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Construction and comparison of three reference-quality genome assemblies for soybean.

Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CY, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT.

Plant J. 2019 Aug 21. doi: 10.1111/tpj.14500. [Epub ahead of print]


Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives.

Zwart RS, Thudi M, Channale S, Manchikatla PK, Varshney RK, Thompson JP.

Front Plant Sci. 2019 Jul 24;10:966. doi: 10.3389/fpls.2019.00966. eCollection 2019.


A systematic dissection of the mechanisms underlying the natural variation of silique number in rapeseed germplasm.

Li S, Zhu Y, Varshney RK, Zhan J, Zheng X, Shi J, Wang X, Liu G, Wang H.

Plant Biotechnol J. 2019 Aug 1. doi: 10.1111/pbi.13224. [Epub ahead of print]


Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice.

Arbelaez JD, Tandayu E, Reveche MY, Jarana A, van Rogen P, Sandager L, Stolt P, Ng E, Varshney RK, Kretzschmar T, Cobb J.

Plant Methods. 2019 Jul 24;15:78. doi: 10.1186/s13007-019-0464-2. eCollection 2019.


Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems.

Sandhu N, Subedi SR, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A.

Sci Rep. 2019 Jun 27;9(1):9334. doi: 10.1038/s41598-019-45770-3.


Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition.

Subedi SR, Sandhu N, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A.

BMC Genomics. 2019 Jun 10;20(1):471. doi: 10.1186/s12864-019-5840-9.


Mitigating Aflatoxin Contamination in Groundnut through A Combination of Genetic Resistance and Post-Harvest Management Practices.

Pandey MK, Kumar R, Pandey AK, Soni P, Gangurde SS, Sudini HK, Fountain JC, 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 RK.

Toxins (Basel). 2019 Jun 3;11(6). pii: E315. doi: 10.3390/toxins11060315. Review.


The role of ramosetron in the prevention of post-spinal shivering in obstetric patients. A prospective randomized double blind study.

Varshney RK, Garg M, Kapoor K, Jheetay GS.

Rom J Anaesth Intensive Care. 2019 Apr;26(1):37-43. doi: 10.2478/rjaic-2019-0006.


QTLian breeding for climate resilience in cereals: progress and prospects.

Choudhary M, Wani SH, Kumar P, Bagaria PK, Rakshit S, Roorkiwal M, Varshney RK.

Funct Integr Genomics. 2019 Sep;19(5):685-701. doi: 10.1007/s10142-019-00684-1. Epub 2019 May 16. Review.


Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.).

Luo H, Pandey MK, Khan AW, Wu B, Guo J, Ren X, Zhou X, Chen Y, Chen W, Huang L, Liu N, Lei Y, Liao B, Varshney RK, Jiang H.

Plant Biotechnol J. 2019 May 13. doi: 10.1111/pbi.13153. [Epub ahead of print]


The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication.

Zhuang W, Chen H, Yang M, Wang J, Pandey MK, Zhang C, Chang WC, Zhang L, Zhang X, Tang R, Garg V, Wang X, Tang H, Chow CN, Wang J, Deng Y, Wang D, Khan AW, 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 SA, 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 PB, Pan RL, Paterson AH, Wang X, Ming R, Varshney RK.

Nat Genet. 2019 May;51(5):865-876. doi: 10.1038/s41588-019-0402-2. Epub 2019 May 1.


The genome sequence of segmental allotetraploid peanut Arachis hypogaea.

Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J.

Nat Genet. 2019 May;51(5):877-884. doi: 10.1038/s41588-019-0405-z. Epub 2019 May 1.


Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits.

Varshney RK, Thudi M, Roorkiwal M, He W, Upadhyaya HD, Yang W, Bajaj P, Cubry P, Rathore A, Jian J, Doddamani D, Khan AW, Garg V, Chitikineni A, Xu D, Gaur PM, Singh NP, Chaturvedi SK, Nadigatla GVPR, Krishnamurthy L, Dixit GP, Fikre A, Kimurto PK, Sreeman SM, Bharadwaj C, Tripathi S, Wang J, Lee SH, Edwards D, Polavarapu KKB, Penmetsa RV, Crossa J, Nguyen HT, Siddique KHM, Colmer TD, Sutton T, von Wettberg E, Vigouroux Y, Xu X, Liu X.

Nat Genet. 2019 May;51(5):857-864. doi: 10.1038/s41588-019-0401-3. Epub 2019 Apr 29.


Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops.

Priya M, Dhanker OP, Siddique KHM, HanumanthaRao B, Nair RM, Pandey S, Singh S, Varshney RK, Prasad PVV, Nayyar H.

Theor Appl Genet. 2019 Jun;132(6):1607-1638. doi: 10.1007/s00122-019-03331-2. Epub 2019 Apr 2. Review.


Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement.

Chen X, Lu Q, Liu H, Zhang J, Hong Y, Lan H, Li H, Wang J, Liu H, Li S, Pandey MK, Zhang Z, Zhou G, Yu J, Zhang G, Yuan J, Li X, Wen S, Meng F, Yu S, Wang X, Siddique KHM, Liu ZJ, Paterson AH, Varshney RK, Liang X.

Mol Plant. 2019 Jul 1;12(7):920-934. doi: 10.1016/j.molp.2019.03.005. Epub 2019 Mar 19.


An "Axiom Cajanus SNP Array" based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea.

Yadav P, Saxena KB, Hingane A, Kumar CVS, Kandalkar VS, Varshney RK, Saxena RK.

BMC Genomics. 2019 Mar 21;20(1):235. doi: 10.1186/s12864-019-5595-3.


Technological perspectives for plant breeding.

Godwin ID, Rutkoski J, Varshney RK, Hickey LT.

Theor Appl Genet. 2019 Mar;132(3):555-557. doi: 10.1007/s00122-019-03321-4. Epub 2019 Mar 19. No abstract available.


InDel markers: An extended marker resource for molecular breeding in chickpea.

Jain A, Roorkiwal M, Kale S, Garg V, Yadala R, Varshney RK.

PLoS One. 2019 Mar 18;14(3):e0213999. doi: 10.1371/journal.pone.0213999. eCollection 2019.


Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.).

Yu B, Huai D, Huang L, Kang Y, Ren X, Chen Y, Zhou X, Luo H, Liu N, Chen W, Lei Y, Pandey MK, Sudini H, Varshney RK, Liao B, Jiang H.

BMC Genet. 2019 Mar 12;20(1):32. doi: 10.1186/s12863-019-0734-z.


Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

Yadav S, Sandhu N, Majumder RR, Dixit S, Kumar S, Singh SP, Mandal NP, Das SP, Yadaw RB, Singh VK, Sinha P, Varshney RK, Kumar A.

Sci Rep. 2019 Feb 22;9(1):2616. doi: 10.1038/s41598-019-39084-7.


Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains.

Abbai R, Singh VK, Nachimuthu VV, Sinha P, Selvaraj R, Vipparla AK, Singh AK, Singh UM, Varshney RK, Kumar A.

Plant Biotechnol J. 2019 Aug;17(8):1612-1622. doi: 10.1111/pbi.13087. Epub 2019 Feb 15.


Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.).

Mannur DM, Babbar A, Thudi M, Sabbavarapu MM, Roorkiwal M, Yeri SB, Bansal VP, Jayalakshmi SK, Singh Yadav S, Rathore A, Chamarthi SK, Mallikarjuna BP, Gaur PM, Varshney RK.

Mol Breed. 2019;39(1):2. doi: 10.1007/s11032-018-0908-9. Epub 2018 Dec 28.


Toward the sequence-based breeding in legumes in the post-genome sequencing era.

Varshney RK, Pandey MK, Bohra A, Singh VK, Thudi M, Saxena RK.

Theor Appl Genet. 2019 Mar;132(3):797-816. doi: 10.1007/s00122-018-3252-x. Epub 2018 Dec 17. Review.


Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.).

Luo H, Pandey MK, Khan AW, Guo J, Wu B, Cai Y, Huang L, Zhou X, Chen Y, Chen W, Liu N, Lei Y, Liao B, Varshney RK, Jiang H.

Plant Biotechnol J. 2019 Jul;17(7):1248-1260. doi: 10.1111/pbi.13050. Epub 2019 Jan 30.


Drought or/and Heat-Stress Effects on Seed Filling in Food Crops: Impacts on Functional Biochemistry, Seed Yields, and Nutritional Quality.

Sehgal A, Sita K, Siddique KHM, Kumar R, Bhogireddy S, Varshney RK, HanumanthaRao B, Nair RM, Prasad PVV, Nayyar H.

Front Plant Sci. 2018 Nov 27;9:1705. doi: 10.3389/fpls.2018.01705. eCollection 2018. Review.


Genotyping-by-sequencing based genetic mapping reveals large number of epistatic interactions for stem rot resistance in groundnut.

Dodia SM, Joshi B, Gangurde SS, Thirumalaisamy PP, Mishra GP, Narandrakumar D, Soni P, Rathnakumar AL, Dobaria JR, Sangh C, Chitikineni A, Chanda SV, Pandey MK, Varshney RK, Thankappan R.

Theor Appl Genet. 2019 Apr;132(4):1001-1016. doi: 10.1007/s00122-018-3255-7. Epub 2018 Dec 11.


Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.).

Shirasawa K, Bhat RS, Khedikar YP, Sujay V, Kolekar RM, Yeri SB, Sukruth M, Cholin S, Asha B, Pandey MK, Varshney RK, Gowda MVC.

Front Plant Sci. 2018 Nov 26;9:1727. doi: 10.3389/fpls.2018.01727. eCollection 2018.


Development and Application of High-Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes.

Saxena RK, Rathore A, Bohra A, Yadav P, Das RR, Khan AW, Singh VK, Chitikineni A, Singh IP, Kumar CVS, Saxena KB, Varshney RK.

Plant Genome. 2018 Nov;11(3). doi: 10.3835/plantgenome2018.01.0005.


Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.).

Khera P, Pandey MK, Mallikarjuna N, Sriswathi M, Roorkiwal M, Janila P, Sharma S, Shilpa K, Sudini H, Guo B, Varshney RK.

Mol Genet Genomics. 2019 Apr;294(2):365-378. doi: 10.1007/s00438-018-1511-9. Epub 2018 Nov 22.


Modelling predicts that soybean is poised to dominate crop production across Africa.

Foyer CH, Siddique KHM, Tai APK, Anders S, Fodor N, Wong FL, Ludidi N, Chapman MA, Ferguson BJ, Considine MJ, Zabel F, Prasad PVV, Varshney RK, Nguyen HT, Lam HM.

Plant Cell Environ. 2019 Jan;42(1):373-385. doi: 10.1111/pce.13466. Epub 2018 Nov 18.


Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.

Garg V, Khan AW, Kudapa H, Kale SM, Chitikineni A, Qiwei S, Sharma M, Li C, Zhang B, Xin L, Kishor PBK, Varshney RK.

Plant Biotechnol J. 2019 May;17(5):914-931. doi: 10.1111/pbi.13026. Epub 2018 Dec 1.


Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach).

Paudel D, Kannan B, Yang X, Harris-Shultz K, Thudi M, Varshney RK, Altpeter F, Wang J.

Sci Rep. 2018 Sep 26;8(1):14419. doi: 10.1038/s41598-018-32674-x.


Development of sequence-based markers for seed protein content in pigeonpea.

Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK.

Mol Genet Genomics. 2019 Feb;294(1):57-68. doi: 10.1007/s00438-018-1484-8. Epub 2018 Sep 1.


Corrigendum: Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis).

Lu Q, Li H, Hong Y, Zhang G, Wen S, Li X, Zhou G, Li S, Liu H, Liu H, Liu Z, Varshney RK, Chen X, Liang X.

Front Plant Sci. 2018 Jul 31;9:1099. doi: 10.3389/fpls.2018.01099. eCollection 2018.


Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.).

Wang X, Xu P, Yin L, Ren Y, Li S, Shi Y, Alcock TD, Xiong Q, Qian W, Chi X, Pandey MK, Varshney RK, Yuan M.

Plant Mol Biol Report. 2018;36(3):518-529. doi: 10.1007/s11105-018-1088-9. Epub 2018 Jun 23.


A western Sahara centre of domestication inferred from pearl millet genomes.

Burgarella C, Cubry P, Kane NA, Varshney RK, Mariac C, Liu X, Shi C, Thudi M, Couderc M, Xu X, Chitikineni A, Scarcelli N, Barnaud A, Rhoné B, Dupuy C, François O, Berthouly-Salazar C, Vigouroux Y.

Nat Ecol Evol. 2018 Sep;2(9):1377-1380. doi: 10.1038/s41559-018-0643-y. Epub 2018 Aug 6.


Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea.

Roorkiwal M, Jarquin D, Singh MK, Gaur PM, Bharadwaj C, Rathore A, Howard R, Srinivasan S, Jain A, Garg V, Kale S, Chitikineni A, Tripathi S, Jones E, Robbins KR, Crossa J, Varshney RK.

Sci Rep. 2018 Aug 3;8(1):11701. doi: 10.1038/s41598-018-30027-2.


Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee SH.

Plant Biotechnol J. 2019 Feb;17(2):517-530. doi: 10.1111/pbi.12995. Epub 2018 Sep 11.


Molecular Mapping of QTLs for Heat Tolerance in Chickpea.

Paul PJ, Samineni S, Thudi M, Sajja SB, Rathore A, Das RR, Khan AW, Chaturvedi SK, Lavanya GR, Varshney RK, Gaur PM.

Int J Mol Sci. 2018 Jul 25;19(8). pii: E2166. doi: 10.3390/ijms19082166.


RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.).

Mahdavi Mashaki K, Garg V, Nasrollahnezhad Ghomi AA, Kudapa H, Chitikineni A, Zaynali Nezhad K, Yamchi A, Soltanloo H, Varshney RK, Thudi M.

PLoS One. 2018 Jun 28;13(6):e0199774. doi: 10.1371/journal.pone.0199774. eCollection 2018.


Progress in understanding drought tolerance: from alleles to cropping systems.

Varshney RK, Tuberosa R, Tardieu F.

J Exp Bot. 2018 Jun 6;69(13):3175-3179. doi: 10.1093/jxb/ery187. No abstract available.


Breeding pigeonpea cultivars for intercropping: synthesis and strategies.

Saxena KB, Choudhary AK, Saxena RK, Varshney RK.

Breed Sci. 2018 Mar;68(2):159-167. doi: 10.1270/jsbbs.17105. Epub 2018 Apr 12. Review.


Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids.

Liang Z, Gupta SK, Yeh CT, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupta R, Yang J, Varshney RK, Schnable PS, Schnable JC.

G3 (Bethesda). 2018 Jul 2;8(7):2513-2522. doi: 10.1534/g3.118.200242.


Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis).

Lu Q, Li H, Hong Y, Zhang G, Wen S, Li X, Zhou G, Li S, Liu H, Liu H, Liu Z, Varshney RK, Chen X, Liang X.

Front Plant Sci. 2018 May 3;9:604. doi: 10.3389/fpls.2018.00604. eCollection 2018. Erratum in: Front Plant Sci. 2018 Jul 31;9:1099.


Genome-Wide Identification and Analysis of Arabidopsis Sodium Proton Antiporter (NHX) and Human Sodium Proton Exchanger (NHE) Homologs in Sorghum bicolor.

Hima Kumari P, Anil Kumar S, Ramesh K, Sudhakar Reddy P, Nagaraju M, Bhanu Prakash A, Shah T, Henderson A, Srivastava RK, Rajasheker G, Chitikineni A, Varshney RK, Rathnagiri P, Lakshmi Narasu M, Kavi Kishor PB.

Genes (Basel). 2018 May 3;9(5). pii: E236. doi: 10.3390/genes9050236.


Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.).

Saxena RK, Patel K, Sameer Kumar CV, Tyagi K, Saxena KB, Varshney RK.

Theor Appl Genet. 2018 Aug;131(8):1605-1614. doi: 10.1007/s00122-018-3101-y. Epub 2018 Apr 28.


Can genomics deliver climate-change ready crops?

Varshney RK, Singh VK, Kumar A, Powell W, Sorrells ME.

Curr Opin Plant Biol. 2018 Oct;45(Pt B):205-211. doi: 10.1016/j.pbi.2018.03.007. Epub 2018 Apr 21. Review.


High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut.

Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias-Akins P, Jackson SA, Varshney RK, Guo B.

Plant Biotechnol J. 2018 Nov;16(11):1954-1967. doi: 10.1111/pbi.12930. Epub 2018 May 15.


The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development.

Kudapa H, Garg V, Chitikineni A, Varshney RK.

Plant Cell Environ. 2018 Sep;41(9):2209-2225. doi: 10.1111/pce.13210. Epub 2018 May 16.


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