Plant Science & Landscape Architecture Research Works
Permanent URI for this collectionhttp://hdl.handle.net/1903/1603
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Item The Fate of Nitrogen During Agricultural Intensification in East Africa: Nitrogen Budgets in Contrasting Agroecosystems(Wiley, 2023-07-09) Tully, K. L.; Hickman, J. E.; Russo, T. A.; Neill, C.; Matata, P.; Nyadzi, G.; Mutuo, P.; Palm, C. A.The intensification of agricultural systems in sub-Saharan Africa (SSA) is necessary to reduce poverty and improve food security, but increased nutrient applications in smallholder systems could have negative consequences for water quality, greenhouse gas emissions, and air quality. We tracked nitrogen (N) inputs and measured maize (Zea mays) biomass, grain yields, N leaching, and nitric oxide (NO) and nitrous oxide fluxes from a clayey soil in Yala, Kenya and a sandy soil in Tumbi, Tanzania, with application rates of 0, 50, 75, 100, 150, and 200 kg N ha−1 yr−1 over two cropping seasons. Maize yields were 4.5 times higher in Yala than Tumbi, but yields plateaued at both sites with fertilizer applications at or above 100 kg N ha−1 yr−1. Partial N budgets in Yala were typically negative, meaning more N was exported in maize biomass plus grain or lost from the system than was added in fertilizer. In Tumbi, N budgets were negative at lower fertilizer levels but positive at higher fertilizer levels. At both sites most (96%) of the N was lost through maize biomass/grain removal and N leaching. Fertilizer additions at or less than 50 kg N ha−1 yr−1 on these two contrasting sites resulted in minor gaseous N losses, and fertilizer additions less than 200 kg N ha−1 yr−1 caused relatively little change to N leaching losses. This indicates that the modest increases in fertilizer use required to improve maize yields will not greatly increase cropland N losses.Item CRISPR-enabled investigation of fitness costs associated with the E198A mutation in β-tubulin of Colletotrichum siamense(Frontiers, 2023-11-02) Cosseboom, Scott D.; Agarwal, Chiti; Hu, MengjunIntroduction: Understanding fitness costs associated with fungicide resistance is critical to improve resistance management strategies. E198A in b-tubulin confers resistance to the fungicide thiophanate-methyl and has been widely reported in several plant pathogens including Colletotrichum siamense. Method: To better understand potential fitness costs associated with the resistance, a ribonucleoprotein (RNP) complex mediated CRISPR/Cas9 system was used to create a point mutation (E198A) through homology directed repair (HDR) in each of the sensitive (E198) C. siamense isolates collected from strawberries, raspberries, and peaches. The RNP complex was delivered into fungal protoplasts using polyethylene glycol-mediated (PEG) transfection. Results: The transformation efficiency, the proportion of transformants of sensitive parental isolates containing the E198A mutation, averaged 72%. No off-target mutations were observed when sequences similar to the b-tubulin target region with a maximum of four mismatch sites were analyzed, suggesting that the CRISPR/Cas9 system used in this study was highly specific for genome editing in C. siamense. Of the 41 comparisons of fitness between mutant and wild type isolates through in vitro and detached fruit assays, mutant isolates appeared to be as fit (24 of 41 comparisons), if not more fit than wild-type isolates (10 of 41 comparisons). Discussion: The use of CRISPR/Cas9 to evaluate fitness costs associated with point mutations in this study represents a novel and useful method, since wild-type and mutant isolates were genetically identical except for the target mutation.Item Fruit Morphology Measurements of Jujube Cultivar ‘Lingwu Changzao’ (Ziziphus jujuba Mill. cv. Lingwuchangzao) during Fruit Development(MDPI, 2021-02-06) Ma, Yaping; Zhang, Dapeng; Wang, Zhuangji; Song, Lihua; Cao, Bing‘Lingwu Changzao’ (Ziziphus jujuba Mill. cv. Lingwuchangzao), a cultivar of Ziziphus in the Rhamnaceae family, is a traditional jujube cultivar in Ningxia, China. For ‘Lingwu Changzao’, morphological traits are prominent in characterizing fruit yield, quality, and consumer acceptance. However, morphological measurements for ‘Lingwu Changzao’ cultivation are limited. Therefore, the objective of this study is to measure the growing patterns of selected morphological traits during ‘Lingwu Changzao’ fruit development. Eight morphological traits, including four fruit traits (fruit length, diameter, weight, and flesh (mesocarp) thickness), three stone traits (stone length, diameter, and weight), and fruit firmness (also known as fruit hardness), were measured over a 3-mo (months) period, covering a completed fruit development period. Results indicate that the growing patterns of fruit traits coincide with double ‘S’ growth curves, which mainly present the growth of ‘Lingwu Changzao’ fruit. Increases of stone traits terminated in the early fruit growth period, while fruit traits continuously increased till the end of the 3-mo period. That implies a high fruit-stone ratio, i.e., a desirable quality attribute for ‘Lingwu Changzao’ as fresh-eating fruits. The results presented in this study can serve as one part of the standard dataset for jujube fruit cultivation in China, and it can also support decisions in plant breeding and field managements for ‘Lingwu Changzao’.Item Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review(MDPI, 2021-02-27) Hu, Mengjun; Chen, ShuningThe rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.Item The Effects of Pedestrian Environments on Walking Behaviors and Perception of Pedestrian Safety(MDPI, 2021-08-05) Kweon, Byoung-Suk; Rosenblatt-Naderi, Jody; Ellis, Christopher D.; Shin, Woo-Hwa; Danies, Blair H.We investigated the effects of pedestrian environments on parents’ walking behavior, their perception of pedestrian safety, and their willingness to let their children walk to school. This study was a simulated walking environment experiment that created six different pedestrian conditions using sidewalks, landscape buffers, and street trees. We used within subjects design where participants were exposed to all six simulated conditions. Participants were 26 parents with elementary school children. Sidewalks, buffer strips, and street trees affected parents’ decisions to: walk themselves; let their children walk to school; evaluate their perception whether the simulated environment was safe for walking. We found that the design of pedestrian environments does affect people’s perceptions of pedestrian safety and their willingness to walk. The presence of a sidewalk, buffer strip, and street trees affected parents’ decision to walk, their willingness to let their children walk to school and perceived the pedestrian environment as safer for walking. The effects of trees on parents’ walking and perception of pedestrian safety are greater when there is a wide buffer rather than a narrow buffer. It was found that parents are more cautious about their children’s walking environments and safety than their own.Item Two Triacylglycerol Lipases Are Negative Regulators of Chilling Stress Tolerance in Arabidopsis(MDPI, 2022-03-21) Wang, Lang; Qian, Bilian; Zhao, Lei; Liang, Ming-Hua; Zhan, Xiangqiang; Zhu, JianhuaCold stress is one of the abiotic stress conditions that severely limit plant growth and development and productivity. Triacylglycerol lipases are important metabolic enzymes for the catabolism of triacylglycerols and, therefore, play important roles in cellular activities including seed germination and early seedling establishment. However, whether they play a role in cold stress responses remains unknown. In this study, we characterized two Arabidopsis triacylglycerol lipases, MPL1 and LIP1 and defined their role in cold stress. The expression of MPL1 and LIP1 is reduced by cold stress, suggesting that they may be negative factors related to cold stress. Indeed, we found that loss-of-function of MPL1 and LIP1 resulted in increased cold tolerance and that the mpl1lip1 double mutant displayed an additive effect on cold tolerance. We performed RNA-seq analysis to reveal the global effect of the mpl1 and lip1 mutations on gene expression under cold stress. The mpl1 mutation had a small effect on gene expression under both under control and cold stress conditions whereas the lip1 mutation caused a much stronger effect on gene expression under control and cold stress conditions. The mpl1lip1 double mutant had a moderate effect on gene expression under control and cold stress conditions. Together, our results indicate that MPL1 and LIP1 triacylglycerol lipases are negative regulators of cold tolerance without any side effects on growth in Arabidopsis and that they might be ideal candidates for breeding cold-tolerant crops through genome editing technology.Item Acclimation and Compensating Metabolite Responses to UV-B Radiation in Natural and Transgenic Populus spp. Defective in Lignin Biosynthesis(MDPI, 2022-08-20) Wong, Tiffany M.; Sullivan, Joe H.; Eisenstein, EdwardPlants have evolved to protect leaf mesophyll tissue from damage caused by UV-B radiation by producing an array of UV-absorbing secondary metabolites. Flavonoids (phenolic glycosides) and sinapate esters (hydroxycinnamates) have been implicated as UV-B protective compounds because of the accumulation in the leaf epidermis and the strong absorption in the wavelengths corresponding to UV. Environmental adaptations by plants also generate a suite of responses for protection against damage caused by UV-B radiation, with plants from high elevations or low latitudes generally displaying greater adaptation or tolerance to UV-B radiation. In an effort to explore the relationships between plant lignin levels and composition, the origin of growth elevation, and the hierarchical synthesis of UV-screening compounds, a collection of natural variants as well as transgenic Populus spp. were examined for sensitivity or acclimation to UV-B radiation under greenhouse and laboratory conditions. Noninvasive, ecophysiological measurements using epidermal transmittance and chlorophyll fluorescence as well as metabolite measurements using UPLC-MS generally revealed that the synthesis of anthocyanins, flavonoids, and lignin precursors are increased in Populus upon moderate to high UV-B treatment. However, poplar plants with genetic modifications that affect lignin biosynthesis, or natural variants with altered lignin levels and compositions, displayed complex changes in phenylpropanoid metabolites. A balance between elevated metabolic precursors to protective phenylpropanoids and increased biosynthesis of these anthocyanins, flavonoids, and lignin is proposed to play a role in the acclimation of Populus to UV-B radiation and may provide a useful tool in engineering plants as improved bioenergy feedstocks.Item School Walk Zone: Identifying Environments That Foster Walking and Biking to School(MDPI, 2023-02-06) Kweon, Byoung-Suk; Shin, Woo-Hwa; Ellis, Christopher D.Today, few children walk or bike to school. According to the National Household Travel Survey, only 11% of children walk or bike to school. In 1969, almost 50% of children walked or biked to school in the US. Although our understanding is limited, previous research has shown that physical environments can influence non-automobile mode choices for travel to school. For example, landscape buffers and trees affect parents’ perceptions of their children’s safety and increase their willingness to let their children walk to school. We investigated how a number of physical attributes in the pedestrian environment influence children’s commutes to school. A total of 186 parents from four school walk zones in College Station, TX, participated in this study. We found that children walked more in neighborhoods with mature trees. Moreover, the mean walking and biking distances differed from each other, and both were influenced by the location of the school within the walk zones. Concerns about traffic safety and convenience were negatively related to walking and biking. The findings here suggest ways to shape better school walk zone guidelines that include neighborhood design, planning, and engagement in support of active and healthy children.Item Reducing the generation time in winter wheat cultivars using speed breeding(Wiley, 2023-05-02) Schoen, Adam; Wallace, Sydney; Holbert, Meghan Fisher; Brown-Guidera, Gina; Harrison, Stephen; Murphy, Paul; Sanantonio, Nicholas; Van Sanford, David; Boyles, Richard; Mergoum, Mohamed; Rawat, Nidhi; Tiwari, VijayReducing generation time is critical to achieving the goals of genetic gain in important crops like wheat (Triticum aestivum). Speed breeding (SB) has been shown to considerably reduce generation times in crop plants. Unlike spring wheat cultivars, winter wheat varieties require typically 6–9 weeks of cold treatment, called vernalization, for flowering which extends the generation time for the development of improved winter wheat cultivars. Here, we optimized the SB method using a set of 48 diverse soft red winter wheat (SRWW) cultivars by testing vernalization duration, light and temperature requirements, and the viability of seeds harvested after different durations post-anthesis under extended daylight conditions. We have found that using a 22-h setting (22 h day/2 h night, 25°C/22°C) in high-density 50-cell trays results in rapid generation advancement. We used genotypic data for a panel of soft red winter wheat varieties from the regional programs to determine the impact of photoperiod and vernalization alleles on the efficiency of the SB approach. Using a set of 48 SRWW cultivars and germplasm from Maryland and four other public breeding programs, we establish that this protocol can allow for the advancement of four generations per year in controlled conditions for winter wheat varieties, experimental lines, or emerging cultivars. Our work shows the potential to reduce generation time by ∼30 days per generation faster than what had been reported in the SB strategies for winter wheat, thus allowing for a quicker turnaround time from original cross to genetically stable experimental genotypes that can be tested in field settings.Item Expanding the targeting scope of FokI-dCas nuclease systems with SpRY and Mb2Cas12a(Wiley, 2022-04-04) Cheng, Yanhao; Sretenovic, Simon; Zhang, Yingxiao; Pan, Changtian; Huang, Ji; Qi, YipingCRISPR-Cas9 and Cas12a are widely used sequence-specific nucleases (SSNs) for genome editing. The nuclease domains of Cas proteins can induce DNA double strand breaks upon RNA guided DNA targeting. Zinc finger nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs) have been popular SSNs prior to CRISPR. Both ZFNs and TALENs are based on reconstitution of two monomers with each consisting of a DNA binding domain and a FokI nuclease domain. Inspired by the configuration of ZFNs and TALENs, dimeric FokI-dCas9 systems were previously demonstrated in human cells. Such configuration, based on a pair of guide RNAs (gRNAs), offers great improvement on targeting specificity. To expand the targeting scope of dimeric FokI-dCas systems, the PAM (protospacer adjacent motif)-less SpRY Cas9 variant and the PAM-relaxed Mb2Cas12a system were explored. Rice cells showed that FokI-dSpRY had more robust editing efficiency than a paired SpRY nickase system. Furthermore, a dimeric FokI-dMb2Cas12a system was developed that displayed comparable editing activity to Mb2Cas12a nuclease in rice cells. Finally, a single-chain FokI-FokI-dMb2Cas12a system was developed that cuts DNA outside its targeting sequence, which could be useful for many versatile applications. Together, this work greatly expanded the FokI based CRISPR-Cas systems for genome editing.