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Amy Lawton-Rauh

Associate Professor
Genetics and Biochemistry Department

Office: 316 Biosystems Research Complex
Phone: 864-656-1507
Email: amylr@clemson.edu
Personal Website: popquantgenomics.org

 

 Educational Background

Ph.D. Genetics, Minor Botany
North Carolina State University 2003

Honors B.S. Biology, Minors Chemistry & Anthropology
University of Missouri, Columbia 1997

 Research Interests

ADAPTIVE GENOMICS OF CROPS, CROP WILD RELATIVES, AND WEEDY SPECIES
Addressing these questions guide us in translating models into tools that improve how agriculture impacts food security, human health, and ecosystems impacted by production:
1) How does breeding impact the genomes of crops during domestication and post-domestication stability?
2) Going beyond pedigree-approaches in breeding: Can we develop genome predictions to inform genome selection strategies in crops using population genetics models of diversity and divergence and the principles of quantitative genetics?
3) What can we learn and use from crop wild relatives and locally adapted weeds to improve the sustainability of bioproduct, food, fuel, and fiber production?
4) Is there a ‘genomic propensity’ for some species to adapt more quickly to management practices (especially herbicides) and thereby become aggressive weedy and invasive species? What can we learn from these species regarding adaptive evolution mechanisms at the population level? Can we use our work to translate basic research models into informative, predictive outcomes to improve agriculture, human health, and ecosystems?

My lab studies the relationships between genome dynamics, domestication and ferality traits, genetic histories of crop-wild relative lineages, and the impact that these relationships have on crop improvement plus population-level management of agroecosystems (including weedy and invasive species). More specifically, we apply models of population and quantitative genetics to study: genetic diversity from crop wild relatives and diverse seed collections of rosaceous crops (esp. peaches, apples, and cherries) to improve elite seeds, the genome dynamics underlying aggressive rapid origins and proliferation of herbicide-resistant weedy Amaranthus species, and the tension between domestication and de-domestication in Oryza spp. (rice). For our work, we do many things including bioinformatics analyses of genome data, conducting wet chemistry experiments in bioassays for measuring phenotypic responses to stressors, conducting genetic crosses in the greenhouse, and employing plus optimizing and creating new computational genomics tools to test population histories and domestication models.

Why Population and Quantitative Genomics:
All populations contain variation in traits amongst individuals, and much of this variation has a genetic basis. Genetic variation is present in humans, cats, peaches, dogs, Palmetto trees, mosquitoes, bacteria… etc. Understanding the processes and mechanisms shaping genetic variation and genomic interactions is important in health, agriculture, and ecology. Many genetic phenomena can only be observed at the population level. Thus, it is important to look at entire populations – not just individuals – when studying genetics. Most processes underlying traits involve multiple alleles at multiple genes and it is the unique combination of alleles across many genes that lead to trait values. Thus, it is also important to study interactions and structural features of the entire genome (“genomics”). We can use population and quantitative genetics principles to improve the effectiveness of personalized medicine, optimize crop cultivation strategies and adapt weedy and invasive species management techniques.

What We Do:
In the Lawton-Rauh Laboratory, we test for mechanisms responsible for observed patterns of genetic and trait variation primarily in plants. We study the genomes of Rosaceous crops (peaches, cherries, apples), crop and weedy rice, and amaranths as model systems for understanding population level processes that lead to adaptation and improved cultivars with optimized trait combinations (such as disease resistance and shelf life). Sometimes crop progenitors and wild relatives also become weeds. So, studying wild relatives and weeds can provide tools for developing more sustainable cultivars that are resilient to stressors such as water (drought and flood), temperature, fungi, insects, pathogens, and pesticides (including herbicides).

Genus Amaranthus:
--Adaptive evolution of herbicide resistance at the population genomic level... We are using diversity and divergence population genomics models to define population connectivities. These connectivities lay the foundation for our further work in identifying the origins and proliferations of herbicide tolerance, resistance, and resilience mechanisms at the genome-level. This project is funded by Cotton Incorporated and is in collaboration with Nilda Burgos (Uni. Arkansas) and James Burton (NCSU).
--Origins and histories of Amaranthus species across the globe (cultivated and wild species)... We sampled across the genus to estimate the phylogenetic relationships amongst Amaranthus species. We are working with collaborators on the adaptive potential of several Amaranthus species for several traits, including crop and weediness.

Rosaceous crops (peach, cherry, apple) and wild relatives:
The Lawton-Rauh Lab is working with collaborators to develop genome selection and prediction methods informed by uniting quantitative genetics models with diversity and divergence models in peaches, cherries, apples, and other Rosaceous species (including wild relatives) in this USDA-Specialty Crops grant (for extensive list of collaborators, please see www.rosbreed.org. We are also working with Sebas Ramos-Onsins at the Center for Research in Agricultural Genomics-Spain on this project).

Weedy rice:
We are investigating the genome dynamics of retention and escape traits during domestication and de-domestication by comparing cultivated and targeted weedy rice populations. This project was funded by the USDA-NIFA Weedy and Invasive Species program Collaborators: Nilda Burgos (University of Arkansas) and Albert Fischer (UC-Davis).

 Publications

Wang Y, Zhou L, Li D, Dai L, Lawton-Rauh A, and 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 DG, Caicedo AL, Gressel J, Lawton-Rauh A, Avila LA, Theisen G, Norsworthy J, Ferrero A, Vidotto F, Johnson DE, Ferreira FG, Marchesan E, Menezes V, Cohn MA, Burgos N, Linscombe S, Carmona L, Tang R, and A Merotto. (2014). 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 E, Liebman E, Maxwell BD, Mesgaran MB, Murray JV, Neve P, Nuñez M, Pauchard A, Queenborough S, and B 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, and A Lawton‐Rauh. 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, Zamir D. (2013). Agriculture: Feeding the Future. Nature. 499(7456):23-24

Vigueira CC, Rauh BL, Mitchell-Olds T, and A. Lawton-Rauh. Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea. (2013). PLoS ONE. 8(3): e58916.

Leach M, Agudelo P, and A Lawton-Rauh. Effect of crop rotations on Rotylenchulus reniformis population structure. (2012). Plant Disease. 96(1): 24-29.

Leach M, Agudelo P, and A Lawton-Rauh. Genetic variability of Rotylenchulus reniformis. (2012). Plant Disease. 96(1): 30-36.

Wang J, Zhang, L, Sun X, Lawton-Rauh A*, and D Tian* (*co-corresponding authors). Genetic signatures of highly-adaptable R-genes in closely-related Arabidopsis species. (2011). Gene. 482(1-2):24-33.

Lawton-Rauh A and NR Burgos. (2010). Cultivated and weedy rice interactions and the domestication process. Molecular Ecology, 19 (16): 3243-3245.

Mather KA, Molina J, Rubinstein S, Flowers JM, Caicedo AL, McNally KL, Rauh BL, Lawton-Rauh A, and MD Purugganan. 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.

Leach M, Agudelo P, and A Lawton-Rauh. Population variability of Rotylenchulus reniformis in cotton agroecosystems. (2010). Journal of Nematology 42(3): 251-252.

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.

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.
Jimenez S. Li ZG, Lawton-Rauh AL, Reighard GL, Abbott AG, Bielenberg DG. (2009). Learning from model species: a case study of comparative genomics in Arabidopsis, Populus, peach and apricot. HortScience 44(3):565.

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

 Links

Lawton-Rauh Lab website on PopQuantGenomics
RosBREED2 project page (USDA-Specialty Crops Grant)
Glimpse magazine coverage of our work in weedy species (feral rice and Palmer amaranth)