Pradeep Reddy Marri


Asst. Research Scientist in the lab of Steve Rounsley
BIO5 Institute, The University of Arizona

Research Interests

  • Comparative genomics of plant and bacterial genomes
  • Bioinformatics
  • Next-generation sequencing technologies
  • Metagenomics
  • Crop Improvement
  • Molecular breeding






Research Experience
2008 -              Asst. Research Scientist, BIO5 Institute, University of Arizona, USA

2006 - 2008     Research Associate, University of Arizona, Tucson, Arizona, USA

2004 - 2006     Postdoctoral Fellow, McMaster University, Hamilton, Ontario, Canada
Ph.D   2003   Plant Sciences, University of Hyderabad, India

MS     1998   Biotechnology, Guru Nanak Dev University, India

BS      1996   Genetics, Osmania University, India
Current Projects
My research transcends both plant and bacterial worlds. My research employs genomic tools to tackle some of the most challenging problems. I use molecular, phylogenetic and bioinformatic approaches to understand variations in gene flux among closely related genomes.

Oryza Genomics


Rice is a staple for over a third of the world's population. With the world population size expected to double in the next 25 years, the challenge is to develop high yielding rice varieties that can sustain harsher climatic conditions and dwindling resources. Wild species of rice provide a very valuable resource of novel genes/alleles that help to improve rice yields. I am a part of the consortium that is involved in sequencing rice genomes to uncover useful genes that could be used in subsequent breeding programs for rice improvement. My specific research objectives include:
  • Identification of novel genes in wild rice species
  • Comparative genomics to understand the gene flux among different Oryza species
  • Understand the processes underlying the origin or loss of genes
Next Generation Sequencing for Cassava Improvement


Cassava (Manihot esculenta) is a root crop that is staple to more than 800 million people in Africa. However, cassava develoment is hampered by abiotic and biotic stresses. New improved cassava varieties are needed to increase cassava yield. However, molecular marker development is in its infancy and rapid progess in this area is critical for cassava improvement. As part of this project, we are utilizing the exisiting genome sequence of Cassava to characterize the genetic variability of Cassava germplasm. We are using next generation sequencing technologies to develop SNP markers for a diverse set of cassava accessions. These markers could be used in subsequenct breeding applications for trait improvement. Some of the specific objectives of this project include:
  • Improvement of cassava genome sequence by generationg BAC end sequences
  • Development of SNP markers for a diverse set of cassava accessions
  • Use SNP markers for fine mapping the QTLs for Cassava Brown Streak Disease (CBSD) resistance in cassava
Role of Microbiome in Asthma
Asthma is a complex disease affecting 300 million people worldwide. The genetic background of the host as well as the environment having a significant bearing on the outcome of disease. It is increasingly believed that the microbiome of human airways may have a role in Asthma. I was awarded a pilot grant from Southwest Environmental Health Sciences Center (SWEHSC) to explore the role of microbiome in Asthma. The project uses a metagenomic approach involving 454 sequencing to characterize the mircrobial community structure and gene content in the induced sputum samples of asthmatic and non-asthmatic individuals to detect mircobial biomarkers for Asthma. The specific objectives of the project include:
  • Characterizing the microbial communities in asthmatics vs. non-asthmatic individuals
  • Identification of differences in bacterial genes/pathways in asthmatics vs. non-asthmatics
  • Finding differences in expression patterns of bacterial genes in asthmatics vs. non-asthmatics

Other Projects
In addition to these three major projects, I am involved in projects that use next generation sequencing technologies for genome sequencing and comparative genomics of bacteria such as Neisseria and Clostridium species.
Ferguson, M.E., Rabbi, I.Y., Kulumbeka,. H.P., Hearne, S.J., Close, T.J., Wanamaker, S., Moskal, W.A., Town, C.D., de Young, J., Marri, P.R. and de Villiers, E.P. 2011. A Transcribed Gene SNP Resource and Integrated SSR and SNP Genetic Linkage Map of Cassava (Manihot esculenta Crantz.) BMC Plant Biology. Submitted

Goicoechea, J.L., Ammiraju, J.S.S., Marri, P.R., Chen, M., Jackson, S., Yu, Y., Rounsley, S. and Wing, R.A. 2010. The future of rice genomics: Sequencing the collective Oryza genome. RICE 3: 89-97. PDF

Rounsley, S., Marri, P.R., Yu, Y., He, R., Sisneros, N., Goicoechea, J.L., Lee, S.J., Angelova, A., Kudrna, D., Luo, M., Affourtit, J., Desany, B., Knight, J., Niazi, F., Egholm, M. and Wing, R.A. 2009. De novo next generation sequencing of plant genomes. RICE 2: 35-43. PDF

Marri, P.R., Sarla, N., Reddy, L.V. and Siddiq, E.A. 2005. Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genetics 6: 33. PDF

Marri, P.R., Sarla, N., Reddy, V.L.N. and Siddiq, E.A. 2004. Introgresion and mapping of yield enhancing QTLs from Oryza rufipogon Rice Genetics Newsletter 21: 25-26. PDF

Marri, P.R., Sarla, N., and Siddiq, E.A. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128: 9-17. PDF

Sarla, N., Marri, P.R., and Siddiq, E.A. 2001. Application of inter simple sequence repeat (ISSR) polymorphism in assessing diversity in crop plants. Indian J. Plant Genet. Resources 14(2): 246-247.

Marri P.R., Stern, D.A., Wright, A.L., Billheimer, D. and Martinez, F.D. 2011. Asthma associated differences in microbial composition of airway sampels. PLoS ONE. Submitted

Marri, P.R., Paniscus, M., Weyand, N.J., Rendon, M.A., Calton, C.M., Hernandez, D.R., Higashi, D.L., Sodergren, E., Weinstock, G.M., Rounsley, S. and So, M. 2010. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. PLoS ONE 5(7): e11835. PDF

Lepp, D., Roxas, B.P., Parreira, V.R., Marri, P.R., Rosey, E.L., Gong, J., Songer, J.G., Vedantam, G., Prescott, J.F. 2010. Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis. PLoS ONE 5(5): e10795. PDF

Marri, P.R., Harris, L.K., Houmiel, K., Slater, S.C. and Ochman, H. 2008. The effect of chromosome structure on genetic diversity. Genetics 179: 511-516. PDF

van Passel, M.W.J*, Marri, P.R.* and Ochman, H. 2008. The emergence and fate of horizontally acquired genes in Escherichia coli . PLoS Comput Biol 4(4):e1000059. PDF

Marri, P.R. and Golding, G.B. 2008. Gene amelioration demonstrated: the journey of nascent genes in bacteria. Genome 51: 164-168. PDF

Marri, P.R.* Hao,W.* and Golding, G.B. 2007. The role of laterally transferred genes in adaptive evolution. BMC Evolutionary Biology 7(Suppl 1):S8. PDF

Marri, P.R.*, Hao, W.* and Golding, G.B. 2006. Gene gain and gene loss in Streptococcus: Is it driven by habitat? Molecular Biology and Evolution 23(12): 2379-2391. PDF

Marri, P.R., Bannantine, J.P. and Golding, G.B. 2006. Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer. FEMS Microbiology Reviews 30(6): 906-925. PDF

Marri, P.R., Bannantine, J.P., Paustian, M.L. and Golding, G.B. 2006. Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis. Can. J. Microbiology 52: 560-569. PDF

* joint first authors