Welcome! 歓迎 Willkommen! 欢迎 Bienvenue! Benvenuto! Boa Vinda! привет 환영


Systems…  Amaranthus species (weeds and cultivated species); Herbicide-resistant and locally adapted weedy species (especially A. palmeri, Echinochloa spp.); Rosaceous crops & wild relatives (peach, cherry, apple, strawberry, etc.); Rice (Oryza) cultivars, weeds, and wild relatives

Methods…  population genomics, genome prediction, diversity genomics, computational genomics, bioinformatics, genome scans, quantitative genomics, genome selection, molecular evolution, phylogenetics

Contributions… population dynamics-driven solutions to weedy and invasive species management, resilient and more sustainable crops, improved understanding of the genomic basis of adaptation, dissection of the contributions of genomes and environmental factors shaping traits, personalized genomics applications, adaptive agricultural practices and management for local conditions with global knowledge.

PalmerCottonFieldGAAmaranthus - Research page - Amy's facebook photoDSC00065Hand-with-fruitFeatured image


We investigate the adaptive genomics of crops, crop wild relatives, and weedy species. Our research is guided by the following questions that help us translate evolutionary principles into tools that improve food security, human health, and ecosystems shaped by production:

  • What can we learn and use from crop wild relatives and locally adapted weeds to improve the sustainability of food, fuel, fiber, and bioproduct production?
  • How does breeding impact the genomes of crops during domestication and post-domestication stability?
  • 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?
  • 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?

The Lawton-Rauh Lab investigates the relationships amongst genome dynamics, domestication and ferality traits, and the genetic histories of crop-wild relative lineages in order to understand 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 help improve germplasm (seeds and cultivar tissues), 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 analyses of nucleotide and amino acid sequence data, bioinformatics analyses of whole 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.

Picture of board from MCMC discussion, PopQuantGenetics connection


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 update weedy and invasive species management techniques.


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 (Oryza spp), and amaranths to understand population level processes that lead to adaptation and improved cultivars with optimized trait combinations (such as disease resistance and shelf life). Sometimes cultivars 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).

A summary of our work in weedy and domesticated species was published in Clemson’s Glimpse magazine Fall 2014 (written by Peter Kent): Glimpse “Pestilence of Pigweed” Fall 2014

Amaranthus palmeri devours cotton field

Cotton field without Amaranthus palmeri (left), and taken over by glyphosate resistant A.palmeri (right).  This project is funded by Cotton Incorporated

Weedy rice

Weedy rice in a crop rice field in Arkansas. Notice the long pigmented awns and taller stature. Funding for this project comes from the USDA-NIFA Weedy and Invasive Species program (2008-12), the Wade Stackhouse graduate fellowship program, Clemson Honors College, HHMI/SCLife, and Clemson University. Collaborators: Nilda Burgos (University of Arkansas) and Albert Fischer (UC-Davis)

RosBREED2 aims to connect multiple traits to improve rosaceous cultivars

The RosBREED2 project spans Rosaceous species. Please visit the RosBREED Consortium site to learn more about this extensive collaborative project. The Lawton-Rauh Lab is co-developing 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 Research Initiative funded project. Other funding extending work to the population and quantitative genomics of Armillaria (root rot) resistance in peach is now funded by Wells Fargo (see Lab News for link)