Luận án Tiến sĩ của Nevin Lawrence: Thích ứng với Biến đổi Khí hậu và Hệ thống Sản xuất Lúa Mì

ADAPTION TO CLIMATE CHANGE AND SMALL GRAIN PRODUCTION SYSTEMS BY BROMUS TECTORUM BY NEVIN CRAIG LAWRENCE A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Crop and Soil Sciences DECEMBER 2015 ©Copyright NEVIN CRAIG LAWRENCE 2015 All Rights Reserved ©Copyright NEVIN CRAIG LAWRENCE 2015 All Rights Reserve To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of NEVIN CRAIG LAWRENCE find it satisfactory and recommend that it be accepted. ______________________________________ Amit Dhingra, Ph. ii ACKNOWLEDGEMENTS I would like to extend my gratitude to the many people who have supported me over the course of my Ph. The REACCH project supported my research financially and allowed me to practice integrated research on a large scale.

In particular I want to thank John Abatzoglou for his support with integrating climate models with my research. My graduate committee has been enormously helpful in improving the quality of my research, writing, and scientific thinking. Through a combination of high expectations and the freedom to make my own decisions and mistakes, Ian Burke has sharpened my skills as scientist and pushed me to a higher standard of scholarship. Amber Hauvermale’s expertise and assistance with molecular biology was essential in finishing my dissertation.

Lastly, the camaraderie among fellow graduate students was a constant motivation throughout my time at Washington State University. iii DEDICATION I dedicate my dissertation to my wife Louise. I began dating Louise only a few months before moving to Pullman, proposed to her during the second year of my PhD, married her during my third year, and together we welcomed a son into the world during my fourth year. Louise has been my unfair advantage.

Not many graduate students have the benefit of a spouse possessing an advanced degree in the same field. If I needed a document proofread, a sounding board for a presentation, or a second opinion on experimental design, at any hour of the day, she was happy to help. Louise is an outstanding scientist, mother, wife, and best friend. iv ADAPTION TO CLIMATE CHANGE AND SMALL GRAIN PRODUCTION SYSTEMS BY BROMUS TECTORUM ABSTRACT by Nevin Craig Lawrence, Ph.

Washington State University December 2015 Chair: Ian C. Burke Bromus tectorum (downy brome) is an invasive winter annual grass species naturalized throughout western North America. Within the small grain production region of the Pacific Northwest (PNW) downy brome is a ubiquitous and competitive weed. Previous research has documented regional specificity of downy brome phenotypic development, while considerable variation in phenotypic development has been noted between regions.

In 2011 and 2012 130 downy brome accessions were collected from across the PNW small grain production region. A genotype- by-sequencing approach was employed to call molecular markers, generate population genetic statistics, and classify 88 of the 130 downy brome accessions into genetically similar clusters. Individuals were assigned to one of six genetic clusters using 384 single-nucleotide polymorphisms and discriminant analysis of principal components clustering approach. Accessions were transplanted to three common garden field sites to document and model the timing of development.

The timing of development stages was modeled against cumulative growing-degree-days (GDD) to develop herbicide application thresholds to aid in control of downy brome within small grain fields. The estimate for mature seed production varied from May 18th to June 20th depending upon the v location of the common garden. Earlier production of mature seed was observed following more severe winters compared to mild winters, implying a role of vernalization regulating the timing of development. Greenhouse experiments were initiated to characterize the response of early, intermediate, and late-to-flower downy brome accessions to various vernalization treatments and quantify expression of Brachypodium distachyon gene vernalization 1 (BdVRN1).

Downy brome flowering in response to vernalization treatments was linked to the expression of BdVRN1, implying the molecular controls of flowering in downy brome are similar to the controls of other temperate grass species. Downscaled climate modeling was paired with Global Climate Change models to project downy brome development thresholds under future climate scenarios. Downy brome development is anticipated to advance 16 to 34 days across the small grain production region of the PNW. The earlier development of downy brome will require earlier control inputs, which may conflict with earlier rainfall projected under future climate scenarios.

vi TABLE OF CONTENTS ACKNOWLEDGEMENTS. iv TABLE OF CONTENTS. vii LIST OF TABLES. xi LIST OF FIGURES .xiii Chapter 1: Review of the Literature .1 Climate Change in the Pacific Northwest Small Grain Production Region .2 Weed Response to Climate Change .1 Downy Brome Population Genetics.2 Variation in Downy Brome Development .4 Vernalization Genetics in Model and Crop Species .5 A Need for Applied Research on Weed Response to Climate Change.

32 Chapter 2: Population Genetics and Structure of Bromus tectorum from within the small grain production region of the Pacific Northwest.1 Previous work on downy brome population genetics .1 Small Grain Production Region of the PNW .2 Materials and Methods .1 Sampling of Plant Materials .2 Genotype-by-Sequencing.4 Analysis of Population Genetics, Spatial Structure, and Population Structure .6 Tables and Figures. 60 Chapter 3: Modeling Bromus tectorum Phenology from the PNW Small Grain Production Region.1 Downy Brome Phenology .2 Methods and Materials .2 Common Garden Experiments and Greenhouse Seed Maturity Experiments .2 Winter Survival and Timing of Development .3 Modeling Panicle Emergence.4 Modeling mature seed set .6 Tables and Figures. Characterization of Vernalization Requirements and Expression of BdVRN1 in Bromus tectorum .1 Greenhouse Vernalization Experiments .3 VRN1 Primer Design .2 RNA Extraction and RT-PCR .1 Greenhouse Vernalization Experiments .6 Tables and Figures. Projecting Bromus tectorum Development in the Pacific Northwest Small Grain Production Region using Downscaled Climate Modeling .1 Weed Management For a Changing Climate.2 Methods and Materials .1 Expanded Modeling of Development .2 Downscaled Climate Projection .2 Contemporary Climate Projections .3 Mid-Century Climate Projections.

Tables and Figures. 130 x LIST OF TABLES Table 2. Accession ID number, GPS coordinates of collection locations, year of collection, heterozygosity of each accession, and cluster membership as determined by DAPC. Pairwise Fst values of the 7 described population clusters.

Accession ID, year of collection, GPS coordinates of collection, and assigned cluster of each accession evaluated in common garden and greenhouse experiments. Growing degree accumulation by month for the three common garden studies. Growing degree days required and S. for 50% panicle emergence for each genetic cluster.

Growing degree days required and S. for 50% mature seed set for each genetic cluster. Locations of four towns in the PNW small grain production region, thirty year average (1981-2010) GDD accumulation for each town, and the 30 year average calendar date that 850, 1000 and 1500 GDD occurred. Class, accession ID, GDD estimates and calendar date of mature seed production, and calendar date of flowering from a 2013 common garden experiment.

Matrix of p-values indicating which accessions responded differently to vernalization treatments. Regression parameter estimating the weeks of vernalization required to induce flowering in 50% of individuals in each accession. Accession ID, year of collection, and GPS coordinates of collection site for the accessions of downy brome used to model development thresholds. Global climate change models from the coupled model intercomparison project phase 5 used to project downy brome development thresholds.

GDD accumulation estimates for mature seed production at three common garden locations. Average calendar days and date when 500 and 1,000 GDD were reached from 1950-2005 in the small grain production region of the PWN. Projections of calendar days required to reach 500 GDD under the RCP 4.5 scenarios from 2031-2060, compared to 1950-2005. Projections of calendar days required to reach 1,000 GDD under the RCP 4.5 scenarios from 2031-2060, compared to 1950-2005.

128 xii LIST OF FIGURES Figure 2. The small grain production region of the PNW. Observed versus expected heterozygosity across all loci and individuals. Positive and negative eigenvalues, corresponding to global and local spatial structure.

Histogram of permuted test statistics from 10,000 Monte Carlo simulations and the observed global structure. Interpolation of the global structure. Cumulative variance explained by retaining each additional Principal Component. Bayesian information criterion value for increasing values of k.

Optimal number of retained principal components for assigning cluster membership. F-statistic associated with each discriminant function. Probability of cluster membership for each individual. Individuals that were assigned to a cluster with less than 90% probability.

Distribution of individuals and clusters across the first, second, and third linear discriminates. Spatial distribution of individuals and cluster membership. The small grain production region of the PNW. Growing degree days required and S.

for 50% panicle emergence. Growing degree days required and S. for 50% mature seed set. Percent individuals flowering from each accession.

Matrix of p-values contrasting the flowering response. Expression of VRN1 in downy brome. Mean calendar date when 1,000 GDD were reached. 129 xiv Chapter 1: Review of the Literature 1.1 Climate Change in the Pacific Northwest Small Grain Production Region The Intergovernmental Panel on Climate Change (IPCC) characterized the evidence forglobal climate warming as unequivocal.

Solomon et al. (2007) attributed global climate change to an increase in radiative forcing, which has increased 1.6 W m-2 of that increase attributed to anthropogenic rather than natural sources. Radiative forcing of the climate system is predominantly due to long-lived greenhouse gases (GHGs): carbon dioxide, methane, and nitrous oxide (Solomon et al. Emissions from GHGs have increased dramatically due to human activities since 1750, with current atmospheric GHG levels exceeding the historic natural range for the past several thousand years.

In particular, atmospheric levels of carbon dioxide and methane are higher now than at any point in the last 650,000 years. Solomon et al. (2007) attribute the cause of observed global warming during the last century to anthropogenic sourced GHGs with a >90% likelihood. Between 1906 and 2005, global average surface temperature increased 0.74°C, with the rate of increase since 1956 nearly twice the rate from 1906 to 1950.

Currently, observed changes to global climate since 1850 include decreases in the frequency of cold periods and frosts, and increase in hot periods and heat waves, an increase in heavy precipitation events, and an increase in sea level rise at a global scale (Solomon et al. While climate change is often related to observed and projected increases in global mean annual temperature, the impacts of climate change to human and natural systems are expected to vary widely on a regional scale (Field et al. Experiments have demonstrated increases in photosynthesis rate and improved grain yield among many agronomic crops when carbon dioxide and temperature are increased to levels projected under climate change scenarios (Field et al. Gains in productivity are most likely to occur in mid to high latitudes where projections include 15 increased moisture along with increased carbon dioxide and temperatures.

Meanwhile, lower latitudes are projected to endure decreasing crop yields in response to decreasing total annual precipitation (Solomon et al. When the interaction between increased temperature and water requirements is factored in, models forecast moderate yield increases with moderate temperature changes (0.5°C global average increase) followed by a drop in productivity with average global temperature increases greater than 1.5°C (Kang et al. Furthermore, factors such as extreme weather events and pest pressure will also be altered by changing climate and have the potential to decrease crop productivity (Tubiello et al. The small-grain production area of the Pacific Northwest (PNW) includes central and eastern Washington, parts of northern Oregon, and northern Idaho and totals 2.2 million ha of non- irrigated cropland (Huggins et al.3 million ha of this region were planted into small grains, with around one million ha planted to winter wheat.

Annual precipitation in the region ranges from less than 300 mm to greater than 600 mm, with a west to east increasing precipitation gradient.