We have developed a multi-layer pipeline that uses transcriptomic data to identify candidate genes associated with complex pathways in plants. We used this multi-layer approach, incorporating microarray, RNA sequencing, polymerase chain reaction (PCR), and protein-protein interaction analyses, to identify 14 genes associated with drought tolerance in potato. We generated transgenic potato lines that over-express bZIP28, one of the genes selected by our pipeline, to confirm the involvement of that gene in drought tolerance. The protein interactions of the products of the screened genes were assessed using yeast two-hybrid and bimolecular fluorescence complementation analyses. Overall, this study demonstrated the utility of our multi-layer approach for deciphering complex biosynthetic pathways using transcriptomic data.

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• Knockdown of 60S ribosomal protein L14-2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton
  Margaret Linyerera SHIRAKU, Richard Odongo MAGWANGA, Xiaoyan CAI, Joy Nyangasi KIRUNGU, Yanchao XU, Teame Gereziher MEHARI, Yuqing HOU, Yuhong WANG, Kunbo WANG, Renhai PENG, Zhongli ZHOU, Fang LIU
  Journal of Cotton Research.2021;[Epub]     CrossRef

Supplying sufficient rice to growing populations is a global challenge. Hybrid indica rice varieties exploiting heterosis have increased yields, but inter-subspecific crosses between indica and japonica varieties are hampered by sterility. Examination and genetic understanding of yield heterosis in indica/japonica crosses addressing yield barriers are basic requirements. In this study, QTLs for heterosis of yield traits were identified in indica-japonica recombinant inbred lines (RILs) using a total of 178 RILs originating from Dasanbyeo (indica) × TR22183 (japonica) (DT-RILs) and their backcrossed populations. Nine of sixty-six major quantitative trait loci (QTLs) identified in DT-RILs exhibited heterosis. Heterosis QTLs clustered with other traits on chromosomes 1, 4, and 8, and clusters were conserved between different RILs. The clusters contained several known yield enhancement genes/QTLs. Specific heterotic allele combinations contributed to four major heterosis QTLs, particularly for panicle and spikelet number traits. Heterosis for yield and yield-related traits was explained by the harmonized effects of overdominance, dominance, and epistatic interactions in inter-subspecific breeding populations.

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• Exploring environmentally stable and novel genetic factors influencing rice grain shape and yield attributes
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  Euphytica.2025;[Epub]     CrossRef
• Quantitative Trait Loci Analysis of Leaf Size Traits Using the Recombinant Inbred Lines Derived from a Cross between ‘Odae’ and ‘Unbong40’
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  Korean Journal of Breeding Science.2024; 56(4): 449.     CrossRef
• Analysis of Agricultural Traits of O. sativa and O. glaberrima under Korean Climatic Conditions
  Jae-Ryoung Park, Hyun-Su Park, Jeonghwan Seo, Chang-Min Lee, Songhee Park, Mina Jin, Keon Mi Lee, Keunpyo Lee, Sukyeung Lee, Ebrima Jallow, O-Young Jeong
  Korean Journal of Breeding Science.2024; 56(2): 97.     CrossRef
• Association Analysis of Yield-Related Traits in Rice Following the Introduction of Brown Planthopper Resistant Genes
  Jae-Ryoung Park, Jeonghwan Seo, Chang-Min Lee, Songhee Park, Mina Jin, Keon Mi Lee, O-Young Jeong, Jung-Pil Suh, Hyun-Su Park
  Korean Journal of Breeding Science.2024; 56(4): 381.     CrossRef
• Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid
  Hui You, Sundus Zafar, Fan Zhang, Shuangbing Zhu, Kai Chen, Congcong Shen, Xiuqin Zhao, Wenzhong Zhang, Jianlong Xu
  The Crop Journal.2022; 10(6): 1705.     CrossRef
• Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid
  Sundus Zafar, Hui You, Fan Zhang, Shuang Bin Zhu, Kai Chen, Congcong Shen, Hezhou Wu, Fangjin Zhu, Conghe Zhang, Jianlong Xu
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon
  Venkateswara Rao Yadavalli, Divya Balakrishnan, Malathi Surapaneni, Krishnamraju Addanki, Sukumar Mesapogu, Kavitha Beerelli, Subrahmanyam Desiraju, Sitapati Rao Voleti, Sarla Neelamraju
  Planta.2022;[Epub]     CrossRef
• Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
  Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen, Jianlong Xu
  Rice.2022;[Epub]     CrossRef
• A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice
  Kelvin Dodzi Aloryi, Nnaemeka Emmanuel Okpala, Aduragbemi Amo, Semiu Folaniyi Bello, Selorm Akaba, Xiaohai Tian
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Mapping of QTLs for Yield Traits Using F2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara
  Kavitha Beerelli, Divya Balakrishnan, Krishnam Raju Addanki, Malathi Surapaneni, Venkateswara Rao Yadavalli, Sarla Neelamraju
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population
  Swapnil Ravindra Kulkarni, S. M. Balachandran, K. Ulaganathan, Divya Balakrishnan, A. S. Hari Prasad, G. Rekha, M. B. V. N. Kousik, S. K. Hajira, Ravindra Ramarao Kale, D. Aleena, M. Anila, E. Punniakoti, T. Dilip, K. Pranathi, M. Ayyappa Das, Mastanbee S
  3 Biotech.2021;[Epub]     CrossRef
• Genetic dissection of heterosis of indica–japonica by introgression line, recombinant inbred line and their testcross populations
  Wenqing Yang, Fan Zhang, Sundus Zafar, Junmin Wang, Huajin Lu, Shahzad Naveed, Jue Lou, Jianlong Xu
  Scientific Reports.2021;[Epub]     CrossRef
• Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping
  Swapnil Ravindra Kulkarni, S. M. Balachandran, K. Ulaganathan, Divya Balakrishnan, M. Praveen, A. S. Hari Prasad, R. A. Fiyaz, P. Senguttuvel, Pragya Sinha, Ravindra R. Kale, G. Rekha, M. B. V. N. Kousik, G. Harika, M. Anila, E. Punniakoti, T. Dilip, S. K
  Scientific Reports.2020;[Epub]     CrossRef
• Mapping and Validation of QTLs for the Amino Acid and Total Protein Content in Brown Rice
  Su Jang, Jae-Hyuk Han, Yoon Kyung Lee, Na-Hyun Shin, Yang Jae Kang, Chang-Kug Kim, Joong Hyoun Chin
  Frontiers in Genetics.2020;[Epub]     CrossRef
• Identification of Yield and Yield-Related Quantitative Trait Loci for the Field High Temperature Condition in Backcross Populations of Rice (Oryza sativaL.)
  Jeonghwan Seo, So-Myeong Lee, Jae-Hyuk Han, Na-Hyun Shin, Hee-Jong Koh, Joong Hyoun Chin
  Plant Breeding and Biotechnology.2019; 7(4): 415.     CrossRef

Plant is frequently exposed to various abiotic stress. Salt stress is particularly an important abiotic stress that seriously affects plant growth and development. BrTSR53 gene, a putative stress-related gene isolated from Brassica rapa, was used to generate overexpression transgenic rice. The over-expression of BrTSR53 in BrTSR53-OX transgenic rice was confirmed by quantitative RT-PCR and western blot analysis. To elucidate the role of BrTSR53 in stress tolerance, responses of BrTSR53-OX transgenic rice plants to salt stress conditions were examined. BrTSR53-OX #12, #28, and #32 lines were treated with salt stress on MS medium containing 100 mM or 200 mM of NaCl for 5 and 14 days. Morphological analysis revealed differences between the three transgenic BrTSR53-OX rice and the wild-type rice. The germination rates of the three transgenic BrTSR53-OX lines of rice were significantly higher than that of the wild type rice, indicating that they were more tolerant to 200 mM NaCl than the wild type rice. In addition, the three transgenic BrTSR53-OX rice lines had significantly longer length of root and shoot compared to the wild type rice. These results suggest that the BrTSR53 gene played an important role in the tolerance of rice to salt stress. Therefore, it might be a potential target for the purpose of improving salt tolerance of rice and other crops.

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  Plant Physiology Reports.2023; 28(1): 8.     CrossRef
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• A Novel Variation in the FRIZZLE PANICLE (FZP) Gene Promoter Improves Grain Number and Yield in Rice
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• Cloning and heterologous expression of Os-AP2/ERF-N22 drought inducible rice transcription factor in E. coli
  VAIBHAV KUMAR, KISHWAR ALI, AMRESH KUMAR, KALPANA TEWARI, NITIN KUMAR GARG, SUSHIL S CHANGAN, ARUNA TYAGI
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