Botany Commons^™

Rice Chalky Grain 5 Regulates Natural Variation For Grain Quality Under Heat Stress, Anil Kumar Nalini Chandran, Jaspreet Sandhu, Larissa Irvin, Puneet Paul, Balpreet K. Dhatt, Waseem Hussain, Tian Gao, Paul E. Staswick, Hongfeng Yu, Gota Morota, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature …

Alfalfa Water Productivity And Yield Gaps In The U.S. Central Great Plains, Kaylin P. Fink, Patricio Grassini, Alexandre Rocateli, Leonardo M. Bastos, Jude Kastens, Luke P. Ryan, Xiaomao Lin, Andres Patrignani, Romulo P. Lollato

Department of Agronomy and Horticulture: Faculty Publications

Context: Yield gap (Yg) analyses using farmer-reported yield and management data have been performed for a number of annual grain crops, but it lacks for perennial forages. The U.S. accounts for 21 % of the global alfalfa production with a large rainfed area located in the central Great Plains, serving as an interesting case-study for Yg in perennial forages. Most existing alfalfa Yg analyses quantified the magnitude of the Yg but failed to identify associated management practices to reduce it. Challenging this analysis, a systematic benchmark for alfalfa water productivity [WP, kg dry matter per mm evapotranspiration (ETc)] that …

Effect Of Water Stress On Weed Germination, Growth Characteristics, And Seed Production: A Global Meta-Analysis, Mandeep Singh, Resham Thapa, Meetpal Singh Kukal, Suat Irmak, Steven Mirsky, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Weeds compete with crops for soil moisture, along with other resources, which can impact the germination, growth, and seed production of weeds; however, this impact has not been systematically recorded and synthesized across diverse studies. To address this knowledge gap, a global meta-analysis was conducted using 1,196 paired observations from 86 published articles assessing the effect of water stress on weed germination, growth characteristics, and seed production. These studies were conducted and published during 1970 through 2020 across four continents (Asia, Australia, Europe, and North America). Imposed water stress was expressed as solution osmotic potential (ψsolution), soil water potential (ψsoil), …

Agronomic And Quality Impact Of A Shortened Translocation For Wheat Streak Mosaic Virus Resistance, Mary J. Guttieri, Robert L. Bowden, Guorong Zhang, Scott Haley, Katherine Anna Frels, Gary L. Hein, Katherine W. Jordan

Department of Agronomy and Horticulture: Faculty Publications

Wheat streak mosaic virus (WSMV) is a mite-vectored virus with substantial economic impact on wheat production. One of the effective sources of resistance to WSMV, Wsm1, is carried on a translocation from Thinopyrum intermedium. The original whole arm form of this translocation (T4DL·4JsS) was highly effective against WSMV but carried a substantial yield penalty in the absence of the virus. Shorter recombinants of the Th. intermedium translocation are now available. This study characterized the agronomic performance of near-isogenic sib-pair families in 10 yield trials using one of these shortened T4DL·4DS-4J^sS translocations, named “rec213,” in the absence …

The Genomic And Bulked Segregant Analysis Of Curcuma Alismatifolia Revealed Its Diverse Bract Pigmentation, Xuezhu Liao, Yuanjun Ye, Xiaoni Zhang, Dan Peng, Mengmeng Hou, Gaofei Fu, Jianjun Tan, Jianli Zhao, Rihong Jiang, Yechun Xu, Jinmei Liu, Jinliang Yang, Wusheng Liu, Luke R. Tembrock, Genfa Zhu, Zhiqiang Wu

Department of Agronomy and Horticulture: Faculty Publications

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy ‘‘flowers’’ through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia ‘‘Chiang Mai Pink’’ and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a …

How Elevation Affects Epiphyte Distribution: An Analysis In Epiphyte Distribution Changes At Different Elevations And Tree Strata In Santa Lucia Cloud Forest Reserve, Ecuador, Nicole L. Melnick

Independent Study Project (ISP) Collection

Cloud forests are unique ecosystems due to their tropical nature, high elevations, and extremely high presence of epiphytes that serve many important roles for the ecosystem’s biotic and abiotic components. As epiphytes can make up anywhere from one-quarter (Foster 2001) to a half (Gómez González et al. 2017) of all local plant species in cloud forests, it is essential to understand how their habitat distributions change with elevation and whether climate change will have a significant effect on that. This study used observational survey methods to record the amount of monocots (separately counted bromeliads and orchids), dicots, ferns, and percent …

Arthropod Assemblages At The Intersection Of Epiphyte And Soil Habitats: An Assessment Of Understory Level Nonvascular Epiphyte Communities And Their Connectivity Within A Tropical Montane Rainforest, David “Max” Jones

Independent Study Project (ISP) Collection

Canopy arthropods communities represent a disproportionate amount of global species richness (Stuntz 2001). Understanding arthropod composition and connectivity of lower epiphyte communities is important in understanding how canopy arthropods communities are formed and will respond to change (Floren and Linsenmair 1998). As such this study examined arthropod assemblages living within nonvascular epiphyte communities (epiphyte mats) living directly upon lower trunk regions of 24 trees in a tropical montane rain forest within the Santa Lucia Nature Reserve in Pichincha, Ecuador. Trees were assessed for size, epiphyte diversity, and epiphyte coverage before arthropod sampling within the epiphyte mats. Soil assessments were taken …

Afforestation And Biodiversity: Bryophyte Richness Changes Between Icelandic Forest Types, Kian Mcdonough

Independent Study Project (ISP) Collection

Forest-dwelling bryophytes (mosses, liverworts, hornworts) greatly contribute to biodiversity and ecosystem function but are largely under-studied in comparison to vascular plants. With Iceland’s large-scale afforestation efforts there is a need to understand how different afforestation species are affecting biodiversity, including bryophyte diversity. This study looked at differences in ground-floor bryophyte richness across Sitka spruce, lodgepole pine, and downy birch forests and found that bryophyte richness was highest in the Sitka spruce forests and lowest in downy birch forests. While this suggests a negative correlation between bryophyte richness and light availability, since the conifer species have the densest copy cover, other …

Investigating Primary Succession Following The Retreat Of The Breiðamerkurjökull Glacier, Iceland, Ella Roelofs

Independent Study Project (ISP) Collection

The accelerating rates of glacier retreat around the world as a result of climate change make the study of primary succession in expanding forefields increasingly important. While this is a well studied topic in many parts of the world, little data exists specific to Iceland. This study investigated vegetation development along a chronosequence of eight time periods in the Breiðamerkurjökull outwash plain. Data was collected on percent vegetation cover, dominant species, the number of unique plant groups, and percent cover of five substrate types at 10 plots (0.55 x 0.55 m quadrats) per time period. Important findings include the fact …

Hummingbird Diversity, Abundance, And Feeding Interactions Across Three Floral Communities On Mount Totumas, Chiriquí, Panamá, Zachary Ginn

Independent Study Project (ISP) Collection

(Trochilidae) are a large Neotropical bird family of nectar-feeders that have evolved as pollinators of many Neotropical plants. Interactions between hummingbirds and plants form mutualistic networks that may change in structure over environmental and anthropogenic gradients. While the unique dynamics of hummingbird diversity and floral interactions have been studied throughout the Neotropics, differing drivers between locations emphasizes the need for further local research. This deficit is especially crucial in biodiverse and understudied locations like the Western Highlands of Panamá. In this study, I investigated how hummingbird diversity, abundance, and floral interactions differed between Cloud Forest, Garden, and Oak Forest on …

2022 Fall Newsletter, Plaster Creek Stewards

Newsletters

Highlights:

Reflections on Our Mission

Fall Event 2022: Future Thriving

Parking Lot Retrofits - A New PCS Strategy

Research Updates

Betty Kliewer Joins the Team

Planting Partners, Interns, and Community Organizations

Support Our Work

Upcoming Event: End-of-Year Celebration

Cyclic Adp Ribose Isomers: Production, Chemical Structures, And Immune Signaling, Mohammad K. Manik, Yun Shi, Sulin Li, Mark A. Zaydman, Neha Damaraju, Samuel Eastman, Thomas G. Smith, Weixi Gu, Veronika Masic, Tamim Mosaiab, James S. Weagley, Steven J. Hancock, Eduardo Vasquez, Lauren Hartley-Tassell, Nestoras Kargios, Natsumi Maruta, Bryan Y.J. Lim, Hayden Burdett, Michael J. Landsberg, Mark A. Schembri, Ivan Prokes, Lijiang Song, Murray Grant, Aaron Diantonio, Jeffrey D. Nanson, Ming Guo, Jeffrey Milbrandt, Thomas Ve, Bostjan Kobe

Department of Agronomy and Horticulture: Faculty Publications

Cyclic adenosine diphosphate (ADP)–ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD+) hydrolysis. We show that v-cADPR (2′cADPR) and v2-cADPR (3′cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2′cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3′cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and …

Spatial Patterns Of Woody Plant Encroachment In A Temperate Grassland, Dillon T. Fogarty, Robert B. Peterson, Dirac Twidwell

Department of Agronomy and Horticulture: Faculty Publications

Context Woody encroachment is the process whereby grasslands transition to a woody-dominated state. This process is a global driver of grassland decline and is ultimately the outcome of increased woody plant recruitment in grasslands. Yet, little is known about how recruitment distances structure spatial patterns of encroachment.

Objectives Here, we develop a recruitment curve to describe the scatter of woody plant recruitment around seed sources and examine how this structures spatial patterns of encroachment.

Methods We developed a recruitment curve for Juniperus virginiana using an encroachment dataset that captures spread from tree plantings into treeless grassland sites in the Nebraska …

The Heterogeneity In The Landscape Of Gene Dominance In Maize Is Accompanied By Unique Chromatin Environments, Liangwei Yin, Gen Xu, Jinliang Yang, Meixia Zhao

Department of Agronomy and Horticulture: Faculty Publications

Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the …

Next-Generation Technologies Unlock New Possibilities To Track Rangeland Productivity And Quantify Multi-Scale Conservation Outcomes, Caleb P. Roberts, David E. Naugle, Brady W. Allred, Victoria M. Donovan, Dillon T. Fogarty, Matthew O. Jones, Jeremy D. Maestas, Andrew C. Olsen, Dirac L. Twidwell Jr

Department of Agronomy and Horticulture: Faculty Publications

Historically, relying on plot-level inventories impeded our ability to quantify large-scale change in plant biomass, a key indicator of conservation practice outcomes in rangeland systems. Recent technological advances enable assessment at scales appropriate to inform management by providing spatially comprehensive estimates of productivity that are partitioned by plant functional group across all contiguous US rangelands. We partnered with the Sage Grouse and Lesser Prairie-Chicken Initiatives and the Nebraska Natural Legacy Project to demonstrate the ability of these new datasets to quantify multi-scale changes and heterogeneity in plant biomass following mechanical tree removal, prescribed fire, and prescribed grazing. In Oregon’s sagebrush …

Cytogenetic And Genomic Characterization Of A Novel Tall Wheatgrass‑Derived Fhb7 Allele Integrated Into Wheat B Genome, Wei Zhang, Tatiana Danilova, Mingyi Zhang, Shuangfeng Ren, Xianwen Zhu, Qijun Zhang, Shaobin Zhong, Linda Dykes, Jason Fiedler, Steven Xu, Katherine Frels, Stephen Wegulo, Jeffrey Boehm Jr., Xiwen Cai

Department of Agronomy and Horticulture: Faculty Publications

A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7^The2, was identified and integrated into the wheat B genome through a small 7B–7E translocation (7BS·7BL–7EL) involving the terminal regions of the long arms. Fhb7^The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7^The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum …

How Digital Is Agriculture In A Subset Of Countries From South America? Adoption And Limitations, Laila A. Puntel, É. L. Bolfe, R. J. M. Melchiori, R. Ortega, G. Tiscornia, A. Roel, F. Scaramuzza, S. Best, A. G. Berger, D. S. S. Hansel, D. Palacios Durán, G. R. Balboa

Department of Agronomy and Horticulture: Faculty Publications

Digital agriculture (DA) can contribute solutions to meet an increase in healthy, nutritious, and affordable food demands in an efficient and sustainable way. South America (SA) is one of the main grain and protein producers in the world but the status of DA in the region is unknown. A systematic review and case studies from Brazil, Argentina, Uruguay, and Chile were conducted to address the following objectives: (1) quantify adoption of existing DA technologies, (2) identify limitations for DA adoption; and (3) summarise existing metrics to benchmark DA benefits. Level of DA adoption was led by Brazil and Argentina followed …

Cropland Reference Ecological Unit: A Land Classification Unit For Comparative Soil Studies, Saurav Das, Bijesh Maharjan

Department of Agronomy and Horticulture: Faculty Publications

There is a growing consensus on a need for measuring the dynamic soil properties of croplands and even comparisons with a reference state or native land. These measurements and paired comparisons will create the capacity to determine soil health management effects and targets. However, the complex soil heterogeneity and climate variations make soil health potential variable and confound the effects of land-use and management practices and comparisons between soils from different sites. Identifying a discrete landmass unit where all soils have similar health potential will be critical in conducting meaningful comparative studies and measuring the impact of conservation practices. This …

Cell-Type-Specific Profiling Of The Arabidopsis Thaliana Membrane Protein-Encoding Genes, Sergio Alan Cervantes-Pérez, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Membrane proteins work in large complexes to perceive and transduce external signals and to trigger a cellular response leading to the adaptation of the cells to their environment. Biochemical assays have been extensively used to reveal the interaction between membrane proteins. However, such analyses do not reveal the unique and complex composition of the membrane proteins of the different plant cell types. Here, we conducted a comprehensive analysis of the expression of Arabidopsis membrane proteins in the different cell types composing the root. Specifically, we analyzed the expression of genes encoding membrane proteins interacting in large complexes. We found that …

Cell-Type-Specific Profiling Of The Arabidopsis Thaliana Membrane Protein-Encoding Genes, Sergio Alan Cervantes-Pérez, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

Membrane proteins work in large complexes to perceive and transduce external signals and to trigger a cellular response leading to the adaptation of the cells to their environment. Biochemical assays have been extensively used to reveal the interaction between membrane proteins. However, such analyses do not reveal the unique and complex composition of the membrane proteins of the different plant cell types. Here, we conducted a comprehensive analysis of the expression of Arabidopsis membrane proteins in the different cell types composing the root. Specifically, we analyzed the expression of genes encoding membrane proteins interacting in large complexes. We found that …