Publications

  1. Dwiningsih, Y., A. Kumar, J. Thomas, C. Ruiz, J. Alkahtani, A. Alhashami, A. Pereira (2021). Identification of genomic regions controlling chalkiness and grain characteristics in a recombinant inbred line rice population based on high-throughput SNPs markers. Genes, 12(11), 1690. https://doi.org/10.3390/genes12111690
  2. Dwiningsih, Y., A. Kumar, J. Thomas, C. Ruiz, J. Alkahtani, N. Baisakh, A. Pereira (2021). Quantitative trait loci and candidate gene identification for chlorophyll content in RIL rice population under drought conditions. Indonesian Journal of Natural Pigments, 3(2), 54. doi.org/10.33479/ijnp.2021.03.2.54
  3. Kumar A, Gupta C, Thomas J, Pereira A (2021) Genetic dissection of grain yield component traits under high nighttime temperature stress in a rice diversity panel. Frontiers Plant Sci., 28 Sept. 2021, doi.org/10.3389/fpls.2021.712167
  4. Gupta, C, Ramegowda V, Basu S, Pereira A (2021) Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance” Frontiers in Genetics, 24 June 2021, doi.org/10.3389/fgene.2021.652189
  5. Addison, Christopher K. and Angira, Brijesh and Cerioli, Tommaso and Groth, Donald E. and Richards, Jonathan K. and Linscombe, Steven D. and Famoso, Adam N.. (2021). Identification and mapping of a novel resistance gene to the rice pathogen, Cercospora janseana. Theoretical and Applied Genetics. 134 (7) 2221 to 2234. Status = Deposited in NSF-PAR doi.org/10.1007/s00122-021-03821-2
  6. Saini, Ajay and Rohila, Jai S. and Govindan, Ganesan and Li, Yong-Fang and Sunkar, Ramanjulu. (2021). Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses. International Journal of Molecular Sciences. 22 (8) 3997. Status = Deposited in NSF-PAR https://doi.org/10.3390/ijms22083997
  7. Berchembrock, Yasmin Vasques and Botelho, Flávia Barbosa and Srivastava, Vibha. (2021). Suppression of ERECTA Signaling Impacts Agronomic Performance of Soybean (Glycine max (L) Merril) in the Greenhouse. Frontiers in Plant Science. 12 . Status = Deposited in NSF-PAR https://doi.org/10.3389/fpls.2021.667825
  8. Gann, Peter James and Esguerra, Manuel and Counce, Paul Allen and Srivastava, Vibha. (2021). Genotype‐dependent and heat‐induced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes. Plant-Environment Interactions. . Status = Deposited in NSF-PAR https://doi.org/10.1002/pei3.10054
  9. Jamsheer K, Muhammed and Kumar, Manoj and Srivastava, Vibha. (2021). SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. Journal of Experimental Botany. . Status = Deposited in NSF-PAR https://doi.org/10.1093/jxb/erab079
  10. Rezaei Cherati, Sajedeh and Shanmugam, Sodha and Pandey, Kamal and Khodakovskaya, Mariya. (2021). Whole-Transcriptome Responses to Environmental Stresses in Agricultural Crops Treated with Carbon-Based Nanomaterials. ACS applied bio materials. 4 (5) 4292–4301. Status = Deposited in NSF-PAR https://doi.org/doi.org/10.1021/acsabm.1c00108
  11. Wang, Yuanyuan and Impa, S. M. and Sunkar, Ramanjulu and Jagadish, S. V.. (2021). The neglected other half ‐ role of the pistil in plant heat stress responses. Plant, Cell & Environment. . Status = Deposited in NSF-PAR https://doi.org/10.1111/pce.14067
  12. Singroha, Garima and Sharma, Pradeep and Sunkur, Ramanjulu. (2021). Current status of microRNA ‐mediated regulation of drought stress responses in cereals. Physiologia Plantarum. 172 (3) 1808 to 1821. Status = Deposited in NSF-PAR https://doi.org/10.1111/ppl.13451
  13. Harb, Amal and Simpson, Craig and Guo, Wenbin and Govindan, Ganesan and Kakani, Vijaya Gopal and Sunkar, Ramanjulu. (2020). The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance. Frontiers in Plant Science. 11 . Status = Deposited in NSF-PAR https://doi.org/10.3389/fpls.2020.618491
  14. Gupta, Chirag and Ramegowda, Vankategowda and Basu, Supratim and Pereira, Andy. (2020). Prediction and characterization of transcription factors involved in drought stress response. bioRxiv. . Status = Deposited in NSF-PAR doi:10.1101/2020.04.29.068379
  15. Baisakh N, Yabes J, Gutierrez A, Mangu V, Ma P, Famoso A, Pereira A (2020) Genetic mapping Identifies consistent quantitative trait loci for yield traits of rice under greenhouse drought conditions. Genes 11 (1), 62 https://doi.org/10.3390/genes11010062
  16. Singh R, Liyanage R, Gupta C, Lay JO Jr, Pereira A, Rojas CM (2020) The Arabidopsis proteins AtNHR2A and AtNHR2B are multi-functional proteins integrating plant immunity with other biological processes. Front Plant Sci. 11:232 https://doi.org/10.3389/fpls.2020.00232
  17. Lee MW, Padilla CS, Gupta C, Galla A, Pereira A, Li J, Goggin FL (2020) The FATTY ACID DESATURASE2 family in tomato contributes to primary metabolism and stress responses. Plant Physiology 182 (2) 1083-1099 https://doi.org/10.1104/pp.19.00487
  18. Nandy, Soumen and Pathak, Bhuvan and Zhao, Shan and Srivastava, Vibha. (2019). Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice. Plant Direct. 3 (5) e00145. Status = Deposited in NSF-PAR doi:10.1002/pld3.145
  19. Pathak, Bhuvan and Srivastava, Vibha. (2020). Recombinase‐mediated integration of a multigene cassette in rice leads to stable expression and inheritance of the stacked locus. Plant Direct. 4 (7) . Status = Deposited in NSF-PAR doi:10.1002/pld3.236
  20. Pathak, Bhuvan P. and Pruett, Eliott and Guan, Huazhong and Srivastava, Vibha. (2019). Utility of I-SceI and CCR5-ZFN nucleases in excising selectable marker genes from transgenic plants. BMC Research Notes. 12 (1) . Status = Deposited in NSF-PAR doi:10.1186/s13104-019-4304-2
  21. de Freitas, Gabriela Moraes and Thomas, Julie and Liyanage, Rohana and Lay, Jackson O. and Basu, Supratim and Ramegowda, Venkategowda and do Amaral, Marcelo Nogueira and Benitez, Letícia Carvalho and Bolacel Braga, Eugenia Jacira and Pereira, Andy and Baisakh, Niranjan. (2019). Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes. PLOS ONE. 14 (6) e0218019. Status = Deposited in NSF-PAR doi:10.1371/journal.pone.0218019
  22. Lee, Min Woo and Padilla, Carmen S. and Gupta, Chirag and Galla, Aravind and Pereira, Andy and Li, Jiamei and Goggin, Fiona L.. (2020). The FATTY ACID DESATURASE2 Family in Tomato Contributes to Primary Metabolism and Stress Responses. Plant Physiology. 182 (2) 1083 to 1099. Status = Deposited in NSF-PAR doi:10.1104/pp.19.00487
  23. Shanmugam, Sudha and Zhao, Shan and Nandy, Soumen and Srivastava, Vibha and Khodakovskaya, Mariya and Tran, Lam-Son Phan. (2020). Modification of soybean growth and abiotic stress tolerance by expression of truncated ERECTA protein from Arabidopsis thaliana. PLOS ONE. 15 (5) e0233383. Status = Deposited in NSF-PAR doi:10.1371/journal.pone.0233383
  24. Baisakh, Niranjan and Yabes, Jonalyn and Gutierrez, Andres and Mangu, Venkata and Ma, Peiyong and Famoso, Adam and Pereira, Andy. (2020). Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions. Genes. 11 (1) 62. Status = Deposited in NSF-PAR doi:10.3390/genes11010062
  25. Singh, Raksha and Liyanage, Rohana and Gupta, Chirag and Lay Jr, Jackson O and Pereira, Andy and Rojas, Clemencia M.. (2020). The Arabidopsis proteins AtNHR2A and AtNHR2B are multi-functional proteins integrating plant immunity with other biological processes. Frontiers in plant science. 11 232. Status = Deposited in NSF-PAR doi:doi.org/10.3389/fpls.2020.00232
  26. Gupta, Chirag and Pereira, Andy. (2019). Recent advances in gene function prediction using context-specific coexpression networks in plants. F1000Research. 8 153. Status = Deposited in NSF-PAR doi:10.12688/f1000research.17207.1
  27. de Freitas GM, Thomas J. (2019). Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes. PloS one. 14 (6) https://doi.org/10.1371/journal.pone.0218019
  28. Moraes de Freitas, Gabriela Peres and Basu, Supratim and Ramegowda, Venkategowda and Thomas, Julie and Benitez, Letícia Carvalho and Braga, Eugenia Bolacel and Pereira, Andy. (2019). Physiological and transcriptional responses to low-temperature stress in rice genotypes at the reproductive stage. Plant Signaling & Behavior. 14 (4) e1581557. Status = Deposited in NSF-PAR doi:10.1080/15592324.2019.1581557
  29. Pathak, Bhuvan and Zhao, Shan and Manoharan, Muthusamy and Srivastava, Vibha. (2019). Dual-targeting by CRISPR/Cas9 leads to efficient point-mutagenesis but only rare targeted deletions in the rice genome. 3 biotech. doi:10.1007/s13205-019-1690-z
  30. Zhao, Yang and Kim, Jae Y. and Karan, Ratna and Jung, Je H. and Pathak, Bhuvan and Williamson, Bruce and Kannan, Baskaran and Wang, Duoduo and Fan, Chunyang and Yu, Wenjin and Dong, Shujie and Srivastava, Vibha and Altpeter, Fredy. (2019). Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane. Plant Molecular Biology. 100 (3) 247 to 263. Status = Deposited in NSF-PAR doi:10.1007/s11103-019-00856-4

Conference Presentations/Papers

  1. Khodakovskaya, M (2019). Assessment of Applications and Implications of Involvement of Carbon-based Nanomaterials (CBNs) in Plant Agriculture. 8th Sustainable Nanotechnology Organization Conference. San Diego, CA. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  2. Khodakovskaya MV (2019). Assessment of effects of carbon-based nanomaterials in plant system using genomics approach. Biological Seminar for Idaho State University. Pocatello, ID. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  3. Srivastava V (2019). CRISPR-Cas9 mediated gene editing in rice for fast track variety development. ABI annual symposium. Jonesboro AR. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  4. Haydon K, Srivastava V, Korth KL (2019). CRISPR-mediated gene editing of lipase and lipoxygenase enzymes in rice (Oryza sativa) to reduce lipid oxidation and enhance storage life of brown rice. Annual meeting of the American Society of Plant Biology. San Jose CA. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  5. Alizada Z and Srivastava V (2020). CRISPR/Cas9 under inducible expression systems. Annual conference of the Society of In Vitro Biology. Virtual. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  6. Berchembrock Y, Botelho F, and Srivastava V (2020). Characterization of the ERECTA gene as QTL for tolerance to environmental stresses. Annual conference of the Society of In Vitro Biology. Virtual. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  7. Gann PJ and Srivastava V (2020). Comprehensive analysis and regulation of starch biosynthesis and degradation genes in rice (Oryza sativa Japonica). Annual conference of the Society of In Vitro Biology. Virtual. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  8. Shanmugam, S. and Khodakovskaya, M. ) (2020). Effects of carbon-based nanomaterials on seed germination, biomass accumulation and tolerance to salt stress of rice and soybean.. 9th Sustainable Nanotechnology Conference. VRTUAL CONFERENCE – ONLINE. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  9. Shanmugam, S. and Khodakovskaya, M (2020). Effects of carbon-based nanomaterials on seed germination, biomass accumulation, and tolerance to salt stress of rice and soybean. PANNANO 2020- The second Pan-American Nanotechnology Conference. Aguas de Lindoia, Brazil. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  10. Berchembrock Y, Botelho F, and Srivastava V (2020). Expression of the Mutant ERECTA and Phenotypic Correlation in Soybean. Annual conference of the Society of In Vitro Biology. Virtual. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  11. Rezaei Cherati S, Shanmugam S, Khodakovskaya MV (2019). Impact of Multi-Walled Carbon Nanotubes (MWCNT) on the Total Metabolome of Exposed Tomato Plants. 2019 SNO Conference. San Diego, CA. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  12. Rezaei Cherati, S., Shanmugam, S., Khodakovskaya, M. (2020). Impact of Multi-Walled Carbon Nanotubes (MWCNT) on the Total Metabolome of Exposed Tomato Plants. 2020 UA Little Rock Student Research & Creative Works Expo. VIRTUAL EVENT – Whova. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  13. Rezaei Cherati, S., Pandey, K., Khodakovskaya, M. (2020). Investigation of effects of Carbon-based Nanomaterials on Plant Transcriptome.. 9th Sustainable Nanotechnology Conference. VIRTUAL CONFERENCE – ONLINE. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  14. Ramanjulu Sunkar, Chandra Obul Reddy Puli, Yun Zheng, Yong-Fang Li, Guru Jagadeeswaran, Angbaji Suo, Bingbing Jiang, Pradeep Sharma, Robert Mann, Govindan Ganesan, Nirmali Gogoi, Asha Srinivasan, Aparna Kakani, Vijaya Gopal Kakani, Abdelali Barakat (2020). MicroRNA profiles in Sorghum exposed to individual or combined abiotic stresses. International conference on Bioinformatics. Virtual. Status = OTHER;  Acknowledgement of Federal Support = Yes
  15. Khodakovskaya MV (2019). Nano-fertilizers: approach, benefits and possible risks. 6th Nano Today Conference. Lisbon, Portugal. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  16. Khodakovskaya Mariya (2020). Nanomaterials as carries for delivery of chemicals widely used in medical and agricultural applications. 9th Sustainable Nanotechnology Conference (organized by Sustainable Nanotechnology Organization (SNO)). VIRTUAL CONFERENCE – ONLINE. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  17. Khodakovskaya MV (2019). Nanotechnological Approach for Improving Productivity and Stress Response of Plants used for Space Exploration. NASA, Seminar for Kennedy Space Center. Merrit Island, FL. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  18. Khodakovskaya, M (2020). New Applications of Nanomaterials for Plant Science and Plant Agriculture”. The second Pan-American Nanotechnology Conference PANNANO 2020. Aguas de Lindoia, Brazil. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  19. Shanmugam, S. and Khodakovskaya, M. (2020). Regulation of growth and stress tolerance of soybean by termination of ERECTA signaling. 2020 UA Little Rock Student Research & Creative Works Expo. VIRTUAL EVENT – Whova. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  20. Shanmugam S, Zhao S, Nandy S, Srivastava V, Khodakovskaya MV (2019). Regulation of growth and stress tolerance of valuable crops by termination of ERECTA signaling. 2019 Plant Biology ASPB meeting. San Jose CA. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  21. Lahiani M, Khodakovskaya MV (2019). Risk Assessment of Tomato Fruits Containing Multi-walled Carbon Nanotube Residues Using Human in vitro Model Systems. Gordon Research Conference. Newry, ME. Status = PUBLISHED;  Acknowledgement of Federal Support = Yes
  22. Kumar, A.,C. Gupta, R. Venkategowda, S. Basu, A. Krishnan, S. Yingling, J. Thomas, A. Pereira (2019). System genetics analysis of heat stress tolerance in rice. Plant & Animal Genome (PAG) XXVII Conference, San Diego, California, USA, January 12nd -16th, 2019 https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/35187
  23. Dwiningsih, Y.. A. Kumar, J. Thomas, S. Yingling, A. Pereira (2019). Molecular genetic analysis of drought resistance and productivity in US rice cultivars. Plant & Animal Genome (PAG)-XXVIII Conference, San Diego, California, USA, January 12-16, 2019.
  24. Kumar, A.,J. Thomas, C. Gupta, S. Yingling, A. Shi, and A. Pereira (2019). Genome-wide association reveals genomic loci associated with variation for photosynthesis and stomatal conductance in rice. 5th Annual Meeting Arkansas Bioinformatics Consortium (ARBIC) 2019 for “Bioinformatics in Food and Agriculture”, February 25th – 26th, 2019, Little Rock, AR USA (1st place awarded).
  25. Dwiningsih, Y.. J. Thomas, A. Kumar,c. Gupta, C. Ruiz, S. Yingling, E. Crowley, A. Pereira (2020). Molecular genetic analysis of drought resistance and productivity mechanisms in rice. Plant & Animal Genome (PAG)-XXVIII Conference, San Diego, California, USA, January 11-15, 2020.
  26. Sunkar, R (2021). Role of microRNAs in drought and heat stress responses in plants. International Plant Physiology Virtual Symposium. Virtual. Status = OTHER;  Acknowledgement of Federal Support = Yes
  27. Kumar, A., J. Thomas, C. Gupta, Y. Dwiningsih, C. Ruiz, N. Gill, A. Pereira (2021). Genetics analysis of heat tolerance contributing to grain yield and quality in rice. Virtual Zoom 82nd Meeting of the Southern Section of the American Society Plant Biologists held on April 16th -18th, 2021.
  28. Dwiningsih, Y., A. Kumar,J. Thomas, C. Gupta, C. Ruiz, J. Alkahtani, N. Baisakh, and A. Pereira (2021). Identification and expression of abscisic acid regulated genes in US RIL rice population under drought conditions. 82nd Meeting of Southern Section of the American Society of Plant Biologists, April 16-18, 2021.

Books

  1. Rohila, JS., Sunkar, R., Rakwal, R., Kim, D-W., Agrawal, GK and Sarkar, A. (2021). Genomic methods for improving abiotic stress tolerance in field crops. Plant Biotechnology: Experience and Future Prospects Second. Ricroch, A., Chopra, S. and Fleischer, S.  Springer.  . Status = ACCEPTED; Acknowledgement of Federal Support = Yes ; Peer Reviewed = Yes

Thesis/Dissertations

  1. Sudha Shanmugam. Enhancement of abiotic stress tolerance in rice and soybean by biotechnological and nanotechnological approached. (2020).  University of Arkansas at Little Rock. Acknowledgement of Federal Support = No
  2. Yheni Dwiningsih. Molecular Genetic Analysis of Drought Resistance and Productivity Traits of Rice Genotypes. (2020).  University of Arkansas System Division of Agriculture. Acknowledgement of Federal Support = Yes

BR Wells Arkansas Rice Research Series

  1. Kumar, A., Y. Dwiningsih, C. Cruiz, J. Thomas, P. Counce, T. J. Sibbenmorgen, K.A.K. Moldenhauer, and A. Pereira (2021). Genome-wide association study to identify potential candidate genomic loci associated with grain yield in Japonica rice under high nighttime temperature. In R. J. Norman R. J.  and Moldenhauer K.A.K. (eds.), B. R. Wells Arkansas Rice Research Studies 2020 under Breeding, Genetics, and Physiology category. Arkansas Agricultural Research Series 676. Division of Agriculture, University of Arkansas pp 47-51.
  2. Kumar, A., S. Yingling, Y. Dwiningsih, C. Ruiz, C. Gupta, J. Thomas, P. Counce, T. J. Sibbenmorgen, K.A.K. Moldenhauer, and A. Pereira (2020). Genome-wide association study for identification of novel genomic loci associated with grain yield and quality traits in Japonica rice under high nighttime temperature. In R. J. Norman R. J.  and Moldenhauer K.A.K. (eds.), B. R. Wells Arkansas Rice Research Studies 2019 under Breeding, Genetics, and Physiology category. Arkansas Agricultural Research Series 667. Division of Agriculture, University of Arkansas pp. 45-48.
  3. Kumar, A., S. Yingling, C. Cruiz, Y. Dwiningsih, C. Gupta, J. Thomas, P. Counce, T. J. Sibbenmorgen, K.A.K. Moldenhauer, and A. Pereira (2019). Screening of Inidca and Japonica subspecies for grain yield and quality under high nighttime temperature. In R. J. Norman R. J.  and Moldenhauer K.A.K. (eds.), B. R. Wells Arkansas Rice Research Studies 2018 under Breeding, Genetics, and Physiology category. Arkansas Agricultural Research Series 659. Division of Agriculture, University of Arkansas pp. 61-66 https://www.cabdirect.org/cabdirect/abstract/20193421294
  4. Kumar, A., S. Yingling, J. Thomas, C. Cruiz, Y. Dwiningsih, C. Gupta, P. Counce, T.J. Sibbenmorgen, K.A.K. Moldenhauer, A. Pereira (2018). Screening of diverse Japonica rice genotypes for grain yield and quality under high nighttime temperature. In R. J. Norman N.J.  and Moldenhauer K.A.K. (eds.), B. R. Wells Arkansas Rice Research Studies 2017 under Breeding, Genetics, and Physiology category. Arkansas Agricultural Research Series 651. Division of Agriculture, University of Arkansas pp. 50-56 https://www.cabdirect.org/cabdirect/abstract/20203540496