Genetics and Biochemistry

Dr. Amy Lawton-Rauh

Amy Lawton-Rauh

Associate Professor

Ph.D. Genetics
2003, North Carolina State University

Contact Information
Office: 316 Biosystems Research Complex
Lab: 317 Biosystems Research Complex
Phone: (864) 656-1507
Web: Lawton-Rauh Lab

Research Focus Areas
Comparative genomics, molecular evolution and population genetics
Genetic interactions amongst crops, wild relatives, and weeds
Evolutionary genetics of pesticide/herbicide resistance


Research Activities

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).


Grant Support

Graduate Students


Sarah Barfield
Katerina Lay
Kameryn McCarty
Kirby McCall
Christopher Robinson

Courses Taught

GEN 4100
Fundamentals of Genetics I

GEN 4110
Fundamentals of Genetics I Laboratory

GEN 8140
Advanced Genetics

GEN 4910
Directred Research

GEN 8300
Methods of Analysis in Population Genetics and Molecular Evolution




Recent Publications

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.

Leach M, Lawton-Rauh A, and P Agudelo. (2011). Ten polymorphic microsatellite loci for reniform nematode, Rotylenchulus reniformis. Molecular Ecology Resources. 11(2): 418-421.

Mather KA, Molina J, Rubinstein S, Flowers JM, Caicedo AL, McNally KL, Rauh BL, Lawton-Rauh A, and MD Purugganan. (2010). Migration, isolation and hybridization in island populations: The case of Madagascar rice. Molecular Ecology, 19 (22): 4892-4905.

Shivrain V, Burgos N, Agrama H, Lawton-Rauh A, Lu B-R, Sales M, Boyett V, Gealy D, Moldenhauer K. (2010). Genetic diversity of weedy red rice populations (Oryza sativa L.) in Arkansas USA. Weed Research, 50 (4): 289-302.

Lawton-Rauh A, Climer C, B Rauh. (2010). Comparative and Evolutionary genomics. in Principles and practices of plant genomics, Volume 3 Advanced genomics. Eds. C. Kole and A.G. Abbott. Book Chapter.

Leach MM, Agudelo P, A Lawton-Rauh. (2009). Effect of crop rotation on Rotylenchulus reniformus population structure. Journal of Nematology, 41 (4): 347-348.

Jimenez S, Lawton-Rauh A, Reighard GL, Abbott AG and DG Bielenberg. (2009). Phylogenetic Analysis and Molecular Evolution of the Dormancy Associated MADS-Box Genes from Peach. BMC Plant Biology Vol. 9, Article 81.

Lawton-Rauh A. (2008). Demographic factors shaping genetic variation. Current Opinion in Plant Biology 11(2):103-109. Invited review.

Lawton-Rauh A, Friar EA, DL Remington. (2007). Collective evolution processes and the tempo of lineage divergence in the Hawaiian silversword alliance adaptive radiation (Heliantheae, Asteraceae). Molecular Ecology, 16(19): 3993-3994.

Lawton-Rauh A, Robichaux RH, and MD Purugganan. (2007). Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae). Molecular Ecology, 16(19): 3995-4013. Cover photo.