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Publications: Centre for Crop and Food Innovation

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Number of items at this level: 46.

Journal Article

Bayer, P.E., Valliyodan, B., Hu, H.ORCID: 0000-0003-1070-213X, Marsh, J.I., Yuan, Y., Vuong, T.D., Patil, G., Song, Q., Batley, J., Varshney, R.K.ORCID: 0000-0002-4562-9131, Lam, H‐M, Edwards, D. and Nguyen, H.T. (2021) Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome, Early View . e20109.

Bellucci, E., Mario Aguilar, O., Alseekh, S., Bett, K., Brezeanu, C., Cook, D., De la Rosa, L., Delledonne, M., Dostatny, D.F., Ferreira, J.J., Geffroy, V., Ghitarrini, S., Kroc, M., Kumar Agrawal, S., Logozzo, G., Marino, M., Mary‐Huard, T., McClean, P., Meglič, V., Messer, T., Muel, F., Nanni, L., Neumann, K., Servalli, F., Străjeru, S., Varshney, R.K.ORCID: 0000-0002-4562-9131, Vasconcelos, M.W., Zaccardelli, M., Zavarzin, A., Bitocchi, E., Frontoni, E., Fernie, A.R., Gioia, T., Graner, A., Guasch, L., Prochnow, L., Oppermann, M., Susek, K., Tenaillon, M. and Papa, R. (2021) The INCREASE project: Intelligent Collections of food‐legume genetic resources for European agrofood systems. The Plant Journal . Early View.

Bhat, J.A., Yu, D., Bohra, A., Ganie, S.A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Features and applications of haplotypes in crop breeding. Communications Biology, 4 (1). Art. 1266.

Bhogireddy, S., Mangrauthia, S.K., Kumar, R., Pandey, A.K., Singh, S., Jain, A., Budak, H., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Kudapa, H. (2021) Regulatory non-coding RNAs: A new frontier in regulation of plant biology. Functional & Integrative Genomics, 21 . pp. 313-330.

Bohra, A., Prasad, G., Rathore, A., Saxena, R.K., Naik, S.J.S., Pareek, S., Jha, R., Pazhamala, L., Datta, D., Pandey, G., Tiwari, A., Maurya, A.K., Soren, K.R., Akram, M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Singh, N.P. (2021) Global gene expression analysis of pigeonpea with male sterility conditioned by A 2 cytoplasm. The Plant Genome . Art. e20132.

Commey, L., Tengey, T.K., Cobos, C.J., Dampanaboina, L., Dhillon, K.K., Pandey, M.K., Sudini, H.K., Falalou, H., Varshney, R.K.ORCID: 0000-0002-4562-9131, Burow, M.D. and Mendu, V. (2021) Peanut seed coat acts as a physical and biochemical barrier against Aspergillus flavus infection. Journal of Fungi, 7 (12). Art. 1000.

Evans, F.H.ORCID: 0000-0002-7329-1289 and Shen, J. (2021) Long-term hindcasts of wheat yield in fields using remotely sensed phenology, climate data and machine learning. Remote Sensing, 13 (13). Article 2435.

Evans, F.H.ORCID: 0000-0002-7329-1289 and Shen, J. (2021) Spatially weighted estimation of broadacre crop growth improves gap-filling of Landsat NDVI. Remote Sensing, 13 (11). Article 2128.

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.B., Durand, N.C., Pandey, M.K., Li, G., Barmukh, R., Wang, X., Chen, X., Lam, H-M, Jiang, H., Zong, X., Liang, X., Liu, X., Liao, B., Guo, B., Jackson, S., Nguyen, H.T., Zhuang, W., Shubo, W., Wang, X., Aiden, E.L., Bennetzen, J.L. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (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 . In Press.

Getahun, T., Tesfaye, K., Fikre, A., Haileslassie, T., Chitikineni, A., Thudi, M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Molecular genetic diversity and population structure in Ethiopian chickpea germplasm accessions. Diversity, 13 (6). Art. 247.

Ghatak, A., Schindler, F., Bachmann, G., Engelmeier, D., Bajaj, P., Brenner, M., Fragner, L., Varshney, R.K.ORCID: 0000-0002-4562-9131, Subbarao, G.V., Chaturvedi, P. and Weckwerth, W. (2021) Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity. Biology and Fertility of Soils .

Jha, U.C., Nayyar, H., Palakurthi, R., Jha, R., Valluri, V., Bajaj, P., Chitikineni, A., Singh, N.P., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Thudi, M. (2021) Major QTLs and potential candidate genes for heat stress tolerance identified in Chickpea (Cicer arietinum L.). Frontiers in Plant Science, 12 . Art. 655103.

Kalema, E.P., Akpo, E., Muricho, G., Ringo, J., Ojiewo, C.O. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Mapping out market drivers of improved variety seed use: The case of sorghum in Tanzania. Heliyon, 8 (1). Art. e08715.

Kumar, A., Bohra, A., Mir, R.R., Sharma, R., Tiwari, A., Khan, M.A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Next generation breeding in pulses: Present status and future directions. Crop Breeding and Applied Biotechnology, 21 . Art. e394221S13.

Kumar, A., Rani, M., Mani, S., Shah, P., Singh, D.B., Kudapa, H. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Nutritional significance and Antioxidant-Mediated antiaging effects of Finger Millet: Molecular insights and prospects. Frontiers in Sustainable Food Systems, 5 . Art. 684318.

Kushwah, A., Bhatia, D., Singh, I., Thudi, M., Singh, G., Bindra, S., Vij, S., Gill, B.S., Bharadwaj, C., Singh, S. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292. PLoS ONE, 16 (8). Art. e0254957.

Li, W., Huang, L., Liu, N., Pandey, M.K., Chen, Y., Cheng, L., Guo, J., Yu, B., Luo, H., Zhou, X., Huai, D., Chen, W., Yan, L., Wang, X., Lei, Y., Varshney, R.K.ORCID: 0000-0002-4562-9131, Liao, B. and Jiang, H. (2021) Key regulators of sucrose metabolism identified through comprehensive comparative transcriptome analysis in peanuts. International Journal of Molecular Sciences, 22 (14). Art. 7266.

Liu, H., Hu, D., Du, P., Wang, L., Liang, X., Li, H., Lu, Q., Li, S., Liu, H., Chen, X., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Hong, Y. (2021) Single‐cell RNA‐seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut ( Arachis hypogaea L.). Plant Biotechnology Journal, 19 (11). pp. 2261-2276.

Manchikatla, P.K., Kalavikatte, D., Mallikarjuna, B.P., Palakurthi, R., Khan, A.W., Jha, U.C., Bajaj, P., Singam, P., Chitikineni, A., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Thudi, M. (2021) MutMap approach enables rapid identification of candidate genes and development of markers associated with early flowering and enhanced seed size in chickpea (Cicer arietinum L.). Frontiers in Plant Science, 12 . Art. 688694.

Montesinos-López, O.A., Montesinos-López, A., Mosqueda-González, B.A., Bentley, A.R., Lillemo, M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Crossa, J. (2021) A new deep learning calibration method enhances Genome-Based prediction of continuous crop traits. Frontiers in Genetics, 12 . Art. 798840.

Muzahid, A.A.M., Wanggen, W., Sohel, F., Bennamoun, M., Hou, L. and Ullah, H. (2022) Erratum to “Progressive conditional GAN-based augmentation for 3D object recognition” [Neurocomputing 460 (2021) 20–30]. Neurocomputing, 473 . Art. 158.

Muzahid, A.A.M., Wanggen, W., Sohel, F., Bennamoun, M., Hou, L. and Ullah, H. (2021) Progressive conditional GAN-based augmentation for 3D object recognition. Neurocomputing, 460 . pp. 20-30.

Nguyen, D.T., Hayes, J.E., Atieno, J., Li, Y., Baumann, U., Pattison, A., Bramley, H., Hobson, K.A., Roorkiwal, M., Varshney, R.K.ORCID: 0000-0002-4562-9131, Colmer, T.D. and Sutton, T. (2021) The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data. Theoretical and Applied Genetics .

Palakurthi, R., Jayalakshmi, V., Kumar, Y., Kulwal, P., Yasin, M., Kute, N.S., Laxuman, C., Yeri, S., Vemula, A., Rathore, A., Samineni, S., Soren, K.R., Mondal, B., Dixit, G.P., Bharadwaj, C., Chaturvedi, S.K., Gaur, P.M., Roorkiwal, M., Thudi, M., Singh, N.P. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Translational Chickpea Genomics Consortium to accelerate genetic gains in chickpea (Cicer arietinum L.). Plants, 10 (12). Article 2583.

Parmar, S., Deshmukh, D.B., Kumar, R., Manohar, S.S., Joshi, P., Sharma, V., Chaudhari, S., Variath, M.T., Gangurde, S.S., Bohar, R., Singam, P., Varshney, R.K.ORCID: 0000-0002-4562-9131, Janila, P. and Pandey, M.K. (2021) Single seed-based high-throughput genotyping and rapid generation advancement for accelerated groundnut genetics and breeding research. Agronomy, 11 (6). Art. 1226.

Patel, J., Khandwal, D., Choudhary, B., Ardeshana, D., Jha, R.K., Tanna, B., Yadav, S., Mishra, A., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Siddique, K.H.M. (2022) Differential physio-biochemical and metabolic responses of peanut (Arachis hypogaea L.) under multiple abiotic stress conditions. International Journal of Molecular Sciences, 23 (2). Art. 660.

Pazhamala, L.T., Kudapa, H., Weckwerth, W., Millar, A.H. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Systems biology for crop improvement. The Plant Genome, 14 (2). Art. e20098.

Roorkiwal, M., Pandey, S., Thavarajah, D., Hemalatha, R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Molecular mechanisms and biochemical pathways for micronutrient acquisition and storage in legumes to support biofortification for nutritional security. Frontiers in Plant Science, 12 . Art. 682842.

Saradadevi, G.P., Das, D., Mangrauthia, S.K., Mohapatra, S., Chikkaputtaiah, C., Roorkiwal, M., Solanki, M., Sundaram, R.M., Chirravuri, N.N., Sakhare, A.S., Kota, S., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Mohannath, G. (2021) Genetic, epigenetic, genomic and microbial approaches to enhance salt tolerance of plants: A comprehensive review. Biology, 10 (12). Art. 1255.

Saradadevi, R., Mukankusi, C., Li, L., Amongi, W., Mbiu, J.P., Raatz, B., Ariza, D., Beebe, S., Varshney, R.K.ORCID: 0000-0002-4562-9131, Huttner, E., Kinghorn, B., Banks, R., Rubyogo, J.C., Siddique, K.H.M. and Cowling, W.A. (2021) Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa. The Plant Genome . Art. e20156.

Saxena, R.K., Jiang, Y., Khan, A.W., Zhao, Y., Kumar Singh, V., Bohra, A., Sonappa, M., Rathore, A., Kumar, C.V.S., Saxena, K., Reif, J. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Characterization of heterosis and genomic prediction‐based establishment of heterotic patterns for developing better hybrids in pigeonpea. The Plant Genome . Early View.

Shen, J. and Evans, F.H.ORCID: 0000-0002-7329-1289 (2021) The potential of Landsat NDVI sequences to explain wheat yield variation in fields in Western Australia. Remote Sensing, 13 (11). Article 2202.

Sinha, P., Singh, V.K., Bohra, A., Kumar, A., Reif, J.C. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits. Theoretical and Applied Genetics, 134 . pp. 1829-1843.

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. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) Global transcriptome profiling identified transcription factors, biological process, and associated pathways for pre-harvest aflatoxin contamination in groundnut. Journal of Fungi, 7 (6). p. 413.

Varshney, R.K.ORCID: 0000-0002-4562-9131 (2021) The Plant Genome special issue: Advances in genomic selection and application of machine learning in genomic prediction for crop improvement. The Plant Genome, 14 (3). Art. e20178.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Bohra, A., Roorkiwal, M., Barmukh, R., Cowling, W., Chitikineni, A., Lam, H-M, Hickey, L.T., Croser, J., Edwards, D., Farooq, M., Crossa, J., Weckwerth, W., Millar, A.H., Kumar, A., Bevan, M.W. and Siddique, K.H.M. (2021) Rapid delivery systems for future food security. Nature Biotechnology, 39 . pp. 1179-1181.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Bohra, A., Roorkiwal, M., Barmukh, R., Cowling, W.A., Chitikineni, A., Lam, H-M, Hickey, L.T., Croser, J.S., Bayer, P.E., Edwards, D., Crossa, J., Weckwerth, W., Millar, H., Kumar, A., Bevan, M.W. and Siddique, K.H.M. (2021) Fast-forward breeding for a food-secure world. Trends in Genetics, 37 (12). pp. 1124-1136.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Bohra, A., Yu, J., Graner, A., Zhang, Q. and Sorrells, M.E. (2021) Designing future crops: Genomics-Assisted breeding comes of age. Trends in Plant Science, 26 (6). pp. 631-649.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N.P., Du, X., Upadhyaya, H.D., Khan, A.W., Wang, Y., Garg, V., Fan, G., Cowling, W.A., Crossa, J., Gentzbittel, L., Voss-Fels, K.P., Valluri, V.K., Sinha, P., Singh, V.K., Ben, C., Rathore, A., Punna, R., Singh, M.K., Tar’an, B., Bharadwaj, C., Yasin, M., Pithia, M.S., Singh, S., Soren, K.R., Kudapa, H., Jarquin, D., Cubry, P., Hickey, L.T., Dixit, G.P., Thuillet, A-C, Hamwieh, A., Kumar, S., Deokar, A.A., Chaturvedi, S.K., Francis, A., Howard, R., Chattopadhyay, D., Edwards, D., Lyons, E., Vigouroux, Y., Hayes, B.J., von Wettberg, E., Datta, S.K., Yang, H., Nguyen, H.T., Wang, J., Siddique, K.H.M., Mohapatra, T., Bennetzen, J.L., Xu, X. and Liu, X. (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature .

Xiao, Y., Liu, H., Li, H., Liu, Q., Lu, Q., Varshney, R.K.ORCID: 0000-0002-4562-9131, Chen, X. and Hong, Y. (2021) Widely targeted metabolomics characterizes the dynamic changes of chemical profile in postharvest peanut sprouts grown under the dark and light conditions. LWT, 152 . Art. 112283.

Yadav, O.P., Gupta, S.K., Govindaraj, M., Sharma, R., Varshney, R.K.ORCID: 0000-0002-4562-9131, Srivastava, R. and Mahala, R.S. (2021) Genetic gains in Pearl Millet in India: Insights into historic breeding strategies and future perspective. Frontiers in Plant Science, 12 . Art. 645038.

Zhang, S., Ghatak, A., Bazargani, M.M., Bajaj, P., Varshney, R.K.ORCID: 0000-0002-4562-9131, Chaturvedi, P., Jiang, D. and Weckwerth, W. (2021) Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. The Plant Journal .

Zhang, X., Pandey, M.K., Wang, J., Zhao, K., Ma, X., Li, Z., Zhao, K., Gong, F., Guo, B., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Yin, D. (2021) Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations. Genome Biology, 22 (1). Art. 315.

Zhao, C., He, L., Xia, H., Zhou, X., Geng, Y., Hou, L., Li, P., Li, G., Zhao, S., Ma, C., Tang, R., Pandey, M.K., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Wang, X. (2021) De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses. Genomics, 113 (3). pp. 1579-1588.


Dang, Hoang Viet (2021) Identification of gene-gene and gene-environment interactions for flowering time and grain yield using a multi-parental mapping population in barley. PhD thesis, Murdoch University.

Ly, Diem Nguyen Phuoc (2021) Developing novel potato properties using gene editing. PhD thesis, Murdoch University.

This list was generated on Fri Jan 21 19:29:15 2022 UTC.