James H Richards

James H Richards
University of California, Davis | UCD · Department of Land, Air and Water Resources

About

134
Publications
22,343
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10,583
Citations
Citations since 2017
4 Research Items
2922 Citations
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20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500

Publications

Publications (134)
Article
Full-text available
Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to g...
Preprint
Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to gr...
Preprint
Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to gr...
Article
Full-text available
English walnut (Juglans regia L.) is an economically important crop with > 99% of US walnuts produced in California. Changes in climate and recent drought cycles have raised concerns regarding the future of nut production and responsible water use in California agriculture. Our study used an association genetics approach to characterize ecophysiolo...
Article
Full-text available
Populus trichocarpa is a biological model and a candidate species for bioethanol production. Although intraspecific variation is recognized, knowledge about genetic variation underlying the properties of its lignocellulosic biomass is still incomplete. Genetic variation is fundamental for continuing genetic improvement. In this study, we carried ou...
Article
Full-text available
The 2,3,5-triphenyltetrazolium chloride (TTC) technique has been used during decades to distinguish between dead and alive tissues of perennial grasses. This technique did not consider, however, that dormant (i.e., viable) tissues could exist within those erroneously considered dead tissues, thus being unable to report the true physiological stage...
Article
Full-text available
The 2,3,5-triphenyltetrazolium chloride (TTC) technique has been used during decades to distinguish between dead and alive tissues of perennial grasses. This technique did not consider, however, that dormant (i.e., viable) tissues could exist within those erroneously considered dead tissues, thus being unable to report the true physiological stage...
Article
Full-text available
Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), ph...
Data
Table S1. Arabidopsis thaliana accessions used in this experiment. Table S2. Standardized nonlinear and correlational selection gradients within the long season and terminal drought treatments.
Article
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Flowering time and water-use efficiency (WUE) are two ecological traits that are important for plant drought response. To understand the evolutionary significance of natural genetic variation in flowering time, WUE, and WUE plasticity to drought in Arabidopsis thaliana, we addressed the following questions: (1) How are ecophysiological traits genet...
Article
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The importance and consequences of extreme events on the global carbon budget are inadequately understood. This includes the differential impact of extreme events on various ecosystem components, lag effects, recovery times, and compensatory processes. In the summer of 2007 in Barrow, Arctic Alaska, there were unusually high air temperatures (the f...
Article
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Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation...
Article
Full-text available
Significance Water is essential for nearly all aspects of plant biology though, for many plants, water is a limited resource. Water use efficiency measures the ratio of photosynthetic carbon fixation to water lost via leaf transpiration and is a critical determinant of plant productivity in field environments. We identify a molecular variant that d...
Article
Full-text available
The importance and mode of action of extreme events on the global carbon budget are inadequately understood. This includes the differential impact of extreme events on various ecosystem components, lag effects, recovery times, and compensatory processes. Summer 2007 in Barrow, Arctic Alaska, experienced unusually high air temperatures (fifth warmes...
Article
Most C3 plant species have partially open stomata during the night especially in the 3-5 hours before dawn. This predawn stomatal opening has been hypothesized to enhance early morning photosynthesis (A) by reducing diffusion limitations to CO2 at dawn. We tested this hypothesis in cultivated Helianthus annuus using whole shoot gas exchange, leaf l...
Article
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The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (...
Article
Full-text available
Ecologists and physiologists have documented extensive variation in water use efficiency (WUE) in Arabidopsis thaliana, as well as association of WUE with climatic variation. Here, we demonstrate correlations of whole-plant transpiration efficiency and carbon isotope composition (δ13C) among life history classes of A. thaliana. We also use a whole-...
Article
Full-text available
An evolutionary response to selection requires genetic variation; however, even if it exists, then the genetic details of the variation can constrain adaptation. In the simplest case, unlinked loci and uncorrelated phenotypes respond directly to multivariate selection and permit unrestricted paths to adaptive peaks. By contrast, 'antagonistic' plei...
Article
Fremont cottonwood seedlings are vulnerable to water stress from rapid water-table decline during river recession in spring. Water stress is usually cited as the reason for reduced establishment, but interactions of water stress with microclimate extremes are more likely causes of mortality. We assessed photosynthetic responses of Fremont cottonwoo...
Conference Paper
Full-text available
The need for alternative sources of energy has led to recent efforts for developing renewable sources for biofuels. Species belonging to Populus genus (poplars) have several advantages impacting the efficiency of cellulosic ethanol production. Traditional genetic improvement of poplars for bioenergy production can be enhanced by genomics-based bree...
Article
Full-text available
An evolutionary response to selection requires genetic variation; however, even if it exists, then the genetic details of the variation can constrain adaptation. In the simplest case, unlinked loci and uncorrelated phenotypes respond directly to multivariate selection and permit unrestricted paths to adaptive peaks. By contrast, 'antagonistic' plei...
Data
Linear relationships between (A) Neff and Nprof (senesced leaf N) and (B) Peff and Pprof (senesced leaf P). Data are mean ± SE (n = 3-8). Black symbols are non-serpentine species, white symbols are serpentine species. Arctostaphylos congeners are circles, Ceanothus congeners are squares, Quercus congeners are diamonds, and Rhamnus congeners are tri...
Article
Fremont cottonwood (Populus fremontii) is an early successional foundation species found in riparian forest ecosystems in the North American Southwest. Along rivers, the upper limit of the seedling establishment zone depends on the proximity of seedling roots to the declining water table. The lower limit is a function of the maximum elevation of in...
Article
Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well-studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variati...
Article
Full-text available
Low-nutrient adapted species have numerous mechanisms that aid in nutrient conservation. Hypothetically, species adapted to nutrient-poor soils should have tighter internal nutrient recycling, as evidenced by greater resorption. However, literature results are mixed. We suggest methodological factors may limit our understanding of this process. We...
Article
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Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural muta...
Article
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Two instrumented test sections were constructed in summer 1999 at the Kiefer Landfill near Sacramento, California to test the hydraulic performance of two proposed alternative final covers. Both test sections simulated monolithic evapotranspiration (ET) designs that differed primarily in thickness. Both were seeded with a mix of two perennial and o...
Article
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Where serpentine soils exist, variation in soil properties affects plant species distribution at both coarse and fine spatial scales. The New Idria (California, USA) serpentine mass has barren areas, supporting only sparse shrub and tree islands, adjacent to areas of densely-vegetated serpentine chaparral. To identify factors limiting growth on bar...
Article
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We investigated genetic differences in salinity tolerance among 20 saltgrass (Distichlis spicata (L.) Greene) genotypes, including constitutive, gender-based and phenotypic plasticity traits, to better understand the basis of adaptation and acclimation by saltgrass in diverse environments. On average, the plants survived NaCl treatments up to ~1 M,...
Article
The Arctic experiences a high-radiation environment in the summer with 24-hour daylight for more than two months. Damage to plants and ecosystem metabolism can be muted by overcast conditions common in much of the Arctic. However, with climate change, extreme dry years and clearer skies could lead to the risk of increased photoxidation and photoinh...
Article
Full-text available
The concept of the modularity of plant growth form was incorporated with the fates of buds and used as a framework to describe the typical branch-level developmental morphology of sagebrush (Artemisia tridentata ssp. vaseyana (Rydb.) Beetle) and bitterbrush (Purshia tridentata (Pursh) D.C.). Typical branches included one 2-year-old long shoot and a...
Article
Plant nutrient resorption prior to leaf senescence is an important nutrient conservation mechanism for aridland plant species. However, little is known regarding the phylogenetic and environmental factors influencing this trait. Our objective was to compare nitrogen (N) and phosphorous (P) resorption in a suite of species in the Asteraceae and Chen...
Article
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Shifts in the seasonal timing of rainfall have the potential to substantially affect the immense terrestrial stores of soil organic carbon (C, SOC). It remains unclear, however, how changes in the timing of rainfall are influencing SOC storage. We hypothesized that a sustained shift in rainfall timing from winter to a spring-summer regime would red...
Article
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats. Of particular interest are accessions with putatively locally adapted phenotypes - that is, accessions with attributes that are likely adaptive at their sites of origin. These genotypes may provide insight into the gene...
Article
Roots influence root litter decomposition through multiple belowground processes. Hydraulic lift or redistribution (HR) by plants is one such process that creates diel drying–rewetting cycles in soil. However, it is unclear if this phenomenon influences decomposition. Since decomposition in deserts is constrained by low soil moisture and is stimula...
Article
C(3) plants dominate many landscapes and are critically important for ecosystem water cycling. At night, plant water losses can include transpiration (E(night)) from the canopy and hydraulic redistribution (HR) from roots. We tested whether E(night) limits the magnitude of HR in a greenhouse study using Artemisia tridentata, Helianthus anomalus and...
Article
Full-text available
Although roots in dry soil layers are commonly rehydrated by internal hydraulic redistribution during the nocturnal period, patterns of tissue rehydration are poorly understood. Rates of nocturnal rehydration were examined in roots of different orders in Vaccinium corymbosum L. 'Bluecrop' (Northern highbush blueberry) grown in a split-pot system wi...
Article
Significant water loss occurs throughout the night via partially open stomata in many C(3) and C(4) plant species. Although apparently wasteful in terms of water use, nighttime transpiration (E(night)) is hypothesized to benefit plants by enhancing nutrient supply. We tested the hypothesis that plants with greater E(night) would have improved plant...
Article
Full-text available
Wild tomatoes occur in habitats from the extremely dry Atacama Desert to moist areas in the Andean highlands, which may have resulted in adaptation of populations or species to differences in soil moisture availability. However, when two accessions representing extremes in habitat water availability from each of the five self-compatible species wer...
Article
Night-time stomatal opening in C(3) plants may result in significant water loss when no carbon gain is possible. The objective of this study was to determine if endogenous patterns of night-time stomatal opening, as reflected in leaf conductance, in Vicia faba are affected by photosynthetic conditions the previous day. Reducing photosynthesis with...
Article
Full-text available
Growing awareness of night-time leaf conductance (gnight) in many species, as well as genetic variation in gnight within several species, has raised questions about how genetic variation and environmental stress interact to influence the magnitude of gnight. The objective of this study was to investigate how genotype salt tolerance and salinity str...
Article
In desert ecosystems, belowground characteristics are influenced chiefly by the formation and persistence of “shrub-islands of fertility” in contrast to barren plant interspaces. If soil microbial communities are exclusively compared between these two biogeochemically distinct soil types, the impact of characteristics altered by shrub species, espe...
Article
Despite compelling evidence that adaptation to local climate is common in plant populations, little is known about the evolutionary genetics of traits that contribute to climatic adaptation. A screen of natural accessions of Arabidopsis thaliana revealed Tsu-1 and Kas-1 to be opposite extremes for water-use efficiency and climate at collection site...
Article
Full-text available
Plants with limited resources adjust partitioning among growth, survival, and reproduction. We tested the effects of water and nutrient amendments on seed production, size, and quality in Sarcobatus vermiculatus (greasewood) to assess the magnitude and importance of changes in reproductive partitioning. In addition, we assessed interactions among t...
Article
Night-time leaf conductance (g(night)) and transpiration may have several adaptive benefits related to plant water, nutrient and carbon relations. Little is known, however, about genetic variation in g(night) and whether this variation correlates with other gas exchange traits related to water use and/or native habitat climate. We investigated g(ni...
Article
Full-text available
Water movement from roots to soil at night in the process of hydraulic lift (redistribution) rehydrates the rhizosphere and has been proposed to improve plant nutrient acquisition. Another process that has now been found in many plant species is nighttime transpiration and this could also affect nutrient relations by influencing supply of mobile nu...
Article
Redistribution of water within plants could mitigate drought stress of roots in zones of low soil moisture. Plant internal redistribution of water from regions of high soil moisture to roots in dry soil occurs during periods of low evaporative demand. Using minirhizotrons, we observed similar lifespans of roots in wet and dry soil for the grapevine...
Article
Full-text available
Establishment of native vegetation is one method of stabilizing shifting soil and minimizing fine particulate dust air pollution from barren, dry lakebeds worldwide. Successful colonization, however, hinges on native seedlings' ability to survive and grow in these stressful environments. We studied the effects of soil amendment on two halophytic sh...
Article
Full-text available
Soil nutrients in arid systems are supplied to plants in brief pulses following precipitation inputs. While these resource dynamics have been well documented, little is known about how this temporal heterogeneity influences competitive interactions. We examined the impacts of the temporal pattern of N supply on competitive intensity and ability in...
Article
Full-text available
Incomplete stomatal closure at night can result in substantial water loss at times when photosynthetic carbon gain is not occurring in C3 and C4 plant species. To investigate the magnitude of nighttime water loss for a crop species in the field, measurements of nighttime water loss by tomato (Lycopersicon esculentum Mill. cv. Heinz 8892) were made...
Article
Full-text available
Incomplete stomatal closure during the night is observed in a diverse range of C3 and C4 species (Fig. 1; Supplemental Table S1) and can lead to substantial nighttime transpirational water loss. Although water loss is an inevitable consequence of stomatal opening for photosynthetic carbon gain, nighttime stomatal opening is unexpected because carbo...
Article
Limiting resources are generally available in brief temporal pulses in arid systems. We compared the abilities of dominant shrubs in a saltbush scrub community to capture N from pulses and evaluated whether N capture and partitioning within this community is influenced by the seasonal timing of pulses. Based on previous research in agronomic system...
Article
1 Soil resources are heterogeneously distributed in natural systems. In arid systems, for example, soil nitrogen (N) is often supplied in pulses. Mechanisms influencing the ability of a species to exploit N pulses through the season, however, are poorly understood despite the strong potential for temporal variation in N supply to impact growth, sur...
Article
It has been suggested previously that Japanese larch (Larix kaempferi) exhibits characteristics of C4 photosynthesis. To further evaluate this suggestion, stable carbon isotope ratios were determined for leaf and bark tissue of Larix gmelini, L. kaempferi, L. laricina, L. Iyallii, L. occidentalis, and L. sibirica. All δ13C values were more negative...
Article
Full-text available
Both water and nutrients are limiting in arid environments, and desert plants have adapted to these limitations through numerous developmental and physiological mechanisms. In the Mono Basin, California, USA, co-dominant Sarcobatus vermiculatus and Chrysothamnus nauseosus ssp. consimilis are differentially N and P limited. We hypothesized that low...
Article
Full-text available
Serpentine soils limit plant growth by NPK deficiencies, low Ca availability, excess Mg, and high heavy metal levels. In this study, three congeneric serpentine and nonserpentine evergreen shrub species pairs were grown in metalliferous serpentine soil with or without NPKCa fertilizer to test which soil factors most limit biomass production and min...
Article
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Predawn plant water potential (Ψw) is used to estimate soil moisture available to plants because plants are expected to equilibrate with the root-zone Ψw. Although this equilibrium assumption provides the basis for interpreting many physiological and ecological parameters, much work suggests predawn plant Ψw is often more negative than root-zone so...
Article
Full-text available
In arid ecosystems, the ability to rapidly capture nitrogen (N) from brief pulses is expected to influence plant growth, survival, and competitive ability. Theory and data suggest that N capture from pulses should depend on plant growth rate and availability of other limiting resources. Theory also predicts trade-offs in plant stress tolerance and...
Article
Water limitation is one of the most important factors limiting crop productivity world-wide and has likely been an important selective regime influencing the evolution of plant physiology. Understanding the genetic and physiological basis of drought adaptation is therefore important for improving crops as well as for understanding the evolution of...
Article
Full-text available
Nutrients, in addition to water, limit desert primary productivity, but nutrient limitations to fecundity and seed quality in desert ecosystems have received little attention. Reduced seed production and quality may affect recruitment, population, and community processes. At the Mono Basin, CA, USA where the alkaline, sandy soil has very low availa...
Article
Summary • We investigated resource limitations in a saltbrush scrub community along a salinity-alkalinity gradient in the Mojave Desert of North America. Previous studies have shown that, as productivity declines with increasing soil stress, there are parallel declines in leaf Ca and Mg, suggesting availability of these resources may limit growth i...
Article
The amount of C sequestered and its permanence in some deserts could be higher than normally appreciated. Limited soil water availability and slow decomposition rates in desert soils may induce the long-term accumulation of soil organic C and coarse woody litter. We inventoried C in soils along a chronosequence of Sarcobatus vermiculatus shrub isla...
Article
Full-text available
Plant species and functionally related species groups from arid and semi-arid habitats vary in their capacity to take up summer precipitation, acquire nitrogen quickly after summer precipitation, and subsequently respond with ecophysiological changes (e.g. water and nitrogen relations, gas exchange). For species that respond ecophysiologically, the...
Article
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Many terrestrial ecosystems are nutrient limited. Koerselman and Meuleman (1996) proposed critical foliar N:P values that could predict wetland nutrient deficiencies (N:P < 14,="" n="" limitation;="" n:p=""> 16, P limitation). Although critical N:P values have potential as ecological and diagnostic tools, species differences in N and P requirements...
Article
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It is widely recognized that old growth forests store a significant amount of carbon (C); however, little attention has been paid to the role of ``old-growth'' deserts in sequestering C. Although productivity in deserts is low, slow decomposition rates could result in significant amounts of stored C, especially when considering that deserts compris...
Article
Natural and anthropogenic changes in basin lake levels in the western U.S. expose saline, alkaline substrates that are commonly colonized by shrubs in the Chenopodiaceae. On a chronosequence of recently exposed substrates at Mono Lake, California, Sarcobatus vermiculatus has greatest biomass accrual, seed production, seedling establishment, and lea...
Article
Natural and anthropogenic changes in basin lake levels in the western U.S. expose saline, alkaline substrates that are commonly colonized by shrubs in the Chenopodiaceae. On a chronosequence of recently exposed substrates at Mono Lake, California, Sarcobatus vermiculatus has greatest biornass accrual, seed production, seedling establishment, and le...
Article
Full-text available
Plants forage for nutrients by increasing their root length density (RLD) in nutrient-rich soil microsites through root morphological changes resulting in increased root biomass density (RBD), specific root length (SRL), or branching frequency (BF). It is commonly accepted that fast-growing species will forage more than slow-growing species. Howeve...