Research Project: Improvement of Genetic Resistance to Multiple Biotic and Abiotic Stresses in Peanut

Location: Crop Genetics and Breeding Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Application of CRISPR/Cas9-Mediated gene editing for abiotic stress management in crop plants - (Peer Reviewed Journal)
Kumar, M., Prusty, M.R., Pandey, M.K., Singh, P.K., Bohra, A., Guo, B., Varshney, R.K. 2023. Application of CRISPR/Cas9-Mediated gene editing for abiotic stress management in crop plants. Frontiers in Plant Science. 14:1157678. https://doi.org/10.3389/fpls.2023.1157678.

Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut - (Peer Reviewed Journal)
Gangurde, S., Pasupuleti, J., Parmar, S., Variath, M.T., Bomireddy, D., Manohar, S.S., Varshney, R.K., Prashant, S., Guo, B., Pandey, M.K. 2023. Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut. Frontiers in Genetics. 14:1128182. https://doi.org/10.3389/fgene.2023.1128182.

Transcriptional networks orchestrating red and pink testa color in peanut - (Peer Reviewed Journal)
Ahmad, N., Zhang, K., Ma, J., Yuan, M., Hao, S., Wang, M., Deng, L., Ren, L., Gangurde, S.S., Pan, J., Ma, C., Li, C., Guo, B., Wang, X., Li, A., Zhao, C. 2023. Transcriptional networks orchestrating red and pink testa color in peanut. BMC Plant Biology. 23:44. https://doi.org/10.1186/s12870-023-04041-0.

Two decades of association mapping: Insights on disease resistance in major crops - (Peer Reviewed Journal)
Gangurde, S., Xavier, A., Naik, Y., Jha, U., Rangari, S., Kumar, R., Channale, S., Elango, D., Rouf Mir, R., Pandey, M., Punnuri, S., Mendu, V., Reddy, U., Guo, B., Gangarao, N., Sharma, V., Wang, X., Zhao, C., Thudi, M. 2022. Two decades of association mapping: Insights on disease resistance in major crops. Frontiers in Plant Science. 13:1064059. https://doi.org/https://doi.org/10.3389/fpls.2022.1064059.

Aspergillus flavus pangenome to capture the diversity in a single reference genome - (Abstract Only)

Mutmap and whole genome re-sequencing to identify gene(s) controlling peanut resistance to early leaf spot and/or late leaf spot diseases - (Abstract Only)

A MAGIC population for genetic and genomic dissection of disease resistance in peanut (Arachis hypogaea) - (Abstract Only)

Discovery of major quantitative trait loci and candidate genes for fresh seed dormancy in groundnut - (Peer Reviewed Journal)
Bomireddy, D., Gangurde, S.S., Variath, M.T., Janila, P., Manohar, S.S., Sharma, V., Parmar, S., Deshmukh, D., Mangala, R., Mohan Reddy, D., Sudhakar, P., Bhaskara Reddy, B., Varshney, R.K., Guo, B., Pandey, M.K. 2022. Discovery of major quantitative trait loci and candidate genes for fresh seed dormancy in groundnut. Agronomy. 12(2):404. https://doi.org/10.3390/agronomy12020404.

Recent advances in genetics, genomics, and breeding for nutritional quality in groundnut - (Book / Chapter)
Parmar, S., Sharma, V., Deekshitha, B., Soni, P., Joshi, P., Gangurde, S.S., Wang, J., Bera, S.K., Bhat, R.S., Desmae, H., Shirasawa, K., Guo, B., Varshney, R.K., Pandey, M.K. 2022. Recent advances in genetics, genomics, and breeding for nutritional quality in groundnut. In Gosal, S.S., Wani, S.H., editors. Accelerated Plant Breeding. Volume 4. New York, NY: Springer Nature. p. 111-137. https://doi.org/10.1007/978-3-030-81107-5_4.

De novo QTL-seq identifies loci linked to blanchability in peanut (Arachis hypogaea) and refines previously identified QTL with low coverage sequence - (Peer Reviewed Journal)
Korani, W., O'Connor, D., Chu, Y., Chavarro, C., Ballen, C., Guo, B., Ozias-Akins, P., Wright, G., Clevenger, J. 2021. De novo QTL-seq identifies loci linked to blanchability in peanut (Arachis hypogaea) and refines previously identified QTL with low coverage sequence. Agronomy. 11(11):2201. https://doi.org/10.3390/agronomy11112201.

Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement - (Peer Reviewed Journal)
Garg, V., Dudchenko, O., Wang, J., Khan, A.W., Gupta, S., Kaur, P., Han, K., Saxena, R.K., Kale, S.M., Pham, M., Yu, J., Chitikineni, A., Zhang, Z., Fan, G., Lui, C., Valluri, V., Meng, F., Bhandari, A., Liu, X., Yang, T., Chen, H., Valliyodan, B., Roorkiwal, M., Shi, C., Yang, H., Durand, N.C., Pandey, M.K., Li, G., Barmukh, R., Wang, X., Chen, X., Lam, H., Jiang, H., Zong, X., Liang, X., Liu, X., Liao, B., Guo, B., Jackson, S., Nguyen, H.T., Zhuang, W., Wan, S., Wang, X., Aiden, E.L., Bennetzen, J.L., Varshney, R.K. 2021. Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. Journal of Advanced Research. 42:315-329. https://doi.org/10.1016/j.jare.2021.10.009.

Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architectures and interaction alterations - (Peer Reviewed Journal)
Zhang, X., Pandey, M.K., Wang, J., Zhao, K., Ma, X., Li, Z., Zhao, K., Gong, F., Guo, B., Varshney, R.K., Yin, D. 2021. Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architectures and interaction alterations. Genome Biology. 22:315. https://doi.org/10.1186/s13059-021-02520-x.

Identification of QTLs for seed dormancy in cultivated peanut using a recombinant inbred line mapping population - (Peer Reviewed Journal)
Wang, M.L., Wang, H., Zhao, C., Tonnis, B.D., Tallury, S.P., Wang, X., Clevenger, J., Guo, B. 2021. Identification of QTLs for seed dormancy in cultivated peanut using a recombinant inbred line mapping population. Plant Molecular Biology Reporter. https://doi.org/10.1007/s11105-021-01315-5.

Lessons learned: the importance of biological curation - (Research Notes)
Fountain, J., Clevenger, J., Vaughn, J.N., Guo, B. 2021. Lessons learned: the importance of biological curation. Microbiology Resource Announcements. Volume 10 Issue 48.

Global transcriptome profiling identified transcription factors, biological process, and associated pathways for pre-harvest aflatoxin contamination in peanut - (Peer Reviewed Journal)
Soni, P., Pandey, A.K., Nayak, S.N., Pandey, M.K., Tolani, P., Pandey, S., Sudini, H.K., Bajaj, P., Fountain, J.C., Singam, P., Guo, B., Varshney, R.K. 2021. Global transcriptome profiling identified transcription factors, biological process, and associated pathways for pre-harvest aflatoxin contamination in peanut. The Journal of Fungi. 7:1-18. https://doi.org/10.3390/jof7060413.

High resolution genetic and physical mapping of a peanut spotted wilt disease resistance locus, PSWD-1, to Tomato spotted wilt virus (TSWV) - (Abstract Only)

Identification of peanut late leaf spot resistance, pRPP13-like, using Nested Association Mapping Approach - (Abstract Only)

New reference genomes and comparative genomics analyses in Aspergillus flavus - (Abstract Only)

Comparative transcriptome analysis identified candidate genes for late leaf spot resistance and cause of defoliation in groundnut - (Peer Reviewed Journal)
Gangurde, S.S., Nayak, S.N., Joshi, P., Shilp, P., Sudini, H.K., Chitikineni, A., Hong, Y., Guo, B., Chen, X., Pandey, M., Varshney, R.K. 2021. Comparative transcriptome analysis identified candidate genes for late leaf spot resistance and cause of defoliation in groundnut. International Journal of Molecular Sciences. 22, 4491:1-23.

Sensitivity of Aspergillus flavus isolates from peanut seeds in Georgia to Azoxystrobin, a Quinone outside Inhibitor (QoI) fungicide - (Peer Reviewed Journal)
Ali, M., Gunn, M., Stackhouse, T., Waliullah, S., Guo, B., Culbreath, A., Brenneman, T. 2021. Sensitivity of Aspergillus flavus isolates from peanut seeds in Georgia to Azoxystrobin, a Quinone outside Inhibitor (QoI) fungicide. Toxins. 7, 284:1-11. https://doi.org/10.3390/jof7040284.

Metabolomics intervention towards better understanding plant traits - (Peer Reviewed Journal)
Sharma, V., Gupta, P., Priscilla, K., Kumar, S., Ashree, B., Veershetty, A., Ramrao, D.P., Kambar, R., Naik, G.R., Kumar, A., Guo, B., Zhuang, W., Varshney, R.K., Pandey, M.K., Kumar, R. 2021. Metabolomics intervention towards better understanding plant traits. Cells. 10(2):346. https://doi.org/10.3390/cells10020346.

Transcriptome analysis identified coordinated control of key pathways regulating cellular physiology and metabolism upon Aspergillus flavus infection resulting in reduced aflatoxin production in groundnut - (Peer Reviewed Journal)
Soni, P., Nayak, S.N., Kumar, R., Pandey, M.K., Singh, N., Sudini, H.K., Bajaj, P., Fountain, J.C., Singam, P., Hong, Y., Chen, X., Zhuang, W., Liao, B., Guo, B., Varshney, R.K. 2020. Transcriptome analysis identified coordinated control of key pathways regulating cellular physiology and metabolism upon Aspergillus flavus infection resulting in reduced aflatoxin production in groundnut. The Journal of Fungi. 6(4):370. https://doi.org/10.3390/jof6040370.

Draft genome sequences of one Aspergillus parasiticus isolate and nine Aspergillus flavus isolates with varying stress tolerance and aflatoxin production - (Peer Reviewed Journal)
Fountain, J.C., Clevenger, J.P., Nadon, B.D., Wang, H., Abbas, H.K., Kemerait, R.C., Scully, B.T., Vaughn, J.N., Guo, B. 2020. Draft genome sequences of one Aspergillus parasiticus idolate and nine Aspergillus flavus isolates with varying stress tolerance and aflatoxin production. Microbiology Resource Announcements. 9e00478-20. https://doi.org/10.1128/MRA.00478-20.

Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production - (Peer Reviewed Journal)
Fountain, J.C., Clevenger, J.P., Nadon, B.D., Youngblood, R.C., Chang, P., Starr, D., Wang, H., Wiggins, R., Kemerait, R.C., Bhatnagar, D., Ozias-Akins, P., Varshney, R.K., Scheffler, B.E., Vaughn, J.N., Guo, B. 2020. Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production. Genes, Genomes, and Genomics. 10(9). https://doi.org/10.1534/g3.120.401405.

Integrated small RNA and mRNA expression profiles reveals miRNAs and their target genes in response to Aspergillus flavus infection in peanut stress - (Peer Reviewed Journal)
Zhao, C., Li, T., Zhao, Y., Zhao, B., Zhao, S., Hou, L., Xia, H., Guo, B., Wang, X. 2020. Integrated small RNA and mRNA expression profiles reveals miRNAs and their target genes in response to Aspergillus flavus infection in peanut stress. RNA Biology. 20:215. https://doi.org/10.1186/s12870-020-02426-z.

Translational genomics for achieving higher genetic gains in groundnut - (Peer Reviewed Journal)
Pandey, M.K., Pandey, A.K., Kumar, R., Nwosu, V., Guo, B., Wright, G., Bhat, R.S., Chen, X., Bera, S.K., Yuan, M., Jiang, H., Faye, I., Radhakrishnan, T., Wang, X., Liang, X., Liao, B., Zhang, X., Varshney, R.K., Zhuang, W. 2020. Translational genomics for achieving genetic gains in post-genome era in groundnut. Theoretical and Applied Genetics. 133:1678-1702. https://doi.org/10.1007/s00122-020-03592-2.

A global gene expression atlas of cultivated groundnut provides insights into seed development, oil biosynthesis and allergens - (Peer Reviewed Journal)
Sinha, P., Bajaj, P., Pazhamala, L.T., Nayak, S.N., Pandey, N.K., Chitikineni, A., Huai, D., Khan, A.W., Desai, A., Jiang, H., Zhuang, W., Guo, B., Liao, B., Varshney, R.K. 2020. A global gene expression atlas of cultivated groundnut provides insights into seed development, oil biosynthesis and allergens. Plant Biotechnology Journal. pp. 1-14. https://doi.org/10.1111/pbi.13374.

Functional biology and molecular mechanisms of host-pathogen interactions for aflatoxin contamination in groundnut (Arachis hypogaea L.) and maize (Zea mays L.) - (Peer Reviewed Journal)
Soni, P., Gangurde, S.S., Ortega-Beltron, A., Kumar, R., Parmar, S., Sudini, H.K., Lei, Y., Ni, X., Huai, D., Fountain, J.C., Njoroge, S., Mahuku, G., Radhakrishnan, T., Zhuang, W., Guo, B., Liao, B., Singam, P., Pandey, M.K., Bandyopadhyay, R., Varshney, R.K. 2020. Functional biology and molecular mechanisms of host-pathogen interactions for aflatoxin contamination in groundnut (Arachis hypogaea L.) and maize (Zea mays L.). Frontiers in Microbiology. 11:Article 227 p. 1-22. https://doi.org/10.3389/fmicb.2020.00227.

Molecular basis of regulations for root nodule symbiosis between Bradyrhizobium and ‘crack-entry’ legume groundnut (Arachis hypogaea L.) - (Peer Reviewed Journal)
Sharma, V., Bhattacharyya, S., Kumar, R., Kumar, A., Ibanez, F., Wang, J., Guo, B., Sudini, H.K., Gopalakrishnan, S., Dasgupta, M., Varshney, R.K., Pandey, M.K. 2020. Molecular basis of regulations for root nodule symbiosis between Bradyrhizobium and ‘crack-entry’ legume groundnut (Arachis hypogaea L.). Plants. 9:276. https://doi.org/10.3390/plants9020276.

Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea) - (Peer Reviewed Journal)
Gangurde, S.S., Wang, H., Yaduru, S., Pandey, M.K., Fountain, J.C., Chu, Y., Isleib, T.G., Holbrook Jr, C.C., Xavier, A., Culbreath, A., Ozias-Akins, P., Varshney, R.K., Guo, B. 2019. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13311.

Recombination bin-map facilitates identification of major QTL on chromosome A01 and potential candidate genes for resistance to Tomato spotted wilt virus in peanut (Arachis hypogaea) - (Peer Reviewed Journal)
Agarwal, G., Clevenger, J., Kale, S.M., Wang, H., Pandey, M.K., Choudhary, D., Yuan, M., Wang, X., Culbreath, A.K., Holbrook Jr, C.C., Lui, X., Jackson, S.A., Varshney, R.K., Guo, B. 2019. Recombination bin-map facilitates identification of major QTL on chromosome A01 and potential candidate genes for resistance to Tomato spotted wilt virus in peanut (Arachis hypogaea). Journal of Experimental Botany. 9:18246. https://doi.org/10.1038/s41598-019-54747-1.

Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time - (Peer Reviewed Journal)
Fountain, J.C., Yang, L., Pandey, M.K., Bajaj, P., Alexander, D., Chen, S., Kemerait, R.C., Varshney, R.K., Guo, B. 2019. Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time. BMC Microbiology. https://doi.org/10.1186/s12866-019-1580-x.

Evaluation of elite maize inbred lines for reduced Aspergillus flavus infection, aflatoxin accumulation, and agronomic traits - (Peer Reviewed Journal)
Pekar, J.J., Murray, S.C., Isakeit, T.S., Scully, B.T., Guo, B., Knoll, J.E., Ni, X., Abbas, H.K., Williams, W.P., Xu, W. 2019. Evaluation of elite maize inbred lines for reduced Aspergillus flavus infection, aflatoxin accumulation, and agronomic traits. Crop Science. 59:2562-2571. https://doi.org/10.2135/cropsci2019.04.0206.

Mitigating aflatoxin contamination in groundnut through a combination of genetic resistance and post-harvest management practices - (Peer Reviewed Journal)
Pandey, M.K., Kumar, R., Pandey, A.K., Soni, P., Gangurde, S.S., Sudini, H.K., Fountain, J.C., Liao, B., Desmae, H., Okori, P., Chen, X., Jiang, H., Mendu, V., Falalou, H., Njoroge, S., Mwololo, J., Guo, B., Zhuang, W., Wang, X., Liang, X., Varshney, R.K. 2019. Mitigating aflatoxin contamination in groundnut through a combination of genetic resistance and post-harvest management practices. Toxins. 11:315. https://doi.org/10.3390/toxins11060315.

Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour - (Peer Reviewed Journal)
Zhao, Y., Ma, J., Li, M., Deng, L., Li, G., Xia, H., Zhao, S., Hou, L., Li, P., Ma, C., Yuan, M., Ren, L., Gu, J., Guo, B., Zhao, C., Wang, X. 2019. Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13175.

Dissecting the role of oxidative stress in host-Aspergillus flavus interactions using genomics and genetic engineering - (Abstract Only)

Genetic transformation to mitigate drought and aflatoxin-related losses in peanut - (Abstract Only)

Fine mapping and identification of candidate genes in chromosome A01 of peanut for resistance to TSWV - (Abstract Only)

Nested association mapping (NAM) population-based joint linkage mapping and GWAS for identification of consistent QTLs/QTNs for disease and pod traits in peanut - (Abstract Only)

The genome sequence of segmental allotetraploid peanut Arachis hypogaea - (Peer Reviewed Journal)
Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A., Pandey, M., Samoluk, S.S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Kim, K.D., Korani, W., Lanciano, S., Lui, C.G., Mirouze, M., Moretzsohn, M.C., Pham, M., Shin, J.H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N.T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E.L., Michelmore, R., Varshney, R.K., Holbrook Jr, C.C., Cannon, E.K., Scheffler, B.E., Grimwwood, J., Ozias-Akins, P., Cannon, S.B., Jackson, S.A., Schmutz, J. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 51:877-884. https://doi.org/10.1038/s41588-019-0405-z.

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication - (Peer Reviewed Journal)
Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M.K., Zhang, C., Chang, W., Zhang, L., Zhang, X., Tang, R., Garg, V., Wang, X., Tang, H., Chow, C., Wang, J., Deng, Y., Wang, D., Khan, A.W., Yang, Q., Cai, T., Bajaj, P., Wu, K., Guo, B., Zhang, X., Li, J., Liang, F., Hu, J., Liao, B., Liu, S., Chitikineni, A., Yan, H., Zheng, Y., Shan, S., Liu, Q., Xie, D., Wang, Z., Khan, S.A., Ali, N., Zhao, C., Li, X., Luo, Z., Zhang, S., Zhuang, R., Peng, Z., Wang, S., Mamadou, G., Zhuang, Y., Zhao, Z., Yu, W., Xiong, F., Quan, W., Yuan, M., Li, Y., Zou, H., Xia, H., Zha, L., Fan, J., Yu, J., Xie, W., Yuan, J., Chen, K., Zhao, S., Chu, W., Chen, Y., Sun, P., Meng, F., Zhuo, T., Zhao, Y., Li, C., He, G., Zhao, Y, Wang, C., Kavikishor, P.B., Pan, R., Paterson, A.H., Wang, X., Ming, R., Varshney, R.K. 2019. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics. 51:865-876. https://doi.org/10.1038/s41588-019-0402-2.

Climate-smart groundnuts for achieving high productivity and improved quality: current status, challenges and opportunities - (Book / Chapter)
Gangurde, S.S., Kumar, R., Pandey, A.K., Burow, M., Laza, H.E., Nyak, S.N., Guo, B., Liao, B., Bhat, R.S., Madhuri, N., Hemalatha, S., Sudini, H.K., Janila, P., Latha, P., Khan, H., Motagi, B.N., Radhakrishnan, T., Puppala, N., Varshney, R.K., Pandey, M.K. 2019. Climate-smart groundnuts for achieving high productivity and improved quality: current status, challenges and opportunities. Book Chapter. p. 133-172. https://doi.org/10.1007/978-3-319-93536-2_3.

Discovering new frontiers in aflatoxin prevention using "omics" and genetic engineering - (Abstract Only)
Fountain, J.C., Yang, L., Chen, S., Chen, Z., Wang, K., Kemerait, R.C., Guo, B. 2018. Discovering new frontiers in aflatoxin prevention using "omics" and genetic engineering [abstract]. Corn Utilization Conference Proceedings.

Genome-wide association study of agronomic and disease resistance traits using peanut nested association maping populations - (Abstract Only)

Recombination bin-map facilitates QTL mapping of disease resistance traits in peanut (Arachis hypogaea L.) using whole genome re-sequencing - (Abstract Only)

Peanut high-desity genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance - (Abstract Only)

The hunt for the "silver bullet": Reference genome development and comparative genomics analysis of field isolates of Aspergillus flavus for identification of aflatoxin regulators - (Abstract Only)

Investigating the role of reactive oxygen species (ROS) in host-Aspergillus flavus interactions under drought stress using genetic engineering - (Abstract Only)

Evolution and characterization of the AhRAF4 NB-ARC gene family induced by Aspergillus flavus inoculation and abiotic stresses in peanut - (Peer Reviewed Journal)
Deng, Y., Chen, H., Zhang, C., Cai, T., Zhang, B., Zhou, S., Fountain, J., Pan, R., Guo, B., Zhuang, W. 2018. Evolution and characterization of the AhRAF4 NB-ARC gene family induced by Aspergillus flavus inoculation and abiotic stresses in peanut. Plant Biology. 20(4):641-802. https://doi.org/10.1111/plb.12726.