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Khan, A W and Garg, V and Sun, S and Gupta, Saurabh and Dudchenko, O and Roorkiwal, M and Chitikineni, A and Bayer, P E and Shi, C and Upadhyaya, H D and Bohra, A and Bharadwaj, C and Mir, R R and Baruch, K and Yang, B and Coyne, C J and Bansal, K C and Nguyen, H T and Ronen, G and Aiden, E L and Veneklaas, E and Siddique, K H M and Liu, X and Edwards, D and Varshney, R K (2024) Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nature Genetics (TSI). ISSN 1061-4036
Song, B and Ning, W and Wei, D and Jiang, M and Zhu, K and Wang, X and Edwards, D and Odeny, D A and Cheng, S (2023) Plant genome resequencing and population genomics: Current status and future prospects. Molecular Plant (TSI), 16. pp. 1252-1268. ISSN 1674-2052
Fernandez, C G T and Bayer, P E and Petereit, J and Varshney, R K and Batley, J and Edwards, D (2023) The conservation of gene models can support genome annotation. The Plant Genome (TSI), 16 (3). pp. 1-7. ISSN 1940-3372
Kaashyap, M and Kaur, S and Ford, R and Edwards, D and Siddique, K H M and Varshney, R K 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 (TSI), 20 (7). pp. 1402-1416. ISSN 1467-7644
Zanini, S F and Bayer, P E and Wells, R and Snowdon, R J and Batley, J and Varshney, R K and Nguyen, H T and Edwards, D and Golicz, A A (2021) Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs. The Plant Genome, 15 (1). pp. 1-18. ISSN 1940-3372
Li, Y and Ruperao, P and Batley, J and Edwards, D and Martin, W and Hobson, K and Sutton, T (2021) Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment. The Plant Genome (TSI), 15 (1). pp. 1-13. ISSN 1940-3372
Varshney, R K and Roorkiwal, M and Sun, S and Bajaj, P and Chitikineni, A and Thudi, M and Singh, N P and Du, X and Upadhyaya, H D and Khan, A W and Wang, Y and Garg, V and Fan, G and Cowling, W A and Crossa, J and Gentzbittel, L and Voss-Fels, K P and Valluri, V K and Sinha, P and Singh, V K and Ben, C and Rathore, A and Punna, R and Singh, M K and Tar’an, B and Bharadwaj, C and Yasin, M and Pithia, M S and Singh, S and Soren, K R and Kudapa, H and Jarquín, D and Cubry, P and Hickey, L T and Dixit, G P and Thuillet, A and Hamwieh, A and Kumar, S and Deokar, A A and Chaturvedi, S K and Francis, A and Howard, R and Chattopadhyay, D and Edwards, D and Lyons, E and Vigouroux, Y and Hayes, B J and Wettberg, E v and Datta, S K and Yang, H and Nguyen, H T and Wang, J and Siddique, K H M and Mohapatra, T and Bennetzen, J L and Xu, X and Liu, X (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599. pp. 622-627. ISSN 1476-4687
Ruperao, P and Thirunavukkarasu, N and Gandham, P and Selvanayagam, S and Govindaraj, M and Nebie, B and Manyasa, E and Gupta, R and Das, R R and Odeny, D A and Gandhi, H and Edwards, D and Deshpande, S P and Rathore, A (2021) Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. Frontiers in Plant Science (TSI), 12. ISSN 1664-462X
Bayer, P E and Valliyodan, B and Hu, H and Marsh, J I and Yuan, Y and Vuong, T D and Patil, G and Song, Q and Batley, J and Varshney, R K and Lam, H M and Edwards, D and Nguyen, H T (2021) Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome (TSI). pp. 1-12. ISSN 1940-3372
Valliyodan, B and Brown, A V and Wang, J and Patil, G and Liu, Y and Otyama, P I and Nelson, R T and Vuong, T and Song, Q and Musket, T A and Wagner, R and Marri, P and Reddy, S and Sessions, A and Wu, X and Grant, D and Bayer, P E and Roorkiwal, M and Varshney, R K and Liu, X and Edwards, D and Xu, D and Joshi, T and Cannon, S B and Nguyen, H T (2021) Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data (TSI), 8 (1). pp. 1-9. ISSN 2052-4463
Khan, A W and Garg, V and Roorkiwal, M and Golicz, A A and Edwards, D and Varshney, R K (2020) Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement. Trends in Plant Science (TSI), 25 (2). pp. 148-158. ISSN 1360-1385
Zhao, J and Bayer, P E and Ruperao, P and Saxena, R K and Khan, A W and Golicz, A A and Nguyen, H T and Batley, J and Edwards, D and Varshney, R K (2020) Trait associations in the pangenome of pigeon pea ( Cajanus cajan ). Plant Biotechnology Journal (TSI). pp. 1-9. ISSN 1467-7644
Valliyodan, B and Cannon, S B and Bayer, P E and Shu, S and Brown, A V and Ren, L and Jenkins, J and Chung, C Y L and Chan, T F and Daum, C G and Plott, C and Hastie, A and Baruch, K and Barry, K W and Huang, W and Patil, G and Varshney, R K and Hu, H and Batley, J and Yuan, Y and Song, Q and Stupar, R M and Goodstein, D M and Stacey, G and Lam, H M and Jackson, S A and Schmutz, J and Grimwood, J and Edwards, D and Nguyen, H T (2019) Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal (TSI), 100 (5). pp. 1066-1082. ISSN 0960-7412
Varshney, R K and Thudi, M and Roorkiwal, M and He, W and Upadhyaya, H D and Yang, W and Bajaj, P and Cubry, P and Rathore, A and Jian, J and Doddamani, D and Khan, A W and Garg, V and Chitikineni, A and Xu, D and Gaur, P M and Singh, N P and Chaturvedi, S K and Gangarao, N V P R and Krishnamurthy, L and Dixit, G P and Fikre, A and Kimurto, P K and Sreeman, S M and Bharadwaj, C and Tripathi, S and Wang, J and Lee, S H and Edwards, D and Kavi Kishor, P B and Penmetsa, R V and Crossa, J and Nguyen, H T and Siddique, K H M and Colmer, T D and Sutton, T and von Wettberg, E and Vigouroux, Y and Xu, X and Liu, X (2019) Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics (TSI), 51 (5). pp. 857-864. ISSN 1061-4036
Mousavi-Derazmahalleh, M and Bayer, P E and Hane, J K and Valliyodan, B and Nguyen, H T and Nelson, M N and Erskine, W and Varshney, R K and Papa, R and Edwards, D (2019) Adapting legume crops to climate change using genomic approaches. Plant, Cell & Environment (TSI), 42 (1). pp. 6-19. ISSN 01407791
Kaashyap, M and Ford, R and Kudapa, H and Jain, M and Edwards, D and Varshney, R K and Mantri, N (2018) Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea. Scientific Reports (TSI), 8 (1) (4855). pp. 1-19. ISSN 2045-2322
Abberton, M and Batley, J and Bentley, A and Bryant, J and Cai, H and Cockram, J and Oliveira, A C D and Cseke, L J and Dempewolf, H and Pace, C D and Edwards, D and Gepts, P and Greenland, A and Hall, A E and Henry, R and Hori, K and Howe, G T and Hughes, S and Humphreys, M and Lightfoot, D and Marshall, A and Mayes, S and Nguyen, H T and Ogbonnaya, F C and Ortiz, R and Paterson, A H and Tuberosa, R and Valliyodan, B and Varshney, R K and Yano, M (2016) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal, 14 (04). 01-04. ISSN 1467-7644
Varshney, R K and Singh, V K and Hickey, J M and Xun, X and Marshall, D F and Wang, J and Edwards, D and Ribaut, J M (2015) Analytical and Decision Support Tools for Genomics-Assisted Breeding. Trends in Plant Science. 01-10. ISSN 1360-1385 (In Press)
Kale, S M and Jaganathan, D and Ruperao, P and Chen, C and Punna, R and Kudapa, H and Thudi, M and Roorkiwal, M and Katta, M A V S K and Doddamani, D and Garg, V and Kavi Kishor, P B and Gaur, P M and Nguyen, H T and Batley, J and Edwards, D and Sutton, T and Varshney, R K (2015) Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports (15296). 01-14. ISSN 2045-2322
Kole, C and Muthamilarasan, M and Henry, R and Edwards, D and Sharma, R and Abberton, M and Batley, J and Bentley, A and Blakeney, M and Bryant, J and Cai, H and Cakir, M and Cseke, L J and Cockram, J and Oliveira, A C and Pace, C D and Dempewolf, H and Ellison, S and Gepts, P and Greenland, A and Hall, A and Hori, K and Hughes, S and Humphreys, M W and Iorizzo, M and Ismail, A M and Marshall, A and Mayes, S and Nguyen, H T and Ogbonnaya, F C and Ortiz, R and Paterson, A H and Simon, P W and Tohme, J and Tuberosa, R and Valliyodan, B and Varshney, R K and Wullschleger, S D and Yano, M and Prasad, M (2015) Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects. Frontiers in Plant Science. ISSN 1664-462X
Doddamani, D and Khan, A W and Katta, M A V S K and Agarwal, G and Thudi, M and Ruperao, P and Edwards, D and Varshney, R K (2015) CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database. 01-07. ISSN 1758-0463
Bayer, P E and Ruperao, P and Mason, A S and Stiller, J and Chan, C K K and Hayashi, S and Long, Y and Meng, J and Sutton, T and Visendi, P and Varshney, R K and Batley, J and Edwards, D (2015) High‑resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics, 128 (6). pp. 1039-1047. ISSN 0040-1706
Saxena, R K and Edwards, D and Varshney, R K (2014) Structural variations in plant genomes. Briefings in Functional Genomics. pp. 1-12. ISSN 2041-2649
Ruperao, P and Chan, C-K K and Azam, S and Karafiatova, M and Hayashi, S and Cizkova, J and Saxena, R K and Simkova, H and Song, C and Vrana, J and Chitikineni, A and Visendi, P and Gaur, P M and Millan, T and Singh, K B and Taran, B and Wang, J and Batley, J and Dolezel, J and Varshney, R K and Edwards, D (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal. ISSN 1467-7652
Khan, A W and Thudi, M and Varshney, R K and Edwards, D (2017) Sequencing the Chickpea Genome. In: The Chickpea Genome. Compendium of Plant Genomes book series (CPG) . Springer, pp. 117-123. ISBN 978-3-319-66115-5
Ruperao, P and Bayer, P and Kenneth Chan, C K and Hayashi, S and Roorkiwal, M and Chitikineni, A and Sutton, T and Batley, J and Varshney, R K and Edwards, D (2017) Constructing improved chickpea genome assemblies using skimGBS. In: InterDrought-V, February 21-25, 2017, Hyderabad, India.
Ruperao, P and Bayer, P E and Chan, C K K and Azam, S and Karafiatova, M and Hayashi, S and Cizkova, J and Saxena, R K and Simkova, H and Song, C and Vrána, J and Chitikineni, A and Visendi, P and Gaur, P M and Millan, T and Singh, K B and Taran, B and Wang, J and Batley, J and Dolezel, J and Varshney, R K and Edwards, D (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. The University of Queensland, Australia.