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Publications: Centre for Crop and Food Innovation

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Number of items at this level: 114.

Journal Article

Agarwal, C., Chen, W., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Vandemark, G. (2022) Linkage QTL Mapping and Genome-Wide Association Study on Resistance in Chickpea to Pythium ultimum. Frontiers in Genetics, 13 . Art. 945787.

Aggarwal, S.K., Singh, A., Choudhary, M., Kumar, A., Rakshit, S., Kumar, P., Bohra, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Pangenomics in microbial and crop research: Progress, applications, and perspectives. Genes, 13 (4). Article 598.

Amrani, A., Sohel, F., Diepeveen, D.ORCID: 0000-0002-1535-8019, Murray, D. and Jones, M.G.K.ORCID: 0000-0001-5002-0227 (2022) Insect detection from imagery using YOLOv3-based adaptive feature fusion convolution network. Crop and Pasture Science . Online Early.

Babele, P.K., Kudapa, H., Singh, Y., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Kumar, A. (2022) Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health. Frontiers in Plant Science, 13 . Art. 902536.

Barmukh, R., Roorkiwal, M., Dixit, G.P., Bajaj, P., Kholova, J., Smith, M.R., Chitikineni, A., Bharadwaj, C., Sreeman, S.M., Rathore, A., Tripathi, S., Yasin, M., Vijayakumar, A.G., Rao Sagurthi, S., Siddique, K.H.M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Foyer, C. (2022) Characterization of ‘QTL-hotspot’ introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. Journal of Experimental Botany . Art. erac348.

Barmukh, R., Roorkiwal, M., Garg, V., Khan, A.W., German, L., Jaganathan, D., Chitikineni, A., Kholova, J., Kudapa, H., Sivasakthi, K., Samineni, S., Kale, S.M., Gaur, P.M., Sagurthi, S.R., Benitez‐Alfonso, Y. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. Plant Biotechnology Journal, 20 (9). pp. 1701-1715.

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, 108 (3). pp. 646-660.

Bharadwaj, C., Jorben, J., Rao, A., Roorkiwal, M., Patil, B.S., Jayalakshmi, ., Ahammed, S.K., Saxena, D.R., Yasin, M., Jahagirdar, J.E., Sontakke, P.L., Pithia, M.S., Chudasama, M.K., Swarup, I., Singh, R.K., Nitesh, S.D., Chitikineni, A., Singh, S., Singh, I., Pratap, A., Dixit, G.P., Srivastava, A.K. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Development of High Yielding Fusarium Wilt Resistant Cultivar by Pyramiding of “Genes” Through Marker-Assisted Backcrossing in Chickpea (Cicer arietinum L.). Frontiers in Genetics, 13 . Art. 924287.

Bhat, J.A., Karikari, B., Adeboye, K.A., Ganie, S.A., Barmukh, R., Hu, D., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Yu, D. (2022) Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. Theoretical and Applied Genetics, 135 . pp. 2407-2422.

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., Kilian, B., Sivasankar, S., Caccamo, M., Mba, C., McCouch, S.R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Reap the crop wild relatives for breeding future crops. Trends in Biotechnology, 40 (4). pp. 412-431.

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, 14 (3). Art. e20132.

Bohra, A., Tiwari, A., Kaur, P., Ganie, S.A., Raza, A., Roorkiwal, M., Mir, R.R., Fernie, A.R., Smýkal, P. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) The key to the future lies in the past: Insights from grain legume domestication and improvement should inform future breeding strategies. Plant and Cell Physiology .

Chen, H., Yang, Q., Fu, H., Chen, K., Zhao, S., Zhang, C., Cai, T., Wang, L., Lu, W., Dang, H., Gao, M., Li, H., Yuan, X., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Zhuang, W. (2022) Identification of key gene networks and deciphering transcriptional regulators associated with peanut embryo abortion mediated by calcium deficiency. Frontiers in Plant Science, 13 . Art. 814015.

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.

Doležalová, A., Sládeková, L., Šimoníková, D., Holušová, K., Karafiátová, M., Varshney, R.K.ORCID: 0000-0002-4562-9131, Doležel, J. and Hřibová, E. (2022) Karyotype differentiation in cultivated chickpea revealed by Oligopainting fluorescence in situ hybridization. Frontiers in Plant Science, 12 . Art. 791303.

Elango, D., Wang, W., Thudi, M., Sebastiar, S., Ramadoss, B.R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Genome-wide association mapping of seed oligosaccharides in chickpea. Frontiers in Plant Science, 13 . Art. 1024543.

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.

Fayaz, H., Tyagi, S., Wani, A.A., Pandey, R., Akhtar, S., Bhat, M.A., Chitikineni, A., Varshney, R.K.ORCID: 0000-0002-4562-9131, Thudi, M., Kumar, U. and Mir, R.R. (2022) Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.). Scientific Reports, 12 (1). Art. 11357.

Fosu-Nyarko, J., Adams, I.P., Jones, M.G.K.ORCID: 0000-0001-5002-0227, Fox, A. and Jones, R.A.C. (2022) Comparisons between sequenced and re-sequenced genomes of historical subterranean clover mottle virus isolates. Journal of Plant Pathology .

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.

Garg, V. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Analysis of Small RNA Sequencing Data in Plants. Methods in molecular biology, 2443 . pp. 497-509.

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, 58 . pp. 291-306.

Ghosh, S., Mahadevaiah, S.S., Gowda, S.A., Gangurde, S.S., Jadhav, M.P., Hake, A.A., Latha, P., Anitha, T., Chimmad, V.P., Mirajkar, K.K., Sharma, V., Pandey, M.K., Shirasawa, K., Nayak, S.N., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Bhat, R.S. (2022) Genetic mapping of drought tolerance traits phenotyped under varying drought stress environments in peanut (Arachis hypogaea L.). Euphytica, 218 (12). Art. 168.

Gupta, P.K. (2022) Earth Biogenome Project: Present status and future plans. Trends in Genetics, 38 (8). P811-820.

Halder, U., Biswas, R., Kabiraj, A., Deora, R., Let, M., Roy, R.K., Chitikineni, A., Majhi, K., Sarkar, S., Dutta, B., Laha, A., Datta, A., Khan, D., Varshney, R.K.ORCID: 0000-0002-4562-9131, Saha, D., Chattopadhyay, S. and Bandopadhyay, R. (2022) Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil. Scientific Reports, 12 (1). Art. 8439.

Haque, Md.R. and Sohel, F. (2022) Deep network with score level fusion and inference-based transfer learning to recognize leaf blight and fruit rot diseases of eggplant. Agriculture, 12 (8). Article 1160.

Hasan, A.S.M.M., Sohel, F., Diepeveen, D.ORCID: 0000-0002-1535-8019, Laga, H.ORCID: 0000-0002-4758-7510 and Jones, M.G.K.ORCID: 0000-0001-5002-0227 (2022) Weed recognition using deep learning techniques on class-imbalanced imagery. Crop and Pasture Science . Online Early.

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.

Jones, M.G.K.ORCID: 0000-0001-5002-0227, Fosu-Nyarko, J., Iqbal, S., Adeel, M., Romero-Aldemita, R., Arujanan, M., Kasai, M., Wei, X., Prasetya, B., Nugroho, S., Mewett, O., Mansoor, S., Awan, M.J.A., Ordonio, R.L., Rao, S.R., Poddar, A., Hundleby, P., Iamsupasit, N. and Khoo, K. (2022) Enabling trade in gene-edited produce in Asia and Australasia: The developing regulatory landscape and future perspectives. Plants, 11 (19). Article 2538.

Kaashyap, M., Ford, R., Mann, A., Varshney, R.K.ORCID: 0000-0002-4562-9131, Siddique, K.H.M. and Mantri, N. (2022) Comparative flower transcriptome network analysis reveals DEGs involved in chickpea reproductive success during salinity. Plants, 11 (3). Art. 434.

Kaashyap, M., Kaur, S., Ford, R., Edwards, D., Siddique, K.H.M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Mantri, N. (2022) Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea. Plant Biotechnology Journal, 20 (7). pp. 1402-1416.

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.

Kamdar, J.H., Jasani, M.D., Chandrashekar, A.B., Janila, P., Pandey, M.K., Georrge, J.J., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Bera, S.K. (2022) Does improved oleic acid content due to marker-assisted introgression of ahFAD2 mutant alleles in peanuts alter its mineral and vitamin composition? Frontiers in Plant Science, 13 . Art. 942617.

Kinhoégbè, G., Djèdatin, G., Saxena, R.K., Chitikineni, A., Bajaj, P., Molla, J., Agbangla, C., Dansi, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PLoS ONE, 17 (7). Art. e0271565.

Kulwal, P.L., Mir, R.R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Cytogenetics to functional genomics: six decades journey of Professor P.K. Gupta. Plant Biotechnology Journal, 20 (6). pp. 1021-1030.

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.

Kumar, T., Tiwari, N., Bharadwaj, C., Roorkiwal, M., Reddy, S.P.P., Patil, B.S., Kumar, S., Hamwieh, A., Vinutha, T., Bindra, S., Singh, I., Alam, A., Chaturvedi, S.K., Kumar, Y., Nimmy, M.S., Siddique, K.H.M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) A comprehensive analysis of Trehalose-6-phosphate synthase (TPS) gene for salinity tolerance in chickpea (Cicer arietinum L.). Scientific Reports, 12 (1). Art. 16315.

Kushwah, A., Bhatia, D., Barmukh, R., Singh, I., Singh, G., Bindra, S., Vij, S., Chellapilla, B., Pratap, A., Roorkiwal, M., Kumar, S., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Singh, S. (2022) Genetic mapping of QTLs for drought tolerance in chickpea (Cicer arietinum L.). Frontiers in Genetics, 13 . Art. 953898.

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, G., Liu, R., Xu, R., Varshney, R.K.ORCID: 0000-0002-4562-9131, Ding, H., Li, M., Yan, X., Huang, S., Li, J., Wang, D., Ji, Y., Wang, C., He, J., Luo, Y., Gao, S., Wei, P., Zong, X. and Yang, T. (2022) Development of an Agrobacterium-mediated CRISPR/Cas9 system in pea (Pisum sativum L.). The Crop Journal . In Press.

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.

Lu, Q., Liu, H., Hong, Y., Liang, X., Li, S., Liu, H., Li, H., Wang, R., Deng, Q., Jiang, H., Varshney, R.K.ORCID: 0000-0002-4562-9131, Pandey, M.K. and Chen, X. (2022) Genome-Wide Identification and Expression of FAR1 Gene Family Provide Insight Into Pod Development in Peanut (Arachis hypogaea). Frontiers in Plant Science, 13 . Art. 893278.

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.

Manthena, V., Jarquin, D., Varshney, R.K.ORCID: 0000-0002-4562-9131, Roorkiwal, M., Dixit, G.P., Bharadwaj, C. and Howard, R. (2022) Evaluating dimensionality reduction for genomic prediction. Frontiers in Genetics, 13 . Art. 958780.

Mendu, L., Cobos, C.J., Tengey, T.K., Commey, L., Balasubramanian, V.K., Williams, L.D., Dhillon, K.K., Sharma, D., Pandey, M.K., Falalou, H., Varshney, R.K.ORCID: 0000-0002-4562-9131, Burow, M.D., Sudini, H.K. and Mendu, V. (2022) Seed coat mediated resistance against Aspergillus flavus infection in peanut. Plant Gene, 32 . Art. 100381.

Mir, A.H., Bhat, M.A., Fayaz, H., Wani, A.A., Dar, S.A., Maqbool, S., Yasin, M., Mir, J.I., Khan, M.A., Sofi, P.A., El-Sappah, A.H., Thudi, M., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Mir, R.R. (2022) SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas. Molecular Biology Reports .

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.

Montesinos-López, O.A., Montesinos-López, J.C., Montesinos-López, A., Ramírez-Alcaraz, J.M., Poland, J., Singh, R., Dreisigacker, S., Crespo, L., Mondal, S., Govidan, V., Juliana, P., Espino, J.H., Shrestha, S., Varshney, R.K.ORCID: 0000-0002-4562-9131, Crossa, J. and Lipka, A. (2021) Bayesian multitrait kernel methods improve multienvironment genome-based prediction. G3 Genes|Genomes|Genetics, 12 (2).

Movahedi, A., Wei, H., Zhou, X., Fountain, J.C., Chen, Z-H, Mu, Z., Sun, W., Zhang, J., Li, D., Guo, B., Varshney, R.K.ORCID: 0000-0002-4562-9131, Yang, L. and Zhuge, Q. (2022) Precise exogenous insertion and sequence replacements in poplar by simultaneous HDR overexpression and NHEJ suppression using CRISPR-Cas9. Horticulture Research, 9 . Art. uhac154.

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 .

Pal, N., Jan, I., Saini, D.K., Kumar, K., Kumar, A., Sharma, P.K., Kumar, S., Balyan, H.S. and Gupta, P.K. (2022) Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.). 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.

Pan, J., Zhou, X., Ahmad, N., Zhang, K., Tang, R., Zhao, H., Jiang, J., Tian, M., Li, C., Li, A., Zhang, X., He, L., Ma, J., Li, X., Tian, R., Ma, C., Pandey, M.K., Varshney, R.K.ORCID: 0000-0002-4562-9131, Wang, X. and Zhao, C. (2022) BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut. Theoretical and Applied Genetics .

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). Article 660.

Patil, P.G., Jamma, S., Manjunatha, N., Bohra, A., Pokhare, S., Dhinesh Babu, K., Murkute, A.A. and Marathe, R.A. (2022) Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate. Frontiers in Plant Science, 13 . Art. 943959.

Patil, P.G., Sharma, J., Nanjundappa, M., Singh, N.V., Bohra, A., Gunnaiah, R., Jamma, S.M., Vinayaka, J., Sangnure, V.R. and Marathe, R.A. (2022) Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate. 3 Biotech, 12 (7). Art. 153.

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.

Pundir, S., Sharma, R., Kumar, D., Singh, V.K., Chaturvedi, D., Kanwar, R.S., Röder, M.S., Börner, A., Ganal, M.W., Gupta, P.K., Sharma, S. and Sharma, S. (2022) QTL mapping for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.). Scientific Reports, 12 (1). Art. 9586.

Rai, R.K., Kumar, S.S., Sen Gupta, S., Parasannanavar, D.J., Anish, T.S.N., Barik, A., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Rajkumar, H. (2022) Shooting shadows: India’s struggle to reduce the burden of anaemia. British Journal of Nutrition . First View.

Raza, A., Sharif, Y., Chen, K., Wang, L., Fu, H., Zhuang, Y., Chitikineni, A., Chen, H., Zhang, C., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Zhuang, W. (2022) Genome-Wide characterization of ascorbate peroxidase gene family in peanut (Arachis hypogea L.) revealed their crucial role in growth and multiple stress tolerance. Frontiers in Plant Science, 13 . Art. 962182.

Raza, A., Tabassum, J., Fakhar, A.Z., Sharif, R., Chen, H., Zhang, C., Ju, L., Fotopoulos, V., Siddique, K.H.M., Singh, R.K., Zhuang, W. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Smart reprograming of plants against salinity stress using modern biotechnological tools. Critical Reviews in Biotechnology . pp. 1-28.

Raza, A., Tabassum, J., Zahid, Z., Charagh, S., Bashir, S., Barmukh, R., Khan, R.S.A., Barbosa, F., Zhang, C., Chen, H., Zhuang, W. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants. Frontiers in Plant Science, 12 . Art. 794373.

Roorkiwal, M., Bhandari, A., Barmukh, R., Bajaj, P., Valluri, V.K., Chitikineni, A., Pandey, S., Chellapilla, B., Siddique, K.H.M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Genome-wide association mapping of nutritional traits for designing superior chickpea varieties. Frontiers in Plant Science, 13 . Art. 843911.

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.

Sachdeva, S., Bharadwaj, C., Patil, B.S., Pal, M., Roorkiwal, M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Agronomic performance of chickpea affected by drought stress at different growth stages. Agronomy, 12 (5). Article 995.

Saeed, F., Chaudhry, U.K., Bakhsh, A., Raza, A., Saeed, Y., Bohra, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Moving beyond DNA sequence to improve plant stress responses. Frontiers in Genetics, 13 . Art. 874648.

Salehi, H., Chehregani Rad, A., Sharifan, H., Raza, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Aerially applied zinc oxide nanoparticle affects reproductive components and seed quality in fully grown bean plants ( Phaseolus vulgaris L.). Frontiers in Plant Science . Art. 808141.

Samantara, K., Bohra, A., Mohapatra, S.R., Prihatini, R., Asibe, F., Singh, L., Reyes, V.P., Tiwari, A., Maurya, A.K., Croser, J.S., Wani, S.H., Siddique, K.H.M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Breeding more crops in less time: A perspective on speed breeding. Biology, 11 (2). Article 275.

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, 14 (3). 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, 14 (3). Art. e20125.

Scholz, A.H., Freitag, J., Lyal, C.H.C., Sara, R., Cepeda, M.L., Cancio, I., Sett, S., Hufton, A.L., Abebaw, Y., Bansal, K., Benbouza, H., Boga, H.I., Brisse, S., Bruford, M.W., Clissold, H., Cochrane, G., Coddington, J.A., Deletoille, A-C, García-Cardona, F., Hamer, M., Hurtado-Ortiz, R., Miano, D.W., Nicholson, D., Oliveira, G., Bravo, C.O., Rohden, F., Seberg, O., Segelbacher, G., Shouche, Y., Sierra, A., Karsch-Mizrachi, I., da Silva, J., Hautea, D.M., Da silva, M., Suzuki, M., Tesfaye, K., Tiambo, C.K., Tolley, K.A., Varshney, R.ORCID: 0000-0002-4562-9131, Zambrano, M.M. and Overmann, J. (2022) Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation. Nature Communications, 13 (1). Art. 1086.

Shafi, S., Saini, D.K., Khan, M.A., Bawa, V., Choudhary, N., Dar, W.A., Pandey, A.K., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Mir, R.R. (2022) Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.). Frontiers in Plant Science, 13 . Art. 966339.

Shammi, S., Sohel, F., Diepeveen, D.ORCID: 0000-0002-1535-8019, Zander, S. and Jones, M.G.K.ORCID: 0000-0001-5002-0227 (2022) A survey of image-based computational learning techniques for frost detection in plants. Information Processing in Agriculture . In Press.

Shammi, S., Sohel, F., Diepeveen, D.ORCID: 0000-0002-1535-8019, Zander, S., Jones, M.G.K.ORCID: 0000-0001-5002-0227, Bekuma, A. and Biddulph, B. (2022) Machine learning-based detection of freezing events using infrared thermography. Computers and Electronics in Agriculture, 198 . Art. 107013.

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.

Singh, M.K., Roorkiwal, M., Rathore, A., Soren, K.R., Pithia, M.S., Yasin, M., Barpete, S., Singh, S., Barmukh, R., Das, R.R., Gangwar, P., Chetariya, C.P., Joshi, P., Chaturvedi, S.K., Javia, R.M., Ramani, V.V., Hamwieh, A., Kumar, S., Bharadwaj, C., Singh, N.P. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Evaluation of global composite collection reveals agronomically superior germplasm accessions for chickpea improvement. Agronomy, 12 (9). Article 2013.

Singh, V., Sinha, P., Obala, J., Khan, A.W., Chitikineni, A., Saxena, R.K. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity, 128 . pp. 411-419.

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.

Srivastava, R.K., Yadav, O.P., Kaliamoorthy, S., Gupta, S.K., Serba, D.D., Choudhary, S., Govindaraj, M., Kholová, J., Murugesan, T., Satyavathi, C.T., Gumma, M.K., Singh, R.B., Bollam, S., Gupta, R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Breeding Drought-Tolerant Pearl Millet using conventional and genomic approaches: Achievements and prospects. Frontiers in Plant Science, 13 . Art. 781524.

Tayade, A.D., Motagi, B.N., Jadhav, M.P., Nadaf, A.S., Koti, R.V., Gangurde, S.S., Sharma, V., Varshney, R.K.ORCID: 0000-0002-4562-9131, Pandey, M.K. and Bhat, R.S. (2022) Genetic mapping of tolerance to iron deficiency chlorosis in peanut (Arachis hypogaea L.). Euphytica, 218 (4). Art. 46.

Turner, K.E., Thompson, A.ORCID: 0000-0001-7121-7459, Harris, I., Ferguson, M. and Sohel, F. (2022) Deep learning based classification of sheep behaviour from accelerometer data with imbalance. Information Processing in Agriculture . In Press.

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 .

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., Jarquín, 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. (2022) Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 604 . Art. E12.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Stein, N. and Liu, S. (2022) Recipients of 2021 CSSA Editor's Citation for Excellence Named. The Plant Genome . Art. e20231.

Wani, S.H., Choudhary, M., Barmukh, R., Bagaria, P.K., Samantara, K., Razzaq, A., Jaba, J., Ba, M.N. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops. Theoretical and Applied Genetics .

Xiao, Y., Liu, H., Du, P., Liang, X., Li, H., Lu, Q., Li, S., Liu, H., Hong, Y., Varshney, R.K.ORCID: 0000-0002-4562-9131 and Chen, X. (2022) Impact of different cooking methods on the chemical profile of high-oleic acid peanut seeds. Food Chemistry, 379 . Art. 131970.

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.

Xiao, Y., Liu, H., Lu, Q., Li, H., Liu, Q., Li, S., Liu, H., Varshney, R.K.ORCID: 0000-0002-4562-9131, Liang, X., Hong, Y. and Chen, X. (2022) Lipid profile variations in high olecic acid peanuts by following different cooking processes. Food Research International, 155 . Art. 110993.

Xiao, Z., Wang, Q., Lin, M-W, Huang, M., Wang, Z., Xie, M., Varshney, R.K.ORCID: 0000-0002-4562-9131, Nguyen, H.T., Chan, T-F and Lam, H-M (2022) Wildsoydb DataHub: A platform for accessing soybean multiomic datasets across multiple reference genomes. Plant Physiology . Art. kiac419.

Xu, Y., Zhang, X., Li, H., Zheng, H., Zhang, J., Olsen, M.S., Varshney, R.K.ORCID: 0000-0002-4562-9131, Prasanna, B.M. and Qian, Q. (2022) Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction. Molecular Plant . pp. 1-32.

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.

Yang, T., Liu, R., Luo, Y., Hu, S., Wang, D., Wang, C., Pandey, M.K., Ge, S., Xu, Q., Li, N., Li, G., Huang, Y., Saxena, R.K., Ji, Y., Li, M., Yan, X., He, Y., Liu, Y., Wang, X., Xiang, C., Varshney, R.K.ORCID: 0000-0002-4562-9131, Ding, H., Gao, S. and Zong, X. (2022) Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nature Genetics, 54 (10). pp. 1553-1563.

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, 107 (3). pp. 669-687.

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.

Book Chapter

Kulwal, P.L., Mir, R.R. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2022) Efficient Breeding of Crop Plants. In: Yadava, D.K., Dikshit, H.K., Mishra, G.P. and Tripathi, S., (eds.) Fundamentals of Field Crop Breeding. Springer Singapore, pp. 745-777.

Thesis

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 Tue Jan 31 00:09:15 2023 UTC.