2003, North Carolina State University
Research Focus Areas
Population and Quantitative Genomics,
Domestication and ferality,
Genetic interactions amongst crops, wild relatives, and weeds
Computational genomics of pesticide/herbicide resistance
Amaranthus is a large and diverse genus, containing over sixty member species including locally adapted nutritious leaf vegetable and grain crops, horticultural varieties, and noxious weeds. Most species in this genus are herbaceous annuals (Mosyakin and Robertson. 1993). Amaranthus species are generally wind pollinated and can produce as many as two hundred thousand seeds per female plant per season (Sosnoskie et al. 2009; Stevens. 1957). Starting in 2002, reports indicated that amaranth species, mainly Amaranthus palmeri and Amaranthus rudis (or A. tuberculatus subs. rudis), were becoming increasingly resistant to standard herbicide applications (Patzoldt and Tranel. 2007). An example of the potential economic impact of this resistance is in Zea mays, with studies indicating that as few as 0.5 A. palmeri plants per row of corn can reduce yield by more than 10% (Massinga et al. 2001).
A goal of our research in this system is to understand the evolutionary genomic mechanisms underlying the rapid adaptation to herbicides (insensitivity, resistance) in the Amaranthus genus. This is particularly important due to the reliance upon the herbicide glyphosate which is used in genetic modification technology-based management strategies that are part of conservation tillage approaches. For this work, we are testing alternative models of divergence population genetics interactions among and between populations and species in this genus. Using high performance computing approaches, we are estimating the probabilities of shared ancestral alleles versus derived new mutations exchanged via gene flow in contemporary populations in populations and potentially genetically interacting species to explain the best fit models describing the rapid adaptation to herbicides and massive increases in contemporary population sizes that have been observed since 2002. In combination with molecular evolution and phylogenetic approaches, we are examining gene trees and species trees in candidate target and non-target genes in this study.
Another goal of our research in this system is to estimate a best fit overall phylogeny in this diverse genus. In addition to facilitating the testing of alternative divergence population genetics and molecular evolution hypotheses for herbicide resistance, our work will shed light on the evolutionary dynamics underlying the origins and diversification of locally adapted leaf and grain crops that are important in many cultures. In these studies, we can compare and contrast the evolutionary signatures of crops that have been bred for local adaptation versus crops that have been bred for large scale agricultural practices that have resulted in crops that are adapted to wider, less specific habitat requirements. Additionally, we can use genetic models to test for the relationships of populations and cultivars that are of ancient and contemporary cultural significance across the globe. Our work in the Amaranthus genus is greatly facilitated by national and international collaborations.
Weedy red rice (Oryza sp.) is a conspecific weed of cultivated rice fields around the world. In Arkansas, red rice continues to persist in agroecosystems with a significant presence in approximately 60% of cultivated rice fields. This persistence results in large decreases in market value due to competition, lodging, and loss in value of harvested crop. Red rice is classified as a noxious weed due to crop-like physiology, high fecundity and seed shattering, protracted emergence and seed dormancy. In California, red rice was completely eradicated, but new emergence has been documented starting in a single county in 2006. Studying the divergence population genetics patterns in this system gives us the opportunity to isolate specific attributes of ‘unintended’ targets of selection as a contrast to the obvious targets of selection in the conspecific crop. Additionally, given the potential for allele movement between these conspecifics, our work contributes towards ongoing discussions on the efficacy of transgenic crops.
We have sequenced 48 Sequence Tagged Sites (STS) that were developed to represent the rice genome in red rice sampled from three specific ecozones in Arkansas and in several fields in California plus South Carolina. Our objectives for this USDA-funded project are: (1) To assess the distribution and infestation level of weedy rice in California (new recruitments) and Arkansas (widespread occurrence); (2) To identify agroecological factors that may be associated with proliferation of weedy rice; (3) To test alternative hypothesis of population structure and gene flow between cultivated and weedy rice localities and populations as they relate to management strategies and ecozones; and (4) To evaluate geographic, edaphic, or crop management variables associated with specific weedy rice genotypes or morphotypes. This project is funded by the USDA and is in collaboration with Nilda Burgos (University of Arkansas) and Albert Fisher (UC-Davis).
Population Genetics of Glyphosate Resistance in Amaranthus palmeri
U.S Department of Agriculture
Evolutionary Dynamics and Management of Weedy Rice in the U.S.
Fundamentals of Genetics I
Fundamentals of Genetics I Laboratory
Methods of Analysis in Population Genetics and Molecular Evolution
Wang Y, Zhou L, Li D, Dai L, Lawton-Rauh A, Srimani PK, Duan Y, F Luo (2015) Genome-Wide Comparative Analysis Reveals Similar Types of NBS Genes in Hybrid Citrus sinensis Genome and Original Citrus clementine Genome and Provides New Insights into Non-TIR NBS Genes. PLoS ONE 10(3): e0121893. doi:10.1371/journal.pone.0121893.
Ziska LH, Gealy DR, Burgos N, Caicedo AL, Gressel JL, Lawton-Rauh AL, Avila LA, Theisen G, Norsworthy J, Ferrero A, Vidotto F, Johnson DE, Ferreira FG, Marchesan E, Menezes V, Cohn MA, Linscombe S, Carmona L, Tang R, A Merotto (2015). Weedy (Red) Rice: An Emerging Constraint to Global Rice Production. Advances in Agronomy 129:181–228
Ward SM, Cousens RD, Bagavathiannan MV, Barney JN, Beckie HJ, Busi R, Davis AS, Dukes JS, Forcella F, Freckleton RP, Gallandt ER, Hall LM, Jasieniuk M, Lawton-Rauh A, Lehnhoff EA, Liebman M, Maxwell BD, Mesgaran MB, Murray JV, Neve P, Nuñez MA, Pauchard A, Queenborough SA, and BL Webber (2014) Agricultural Weed Research: A Critique and Two Proposals. Weed Science 62:4, 672-678
Gressel J, Stewart CN, Giddings LV, Fischer AJ, Streibig JC, Burgos NR, Trewavas A, Merotto A, Leaver CJ, Ammann K, Moses V, Lawton‐Rauh A (2014). Overexpression of epsps transgene in weedy rice: insufficient evidence to support speculations about biosafety. New Phytologist 202:2, 360-362.
McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, and D Zamir (2013). Agriculture: Feeding the Future. Nature 499 (7456), 23-24.
Vigueira C, Rauh B, Mitchell-Olds T and A Lawton-Rauh (2013). Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea. PLoSONE 8:3, e58916.
Leach M, Agudelo P, and A Lawton-Rauh. (2012). Genetic Variability of Rotylenchulus reniformis. Plant Disease 96:1, 30-36.
Leach M, Agudelo P, and A Lawton-Rauh (2012). Effect of Crop Rotations on Rotylenchulus reniformis Population Structure. Plant Disease 96:1, 24-29
Lawton-Rauh A and NR Burgos. (2010). Cultivated and weedy rice interactions and the domestication process. Molecular Ecology, 19 (16): 3243-3245.
Wang J, Zhang L, Li J, Lawton-Rauh A* and D Tian*. (2011). Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species. Gene, 482(1-2):24-33.