Dr. Padma Nimmakayala

Vegetable genomics and breeding
Dr. Nimmakayala's research focuses on molecular marker development, genetic and physical mapping, marker assisted selection in vegetable crops (pepper, watermelon, sweetpotato and other cucurbits).

Quantitative genetics, DNA marker assisted plant breeding


Lab: 304-766-5246

Research Interests:

Our research program focuses on vegetable breeding, genetics and genomics. Our research aims in developing molecular markers for pepper, pumpkin, Melon and watermelon, and integrating these tools for marker assisted breeding to improve fruit traits.
We developed the first whole genome sequence for Cucurbita pepo genome. We have also identified pumpkin types that have high antioxidants and tocopherols that can be used for nutraceutical purposes. 
Presently, little is known about the genes controlling flavor and fruit architecture in pepper germplasm that is relevant to breeding. We have already generated extensive SNP data that can make Genome-wide Association Study (GWAS) feasible to identify molecular markers linked to phytonutrients and fruit architecture.
Teaching:  I Participate in team taught course- Biotechniques II (BT-572) and teach plant genetic engineering. I also teach crop evolution and biodiversity (Biol.363).
 

Education: 

B.Sc. (Agric): Andhra Pradesh Agricultural University, Hyderabad, India (1981-85).
M.Sc. (Genetics & Plant Breeding): Tamil Nadu Agricultural University, Coimbatore, India (1986-88).
Ph.D. (Genetics&Plant Breeding): University of Agriculture sciences, Bangalore, India (1989-1992)
Research Scientist (Genetics & Plant Breeding), Indian Council of Agriculture Research (1992-98)
Post-doctoral Associate: Texas A&M University, College Station, TX (1998-2001)
 

Awards/Grants:

USDA-NIFA Proposal no. 2012-02508. Genome-wide association mapping for improving nutraceutical traits in pumpkin and squash (01 SEP 2012 -31 AUG 2016), $299,832 (Research grant; as Principal investigator).
USDA-NIFA Proposal no. 2013-04053. Summer academy of plant breeding: A platform to develop minority workforce in molecular plant breeding (01 SEP 2013 - 31 AUG 2016), $120,000 (Teaching grant; as Principal investigator).
USDA-NIFA Proposal no. 2010-02247. Stories of crop evolution, biodiversity and domestication and methods of genomic assisted crop improvement for curricula development (01 SEP 2011 - 31 AUG 2015), $299,986 (Teaching grant; as Principal investigator).
USDA-NIFA Proposal no. 2013-03685. Diversifying the watermelon cultivar genetic base using genomic selection to improve nutraceutical traits and use them as parental lines (01 SEP 2013 - 31 AUG 2016), $444,346 (Research grant; as co-investigator).
 

Selected Publications (2010-2016):

1. Perla, V., Nimmakayala, P., Nadimi, M., Alaparthi, S., Hankins, G. R., Ebert, A. W., & Reddy, U. K. (2016). Vitamin C and reducing sugars in the world collection of Capsicum baccatum L. genotypes. Food Chemistry, 202, 189-198. doi: http://dx.doi.org/10.1016/j.foodchem.2016.01.135
2. Singh, N. V., Abburi, V. L., Ramajayam, D., Kumar, R., Chandra, R., Sharma, K. Sharma J, Babu KD, Pal R, Mundewadikar D, Saminathan T, Cantrell R, Nimmakayala P Reddy, U. K. (2015). Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.  Molecular Genetics and Genomics, 290(4), 1393-1402. doi: 10.1007/s00438-015-1003-0
3. Saminathan T,, Malkaram SA, Patel D, Taylor K, Hass A, Nimmakayala P, Huber DH, and Umesh K. Reddy (2015). Differential gene expression and alternative splicing between diploid and tetraploid watermelon. Journal of experimental botany, 66(5), 1369-1385. doi:10.1093/jxb/eru486
4. Saminathan T,, Malkaram SA, Patel D, Taylor K, Hass A, Nimmakayala P, Huber DH, and Umesh K. Reddy.(2015).Transcriptome Analysis of Invasive Plants in Response to Mineral Toxicity of Reclaimed Coal-Mine Soil in the Appalachian Region. Environmental Science & Technology.DOI: 10.1021/acs.est.5b01901
5. Saminathan, T., Malkaram, S. A., Patel, D., Taylor, K., Hass, A., Nimmakayala, P. Huber DH, and Reddy, U. K. (2015). Transcriptome Analysis of Invasive Plants in Response to Mineral Toxicity of Reclaimed Coal-Mine Soil in the Appalachian Region. Environmental Science & Technology, 49(17), 10320-10329. doi: 10.1021/acs.est.5b01901
6. Reddy, U., Abburi, L., Abburi, V., Saminathan, T., Cantrell, R., Vajja, V., Reddy R., Tomason YR., Levi A, Wehner, TC., Nimmakayala P. (2015). A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon. The Journal of heredity, 106(2), 166.
7. Venkatesan T, Sridhar V, Tomason YR, Jalali SK,. Behere GT, Shanthi RM, Kumar R, Vajja VG, Nimmakayala P, Umesh K. Reddy. 2015. Use of expressed sequence tag microsatellite markers for population genetic research of Helicoverpa armigera (Lepidoptera: Noctuidae) from India. Can. Entomol. 00: 1–13 (2015)
8. Reddy, U. K., Nimmakayala, P., Levi, A., Abburi, V. L., Saminathan, T., Tomason, Y. R., Vajja G, Reddy R, Abburi L, Wehner TC, Ronin Y Karol, A. (2014). High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon. G3: Genes|Genomes|Genetics, 4(11), 2219-2230. doi: 10.1534/g3.114.012815
9. Reddy, U. K., Almeida, A., Abburi, V. L., Alaparthi, S. B., Unselt, D., Hankins, G., Park M, Choi D, Nimmakayala, P. (2014). Identification of Gene-Specific Polymorphisms and Association with Capsaicin Pathway Metabolites in Capsicum annuum L. Collections. PLoS ONE, 9(1), e86393. doi: 10.1371/journal.pone.0086393
10. Nimmakayala, P., Levi, A., Abburi, L., Abburi, V. L., Tomason, Y. R., Saminathan, T., Vajja VG, Malkaram S, Reddy R, Wehner T, and Reddy, U. K. (2014). Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC genomics, 15(1), 1-15. doi: 10.1186/1471-2164-15-767
11. Nimmakayala, P., Abburi, V. L., Bhandary, A., Abburi, L., Vajja, V. G., Reddy, R., Malkaram S, Venkatramana P, Asela Wijeratne, Tomason Y, Levi A, Wehner T Reddy, U. K. (2014). Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Molecular Breeding, 34(2), 537-548. doi: 10.1007/s11032-014-0056-9
12. Nimmakayala, P., Abburi, V. L., Abburi, L., Alaparthi, S. B., Cantrell, R., Park, M.,  Doil Choi, Hankins G, Malkaram S., and Reddy, U. K. (2014). Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping. Molecular Genetics and Genomics, 289(4), 513-521. doi: 10.1007/s00438-014-0827-3
13. Tomason, Y., Nimmakayala, P., Levi, A., & Reddy, U. K. (2013). Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon. Molecular Breeding, 31(4), 829-841.
14. Umesh K. Reddy, Nischit Aryal, Nurul Islam-Faridi, Yan Tomason, Amnon Levi and Padma Nimmakayala. 2013. Cytomolecular characterization of rDNA distribution in various Citrullus species using fluorescent in situ hybridization. Genetic Resources and Crop Evolution. DOI 10.1007/s10722-013-9976-1.
15. Manohar S.,  Jagadeeswaran G., Nimmakayala P., Tomason Y.,  Almeida A., Sunkar R., Levi  A., Reddy UK. (2012) Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit species. Plant Mol. Biol. Rep ;31 335-343
16. Nimmakayala P, Vajja G, Gist R, Tomason YR, Levi A, Reddy UK.2011. Effect of DNA methylation on molecular diversity of watermelon heirlooms and stability of methylation specific polymorphisms across the genealogies.  Euphytica. 177: 79-89.
17. Guru J, Nimmakayala P, Zheng Y, Gouda K, Reddy U and Sunkar R. 2011. Characterization of the small RNA component of the transcriptome in leaves and fruits of four cucurbits revealed dynamic regulation of conserved and novel miRNAs. BMC Genomics 2012, 13:329 http://www.biomedcentral.com/1471-2164/13/329.
18. Reddy UK, Rong JK, Nimmakayala P, Vajja G, Rahman M, Yu JZ, Soliman K, Heller-Uszynska K, Kilian A, and Paterson A.H. 2011. Use of DArT markers for integration into cotton reference map and anchoring to a RIL map. Genome 54(5): 349-359.
19. Nimmakayala P, Perumal R, Sujatha M and U K. Reddy. 2011. Sesamum. (Book chapter). Wild Crop Relatives: Genomic and Breeding Resources, oilseeds. Springer-Verlag, Berlin Heidelberg. 261-273.
20. Nimmakayala P, Faridi NI, Tomason YR, Lutz F, Levi A and U K. Reddy. 2011. Citrullus. (Book chapter). Wild Crop Relatives: Genomic and Breeding Resources, Vegetables. Springer-Verlag, Berlin Heidelberg. Pages 59-66.
21. Nimmakayala P, Vajja G and U K. Reddy. 2011. Ipomoea. (Book chapter). Wild Crop Relatives: Genomic and Breeding Resources, Industrial crops. Springer-Verlag, Berlin Heidelberg. 123-132.
22. Nimmakayala P, Jeong J, Tomason Y, Levi A, Ramasamy P, UK. Reddy.2010. Genetic reticulation and interrelationships among Citrullus species as revealed by joint analysis of shared AFLPs and species-specific SSR alleles. Plant Genetic Resources 8 (1): 16-25.
23. Nimmakayala P, Tomason Y, Jeong J, Vajja G, Levi A, Gibson P, UK. Reddy.2010. Molecular diversity in the Ukrainian melon collection as revealed by AFLPs and microsatellites. Plant Genetic Resources 7: 127-134.

Conference presentations (2010-2015):

1. Sequencing and Assembly of the Genome of an American Watermelon Ecotype, Charleston Gray. International Plant & Animal Genome XXI Conference, January 10-14, 2015 - San Diego, CA. (oral presentation)
2. Abiodun B, Saminathan T, Nimmakayala P and Umesh K.Reddy 2015.Genome Wide Association (GWAS) Mapping of Trichome Density and Length in Watermelon. International Plant & Animal Genome XXI Conference, January 10-14, 2015 - San Diego, CA. (oral presentation)
3. Nimmakayala P, Abburi VL, Tomason Y, Wehner T, Levi A and Reddy UK. 2014. Genome-wide Association Mapping of Fruit Traits in Watermelon. International Plant & Animal Genome XXII. Conference. January 12-16, 2014.
4. Levi A, Patrick Wechter, Laura Massey, Ryan Donahoo, Robert Jarret, Padma Nimmakayala, Umesh K. Reddy, Zhangjun Fei.2014. Gene Sequences Present in Citrullus sp. and having been Lost during Domestication of Watermelon. International Plant & Animal Genome XXII. Conference. January 12-16, 2014.
5. Nimmakayala P, Abburi VL, Abburi L, Gopinath V and Reddy UK.2013.Population structure and association mapping of fruit traits and capsicum content in Capsicum annuum. International Plant & Animal Genome XXI Conference, January 12-16, 2013-San Diego, CA
6. Dalton HL, Reddy UK, Manohar S, Tomason Y, Levi A, Nimmakayala P. 2013. Differential expression of miRNA across the grafted tissues collected from heterografts involving different genera of Cucurbitaceae family. International Plant & Animal Genome XXI Conference, January 12-16, 2013- San Diego, CA (oral presentation)
7. Levi A, Reddy UK, Nimmakayala P , Wechter P, Ling KS , Kousik S, Thies J, Mitchell SE, Fei Z.2013.Using Genomic tools to explore genetic diversity and enhance watermelon cultivars. International Plant & Animal Genome XXI Conference, January 12-16, 2013- San Diego, CA.
8. Reddy UK, Manohar S, Jagadeeswaran G, Sunkar R, Tomason Y, Thompson J, Levi A and Nimmakayala P. 2013. Gene expression across ploidy levels of watermelon. International Plant & Animal Genome XXI Conference, January 12-16, 2013- San Diego, CA
9. Tomason Y, Reddy UK and Nimmakayala P. 2013.Map based phylogenies, linkage disequilibrium and association mapping for fruit traits in melon. International Plant & Animal Genome XXI Conference, January 12-16, 2013- San Diego, CA
10. Nimmakayala P, Tomason Y, Vajja VG, Abburi L, Pegadaraju V, Wijeratne A, Levi A, Reddy UK.2012. Identification of SNP Haplotypes and Prospects of Association Mapping in Watermelon. International Plant & Animal Genome XX Conference, January 14-18, 2012- San Diego, CA.http://pag.confex.com/pag/xx/webprogram/Session1016.html
11. Nimmakayala P, Scheuring C, Aryal N, Vajja VG, Zhang Y, Zhang H, Reddy UK.2012. Mining and mapping of SSR motifs from BAC-end sequences of watermelon. International Plant & Animal Genome XX Conference, January 14-18, 2012- San Diego, CA. http://pag.confex.com/pag/xx/webprogram/Session1043.html
12. Almeida Aldo, Nimmakayala P, Aryal N, Manohar S, Vajja VG, Chatfield M, Kaushal G, Reddy UK.2012. Genomic strategies to mine alleles that control capsaicin, dihydrocapsaicin and related compounds. International Plant & Animal Genome XX Conference, January 14-18, 2012- San Diego, CA.
13. Tomason Y, Reddy UK, Nimmakayala P.2012. Association mapping for melon fruit traits. International Plant & Animal Genome XX Conference, January 14-18, 2012- San Diego, CA.
14. Levi A, Wechter P, Thies J, Nimmakayala P, Reddy UK.2012. Genetic Diversity among Watermelon Citrullus spp. Accessions Based on HFO-TAG Markers. International Plant & Animal Genome XX Conference, January 14-18, 2012- San Diego, CA.
15. Nimmakayala P, Tomason YR, Vajja VG and Reddy UK. 2010. Population Structure and Association Mapping in Watermelon. 108th Annual conference of the American Society for Horticultural Science, August 2-5, 2010. (Oral Presentation).
16. Tomason YR, Nimmakayala P, Vajja VG, Levi A, Gibson P and Reddy UK. 2010. LD Mapping for Melon fruit related traits. 108th Annual conference of the American Society for Horticultural Science, August 2-5, 2010. (Oral Presentation).
17. Aryal N, Nimmakayala P, Tomason YR, Vajja VG, Levi A and Reddy UK. Molecular and cytogenetic characterization of watermelon using DNA Markers and FISH. 108th Annual conference of the American Society for Horticultural Science, August 2-5, 2010.
18. Lutz FG, Nimmakayala P, Tomason YR, Levi A and Reddy UK. 2010. Syntenic Analysis of Cucurbit Cultivar Complex Using Microsatellite Markers. 108th Annual conference of the American Society for Horticultural Science, August 2-5, 2010. (Oral Presentation).
19. Yan R. Tomason, Nimmakayala P, Gopinath Vajja, Amnon Levi Paul Gibson, Umesh K. Reddy. LD Mapping For Melon Fruit Related Traits. . International Plant & Animal Genome XVIII Conference.  January 12-16, 2010.
20. Nimmakayala P, Yan R. Tomason, Gopinath Vajja, Amnon Levi, Umesh K. Reddy.  Genetic Characterization of Interspecific Breakdown in Cucurbita spp. International Plant & Animal Genome XVIII. Conference.  January 12-16, 2010.
21. Nimmakayala P, Yan R. Tomason, Jeong J, Vajja G, Levi A, Paul Gibson, Reddy UK. Population Structure and Association Mapping In Watermelon Heirloom Collections. International Plant & Animal Genome XVIII. Conference.  January 12-16, 2010
22. Nimmakayala P, Yan R. Tomason, Jooha Jeong, Gopinath Vajja, Amnon Levi, Umesh K. Reddy Molecular And Cytogenetic Characterization Of Watermelon Using DNA Markers And FISH . International Plant & Animal Genome XVIII. Conference.  January 12-16, 2010.