second chapter assesses phenotypic response to selection based on resident rhizobia populations from long-term agricultural plots varying in host (soybean) or non-host (maize) frequency over years. The mean PHB per cell (measured in nodules) was two times higher in rhizobia populations from plots with 5 or 30 years of continuous maize than from plots where soybean was grown in the previous year. An apparent decrease in mean PHB per cell after the first year of soybean following five years of maize supports the hypothesis that low-PHB rhizobia have higher reproduction in nodules, perhaps due to host sanctions against rhizobia that divert more resources to PHB. A model used to interpret the results suggests that, 1) PHB acquired during symbiosis may contribute to fitness variation for several years after the last host crop, and 2) host sanctions against less-beneficial rhizobia may be stronger in the first soybean crop due to a combination of lower initial rhizobia population size and negative frequency-dependent selection during symbiosis. Collectively, these findings provide empirical support for previously unsubstantiated hypotheses about how conflicts-of-interest over resource allocation contribute to the evolution of the legume-rhizobia mutualism and develop a more nuanced framework for future research.
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    Fitness and Adaptive Capacity in a Minnesota Prairie
    (2016-12) Eule-Nashoba, Amber
    Wild populations are subject to environments that are changing at unprecedented rates. Assessing natural selection and the capacity to adapt in wild populations is crucial to planning for and understanding how species will fare under climate change. The goal of this research was to empirically examine selection and adaptive capacity in a natural population of Chamaecrista fasciculata. In Chapter 1, I present an empirical quantitative genetic study of C. fasciculata to predict the rate of change in mean fitness using Fisher’s Fundamental Theorem of Natural Selection (FTNS). The additive genetic variance for fitness was found to be substantial and statistically significant in both 2013 and 2014. Application of FTNS predicts increases in mean fitness of 1.68 (2013) seeds and 8.08 (2014) seeds in the next generation. These findings demonstrate that this population has the genetic capacity to respond to natural selection and is predicted to increase in fitness and thus, become better adapted to their environment. The objective of Chapter 2 is to compare predicted and observed mean fitness of C. fasciculata in a natural selective environment. Observed mean fitness of both second-generation cohorts was, however, lower than predicted by the FTNS and lower than their respective first-generation cohorts. However, comparison of first and second-generation cohorts growing in the same year and, hence, common conditions, demonstrated an increase in mean fitness. Thus, environmental differences between years, as well as genotype-by-environment interaction, contribute to the deviation of observed from predicted mean fitness. In Chapter 3, I performed a quantitative genetic study of phenotypic selection on C. fasciculata to examine the effect of selection and environment on the phenology of germination and reproductive initiation. In this population, selection for advancement in reproductive stage was detected, as well as a response of 2.2 days earlier flowering in the second generation. Overall, findings of these chapters present a population that has demonstrated a response to selection in flowering phenology and significant genetic variation for evolutionary fitness. This evidence of adaptation and substantial adaptive capacity conveys crucial information regarding the likelihood of population persistence, information that could be utilized for other species towards conservation goals.
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    Intermediate Wheatgrass Nitrogen Dynamics: Nitrate Leaching Prevention and Nitrogen Supply via Legume Intercrops
    (2021-07) Reilly, Evelyn
    We compared soil and soil water nitrate concentrations, root biomass, and yield in intermediate wheatgrass (IWG; Thinopyrum intermedium) and a corn-soybean rotation over three years. Nitrate was 77-96% lower under IWG than the annual system, while root biomass was higher. IWG grain yields were 854, 434, and 222 kg ha-1 for Years 1-3 and biomass averaged 4.65 Mg ha-1 yr-1. IWG effectively reduces soil solution NO3--N concentrations even on sandy soils, supporting its potential for broader adoption on vulnerable land. We also assessed grain and biomass yield and N dynamics in response to mineral fertilizer and six legume intercrops. Treatments affected N dynamics and IWG biomass but not grain yields. N transfer rates ranged from 0 to 27% but legume biomass was negatively associated with IWG grain yield, suggesting competition in addition to nitrogen supply. Overall, alfalfa, red clover, and birdsfoot trefoil were among the best options for intercrops.
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    Legume cover crops in high tunnels: Field evaluation for soil health and controlled environment freezing tolerance
    (2018-02) Perkus, Elizabeth
    This thesis explores legume cover crops as a possible management tool for nitrogen fertility and soil health maintenance in high tunnels. Projects include: 1) a two-year field evaluation of three fall planted cover crop mixes for winter annual production, 2) a controlled environment freezing tolerance study of hairy vetch (Vicia villosa) and red clover (Trifolium pratense) using simulated high tunnel conditions, and 3) a one-year field evaluation of three spring planted cover crop mixes. Cover crop mixes used in projects 1 and 3 consisted of: a) red clover monoculture (T. pratense), b) Austrian winter pea/winter rye 1:1 biculture (Pisum sativum and Secale cereal), and c) hairy vetch/tillage radish/winter rye 4:1:15 mix (V. villosa, Raphanus sativus, and S. cereal). Winter annual legume results show a wide range of biomass nitrogen additions (19.7 to 365.0 kg N ha-1), with no negative impact cash crop yield or soil health measures.
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    SINful Consequences of Cover Cropping: Soil Inorganic Nitrogen (SIN) Provision and Retention from Warm-Season Cover Crops for Northern US Region Vegetable Production
    (2023) Moses, Ezra
    Warm-season cover crops are promising tools to meet vegetable crop nitrogen (N) demands while preventing N losses but more information is needed to achieve these goals in the northern US region. We explored warm-season cover crops in two rotations in Minnesota to evaluate biomass production, N provision and retention benefits, and impacts on vegetable yields. Warm-season cover crop biomass production ranged from 628-13,350 kg ha-1 and did not frequently exceed a weedy control. Soil nitrate decreased beneath cover crops and increased post-termination, demonstrating seasonal patterns potentially synchronous with vegetable demand. Cover crops reduced nitrate leaching to buried resin lysimeters by up to 50% but not significantly. Vegetable yields were often decreased following cover crop treatments, though legumes boosted vegetable yield in limited site-years. Evidence from this study suggests that warm-season cover crops could synchronize seasonal N patterns with vegetable demand but may not boost vegetable yields.