Vikram E. Chhatre
Population Genomics & Computational Biology


Brief chronology of my work


I grew up in India and have studied and worked in Sweden, Canada and the United States during the last 20 years. My professional training is in the field of population genetics and much of my work is on natural populations of widely distributed forest tree species. My early work focused on conservation genetics of Norway spruce and central marginal hypothesis testing in old and second growth forests of eastern white pine.


In the intervening years before I began my graduate studies, I worked as a research technician with Patrick Abbot at Vanderbilt University. During the course of five years, I learned a great deal about molecular population genetics and social evolution in aphids. I also performed thousands of PCR reactions and genotyped large numbers of aphids and treehoppers using polyacrylamide gels. My participation in this work showed that movement of aphids between galls is not restricted by kinship. Together with Kathleen Grogan, we further developed this work resulting in a publication on the cost of conflict in aphid societies. While at Vanderbilt, I also did a brief stint with Lila Sonica-Krezel working on TILLING, a reverse genetics approach in zebrafish.


My PhD dissertation at Texas A&M was on the more applied science topic of forest tree improvement and quantitative genetics. My work developed an understanding of the captured genetic variation as well as inbreeding during the two cycles of phenotypic selection within the breeding stock of loblolly pine (Pinus taeda L.) operated by the Western Gulf Forest Tree Improvement Program.

It was also during my PhD that I developed the now popular STRUCTURE analysis automation utility - StrAuto which has now been cited by 80 peer-reviewed publications and downloaded over 2000 times by scientists in over 50 countries. Parallelization was subsequently implemented by Kevin Emerson. Paper describing StrAuto can be found here.


I continued my applied work on quantitative genetics of southern pines during my first postdoc at the Southern Institute of Forest Genetics. This work culminated in the development of a dense genetic linkage map for loblolly and slash pine.


Working with Steve Keller, I switched gears to go back to my roots in plant evolutionary genetics. With a new and easier to work model system at hand (poplars), I developed understanding of the next generation sequencing and the bioinformatics analysis of this data to address questions in population and evolutionary genomics. Our analysis of hybridization in poplar species at their range margins showed that introgression can be adaptive if it is beneficial for survival in suboptimal conditions. Another thread of work on flowering time gene network in balsam poplar provided greater insights into influence of range position for local adaptation.


Between Dec 17 and 18, I was appointed to a study commmittee of the National Academy of Sciences. The committee was convened at the request of various federal agencies and was tasked with investigating the role biotechnology could play in saving forests in the face of various threats. You can read about the study process at the committee’s website: Potential for biotechnology to address forest health. A consensus report based on the committee’s findings was published by the National Academies Press in January 2019. It is titled Forest Health and Biotechnology: Possibilities and Considerations which can be downloaded for free.


In the current position, I have developed a number of collaborations in various biological subdisciplines. The following projects are at various stages in data analysis and manuscript preparation:

  • Age and sex dependent analysis of heart pathogenesis in mouse (RNA sequencing)

  • Genetic mechanisms underlying chloroplast stromule function in Arabidopsis thaliana (RNA sequencing)

  • Detecting novel agents of viral infection in the transcriptome sequences of affected Canidae and Equidae. (Whole genome sequencing)

  • Differential gene expression underlying social interactions in Myxococcus bacteria. (RNA sequencing)

  • Understanding genetic regulation of delayed implantation in western spotted skunk (Spilogale gracilis). (Whole genome sequencing and genotyping by sequencing)

  • Genetic architecture of stress tolerance in Wyoming grapevine varieties. (RNA sequencing)

  • Identification of major QTL underlying traits of agronomic importance in Brassica sp. (genotyping by sequencing)

  • Differential gene expression analysis of heart in Rattus norvegicus under various developmental stages. (RNA sequencing)