Groundnut Entered Post-genome Sequencing Era: Opportunities and Challenges in Translating Genomic Information from Genome to Field

  • Manish K. PandeyEmail author
  • Rajeev K. Varshney


Cultivated groundnut or peanut (Arachis hypogaea) is an allopolyploid crop with a large complex genome and genetic barrier for exchanging genetic diversity from its wild relatives due to ploidy differences. Optimum genetic and genomic resources are key for accelerating the process for trait mapping and gene discovery and deploying diagnostic markers in genomics-assisted breeding. The better utilization of different aspects of peanut biology such as genetics, genomics, transcriptomics, proteomics, epigenomics, metabolomics, and interactomics can be of great help to groundnut genetic improvement program across the globe. The availability of high-quality reference genome is core to all the “omics” approaches, and hence optimum genomic resources are a must for fully exploiting the potential of modern science into conventional breeding. In this context, groundnut is passing through a very critical and transformational phase by making available the required genetic and genomic resources such as reference genomes of progenitors, resequencing of diverse lines, transcriptome resources, germplasm diversity panel, and multi-parent genetic populations for conducting high-resolution trait mapping, identification of associated markers, and development of diagnostic markers for selected traits. Lastly, the available resources have been deployed in translating genomic information from genome to field by developing improved groundnut lines with enhanced resistance to root-knot nematode, rust, and late leaf spot and high oleic acid. In addition, the International Peanut Genome Initiative (IPGI) have made available the high-quality reference genome for cultivated tetraploid groundnut which will facilitate better utilization of genetic resources in groundnut improvement. In parallel, the development of high-density genotyping platforms, such as Axiom_Arachis array with 58 K SNPs, and constitution of training population will initiate the deployment of the modern breeding approach, genomic selection, for achieving higher genetic gains in less time with more precision.


Genomic resources Trait mapping Gene discovery Diagnostic markers Genomics-assisted breeding Molecular breeding products 



Financial support is acknowledged from the Peanut Foundation, MARS Inc., Bill & Melinda Gates Foundation (Tropical Legumes I, II, and III), National Agricultural Science Fund (NASF) of Indian Council of Agricultural Research (ICAR), Government of India, and World Bank Assisted Watershed Development Project II (KWDP-II) by Government of Karnataka, India. The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of the CGIAR.


  1. Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo AC, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimarães PM, Isobe S, Guo B, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R, Ozias-Akins (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446Google Scholar
  2. Chen Z, Wang ML, Barkley NA, Pittman RN (2010) A simple allele-specific PCR assay for detecting FAD2 alleles in both a and B genomes of the cultivated peanut for high-oleate trait selection. Plant Mol Biol Report 28:542–548CrossRefGoogle Scholar
  3. Chen X, Li H, Pandey MK, Yang Q, Wang X, Garg V, Li H, Chi X, Doddamani D, Hong Y, Upadhyaya HD, Guo H, Khan AW, Zhu F, Zhang X, Pan L, Pierce GJ, Zhou G, Krishnamohan KAVS, Chen M, Zhong N, Agarwal G, Li S, Chitikineni A, Zhang G, Sharma S, Chen N, Liu N, Janila P, Li S, Wang M, Wang T, Sun J, Li X, Li C, Wang M, Yu L, Wen S, Singh S, Yang Z, Zhao J, Zhang C, Yu Y, Bi J, Zhang X, Liu Z, Paterson AH, Wang S, Liang X, Varshney RK, Yu S (2016) Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis and allergens. Proc Natl Acad Sci USA 113(24):6785–6790CrossRefPubMedGoogle Scholar
  4. Chu Y, Holbrook CC, Timper P, Ozias-Akins P (2007) Development of a PCR-based molecular marker to select for nematode resistance in peanut. Crop Sci 47:841–847CrossRefGoogle Scholar
  5. Chu Y, Holbrook CC, Ozias-Akins P (2009) Two alleles of ahFAD2B control the high oleic acid trait in cultivated peanut. Crop Sci 49:2029–2036CrossRefGoogle Scholar
  6. Chu Y, Wu CL, Holbrook CC, Tillman BL, Person G, Ozias-Akins P (2011) Marker-assisted selection to pyramid nematode resistance and the high oleic trait in peanut. Plant Genome 4:8CrossRefGoogle Scholar
  7. Clevenger J, Chu Y, Scheffler B, Ozias-Akins P (2016) A developmental transcriptome map for allotetraploid Arachis hypogaea. Front Plant Sci 7:1446CrossRefPubMedCentralPubMedGoogle Scholar
  8. Clevenger J, Chu Y, Chavarro C, Agarwal G, Bertioli DJ, Leal-Bertioli SCM, Pandey MK, Vaughn J, Abernathy B, Barkley NA, Hovav R, Burow M, Nayak SN, Chitikineni A, Isleib TG, Holbrook CC, Jackson SA, Varshney RK, Ozias-Akins P (2017) Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut. Mol Plant 10:309–322CrossRefPubMedCentralPubMedGoogle Scholar
  9. Janila P, Pandey MK, Shasidhar Y, Variath MT, Sriswathi M, Khera P, Manohar SS, Nagesh P, Vishwakarma MK, Mishra GP, Radhakrishnan T, Manivannan N, Dobariya KL, Vasanthi RP, Varshney RK (2016a) Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes. Plant Sci 242:203–213CrossRefPubMedCentralPubMedGoogle Scholar
  10. Janila P, Pandey MK, Manohar SS, Variath MT, Premlatha N, Nadaf HL, Sudini HK, Bhat R, Manivannan N, Varshney RK (2016b) Foliar fungal disease resistant introgression lines of groundnut (Arachis hypogaea L.) record higher pod and haulm yield in multi-location testing. Plant Breed 135(3):355–366CrossRefGoogle Scholar
  11. Ozias-Akins P, Cannon EKS, Cannon SB (2017) Genomics resources for peanut improvement. In: Varshney RK, Pandey MK, Puppala N (eds) The peanut genome., ISBN 978-3-319-63935-2. Springer International Publishing AG, Cham, pp 69–92CrossRefGoogle Scholar
  12. Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK (2012) Advances in Arachis genomics for peanut improvement. Biotechnol Adv 30(3):639–651CrossRefPubMedCentralPubMedGoogle Scholar
  13. Pandey MK, Guo B, Holbrook CC, Janila P, Zhang X, Bertioli DJ, Isobe S, Liang X, Varshney RK (2014) Molecular markers, genetic maps, and QTLs for peanut molecular breeding. In: Mallikarjuna N, Varshney RK (eds) Genetics, genomics and breeding of peanuts. CRC Press, Taylor & Francis Group, Boca Raton, pp 79–113Google Scholar
  14. Pandey MK, Roorkiwal M, Singh V, Lingam A, Kudapa H, Thudi M, Chitikineni A, Rathore A, Varshney RK (2016) Emerging genomic tools for legume breeding: current status and future perspectives. Front Plant Sci 7:455PubMedPubMedCentralGoogle Scholar
  15. Pandey MK, Agarwal G, Kale SM, Clevenger J, Nayak SN, Sriswathi M, Chitikineni A, Chavarro C, Chen X, Upadhyaya HD, Vishwakarma MK, Leal-Bertioli S, Liang X, Bertioli DJ, Guo B, Jackson SA, Ozias-Akins P, Varshney RK (2017a) Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58K SNPs for accelerating genetics and breeding in groundnut. Sci Rep 7:40577CrossRefPubMedCentralPubMedGoogle Scholar
  16. Pandey MK, Khan AW, Singh VK, Vishwakarma MK, Shasidhar Y, Kumar V, Garg V, Bhat RS, Chitikineni A, Janila P, Guo B, Varshney RK (2017b) QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnol J 15(8):927–941CrossRefPubMedCentralPubMedGoogle Scholar
  17. Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK (2012) Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 32(2):773–788CrossRefGoogle Scholar
  18. Variath MT, Janila P (2017) Economic and academic importance of peanut. In: Varshney RK, Pandey MK, Puppala N (eds) The peanut genome., ISBN 978-3-319-63935-2. Springer International Publishing AG, Cham, pp 7–26CrossRefGoogle Scholar
  19. Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar S, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Anuradha G, Babbar A, Chaudhary AK, Mhase MB, Bharadwaj CH, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL (2013) Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 31:1120–1134CrossRefPubMedGoogle Scholar
  20. Varshney RK, Pandey MK, Janila P, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishnan T, Manohar SS, Nagesh P (2014a) Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor Appl Genet 127(8):1771–1781CrossRefPubMedCentralPubMedGoogle Scholar
  21. Varshney RK, Terauchi R, McCouch SR (2014b) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12(6):e1001883CrossRefPubMedCentralPubMedGoogle Scholar
  22. Varshney RK, Pandey MK, Puppala N (2017) Future prospects for peanut improvement. In: Varshney RK, Pandey MK, Puppala N (eds) The peanut genome., ISBN 978-3-319-63935-2. Springer International Publishing AG, Cham, pp 150–165CrossRefGoogle Scholar
  23. Varshney RK, Thudi M, Pandey MK, Tardieu F, Ojiewo C, Vadez V, Whitbread AM, Siddique KHM, Nguyen HT, Carberry PS, Bergvinson D (2018) Accelerating genetic gains in legumes for prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. J Exp Bot
  24. Vishwakarma MK, Nayak SN, Guo B, Wan L, Liao B, Varshney RK, Pandey MK (2017a) Classical and molecular approaches for mapping of genes and quantitative trait loci in peanut (Arachis hypogaea L.). In: Varshney RK, Pandey MK, Puppala N (eds) The peanut genome., ISBN 978-3-319-63935-2. Springer International Publishing AG, Cham, pp 93–116CrossRefGoogle Scholar
  25. Vishwakarma MK, Kale SM, Sriswathi M, Naresh T, Shasidhar Y, Garg V, Pandey MK, Varshney RK (2017b) Genome-wide discovery and deployment of insertions and deletions markers provided greater insights on species, genomes, and sections relationships in the genus Arachis. Front Plant Sci 8:2064CrossRefPubMedCentralPubMedGoogle Scholar
  26. Wang H, Guo X, Pandey MK, Ji X, Varshney RK, Nwosou V, Guo B (2017) History and impact of the International Peanut Genome Initiative: the exciting journey toward peanut whole genome sequencing. In “The Peanut Genome” (eds RK Varshney, MK Pandey and N Puppala), ISBN 978-3-319-63935-2Google Scholar
  27. Zhao C, Qiu J, Agarwal G, Wang J, Ren X, Xia H, Guo B, Ma C, Wan S, Bertioli DJ, Varshney RK, Pandey MK, Wang X (2017) Genome-wide discovery of microsatellite markers from diploid progenitor species, Arachis duranensis and A. ipaensis, and their application in cultivated peanut (A. hypogaea). Front Plant Sci 8:1209CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)HyderabadIndia

Personalised recommendations