Loading...

Legume Research

Molecular markers and genomic resources for disease resistance in peanut-A review

DOI: 10.18805/LR-409    | Article Id: LR-409 | Page : 137-144
Citation :- Molecular markers and genomic resources for disease resistance in peanut-A review.Legume Research.2019.(42):137-144
Divya Choudhary, Gaurav Agarwal, Hui Wang, Manish K. Pandey, Albert K. Culbreath, Rajeev K. Varshney and Baozhu Guo Baozhu.Guo@ars.usda.gov
Address : USDA-Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA, 31793, USA.
Submitted Date : 13-02-2018
Accepted Date : 28-06-2018
First Online:

Abstract

Recent polyploidation of peanut genome and geographical isolation has rendered peanut to be a highly monomorphic species. Due to its narrow genetic base, cultivated peanut has been susceptible to various diseases, causing economic loss to farmers. Availability of only a few disease resistance sources in cultivated peanut has resulted in limited success using the conventional breeding practices. Also, scarcity of markers has been the major limiting factor to precisely identify the disease resistance genomic regions. Recent identification of large number of molecular markers using advanced genomic resources and high throughput sequencing technologies has and will continue to assist in improvement of peanut diversity and breeding. This review gives an update on recent discovery of molecular markers associated with major diseases and the available genomic resources in peanut.

Keywords

Diseases Genetic Markers Genomics QTL

References

  1. Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H. et al. (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnol. 30:174-178.
  2. Agarwal, G., Clevenger, J., Pandey, M.K., Wang, H., Shasidhar, Y., Chu, Y., Fountain, J.C., Choudhary, D., Culbreath, A.K., Liu, X., Huang, G., Wang, X., Deshmukh, R., Holbrook, C.C., Bertioli, D.J., Ozias-Akins, P., Jackson, S.A., Varshney, R.K., Guo, B. (2018). High€ density genetic map using whole€ genome re€ sequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnol. J. doi.org/10.1111/pbi.12930.
  3. Baltensperger, D.D., Dunn, R.A., Prine, G.M. (1986). Root-knot nematode resistance in Arachis glabrata. Peanut Sci.13:78-80.
  4. Bertioli, D.J., Cannon, S.B., Froenicke, L., Huang, G., Farmer, A.D., Cannon, E.K.S., Liu, X. et al. (2016). The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genet. 48:438-446. 
  5. Bertioli, D.J., Leal-Bertioli, S.C.M., Lion, M.B., Santos, V.L., Pappas, G.J., Cannon, S.B., Guimaraes, P.M. (2003). A large scale analysis of resistance gene homologues in Arachis. Mol. Genet. Genomics.270:34-45.
  6. Bosamia, T.C., Mishra, G.P., Radhakrishnan, T., Dobaria, J.R. (2015). Novel and stress relevant EST derived SSR markers developed and validated in peanut. PLoS One.10: e0129127. doi.org/10.1371/journal.pone.0129127
  7. Burow, M.D., Simpson, C.E., Paterson, A.H., Starr, J.L. (1996). Identification of peanut (Arachis hypogaea L.) RAPD markers diagnostic of root-knot nematode (Meloidogyne arenaria (Neal) Chitwood) resistance. Mol. Breed. 2:369-379.
  8. Burow, M.D., Simpson, C.E., Starr, J.L., Paterson, A.H. (2001). Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genet. 159:823-837.
  9. Chen, X., Li, H., Pandey, M.K., Yang, Q., Wang, X., Garg, V., Li, H. et al. (2016). Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proc. Nat. Acad. Sci. U.S.A.113:6785-6790.
  10. Choi, K., Burow, M.D., Church, G., Burow, G., Paterson, A.H., Simpson, C.E., Starr, J.L. (1999). Genetics and mechanism of resistance to Meloidogyne arenaria in peanut germplasm. J. Nematol. 31:283-290.
  11. Chu, Y., Wu, C.L., Holbrook, C.C., Tillman, B.L., Person, G., Ozias-Akins, P. (2011). Marker-assisted selection to pyramid nematode resistance and the high oleic trait in peanut. Plant Genome. 4:110-117.
  12. Church, G.T., Simpson, C.E., Burow, M.D., Paterson, A.H., Starr, J.L. (2000). Use of RFLP markers for identification of individuals homozygous for resistance to Meloidogyne arenaria in peanut. Nematol. 2:575-580.
  13. Clevenger, J., Chu, Y., Chavarro, C., Agarwal, G., Bertioli, D.J., Leal-Bertioli, S.C.M. Pandey, M.K. et al. (2017). Genome-wide SNP genotyping resolves signatures of selection and tetrasomic recombination in peanut. Mol. Plant. 10:309-322.
  14. Food Agriculture Organization of United Nations (2014). Available online at: http://faostat.fao.org/DesktopDefault.aspx?PageID=339
  15. Fu, G., Zhong, Y., Li, C., Li, Y., Lin, X., Liao, B., Tsang, E.W. et al. (2010). Epigenetic regulation of peanut allergen gene Arah3 in developing embryos. Planta. 231:1049-1060.
  16. Garcia, G.M., Stalker, H.T., Shroeder, E., Kochert, G. (1996). Identification of RAPD, SCAR and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea. Genome.39:836-845.
  17. Guo, B., Chen, X., Dang, P., Scully, B.T., Liang, X., Holbrook, C.C., Yu, J., Culbreath, A.K. (2008). Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection. BMC Dev. Biol.8:12.
  18. Guo, B., Chen, X., Hong, Y., Liang, X., Dang, P., Brenneman, T., Holbrook, C.C., Culbreath, A.K. (2009). Analysis of gene expression profiles in leaf tissues of cultivated peanuts and development of EST-SSR markers and gene discovery. Int. J. Plant Genomics. 2009. doi.org/10.1155/2009/715605
  19. Hilu, K.W. and Stalker, H.T. (1995).Genetic relationships between peanut and wild species of Arachis sect. Arachis (Fabaceae): evidence from RAPDs. Plant Syst.Evol. 198:167-178.
  20. Holbrook, C.C. and Dong, W. (2005). Development and evaluation of a mini core collection for the U.S. peanut germplasm collection. Crop Sci. 45:1540-1544.
  21. Holbrook, C.C., Anderson, W.F., Pittman, R.N. (1993). Selection of a core collection from the United States germplasm collection of peanut. Crop Sci. 33:859-861.
  22. Holbrook, C.C., Isleib, T.G., Ozias-Akins, P., Chu, Y., Knapp, S.J., Tillman, B., Guo, B., Gill, R., Burow, M.D. (2013). Development and phenotyping of recombinant inbred line (RIL) populations for peanut (Arachis hypogaea). Peanut Sci. 40:89-94.
  23. Holbrook, C.C., Timper, P., Culbreath, A.K., Kvien, C.K. (2008). Registration of ‘Tifguard’peanut. J. Plant Regist. 2:92-94.
  24. Huang, B.E., Verbyla, K.L., Verbyla, A.P., Raghavan, C., Singh, V.K., Gaur, P., Leung, H. et al. (2015). MAGIC populations in crops: current status and future prospects. Theor. Appl. Genet. 128: 999-1017.
  25. Jiang, H.F., Ren, X.P., Liao, B.S., Huang, J.Q., Lei, Y., Chen, B.Y., Guo, B.Z., Holbrook, C.C., Upadhyaya, H.D. (2008).Peanut core collection established in china and compared with ICRISAT mini core collection. Acta Agronomica Sinica. 34:25-30. 
  26. Jiang, H.F., Ren, X.P., Zhang, X.J., Huang, J.Q., Lei, Y., Yan, L.Y., Liao, B.S., Upadhyaya H.D., Holbrook, C.C.(2010). Comparison of genetic diversity based on SSR markers between peanut mini core collections from China and ICRISAT. Acta Agronomica Sinica. 36:1084-1091.
  27. Jiang, H., Ren, X., Chen, Y., Huang, L., Zhou, X., Huang, J., Froenicke, L. et al. (2012). Phenotypic evaluation of the Chinese mini-    core collection of peanut (Arachis hypogaea L.) and assessment for resistance to bacterial wilt disease cause by Ralstonia solanacearum. Plant Genet. Resour. 11: 77-83. 
  28. Khedikar, Y.P., Gowda, M.V., Sarvamangala, C., Patgar, K.V., Upadhyaya, H.D., Varshney, R.K. (2010). A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 121:971-984.
  29. Khera, P., Pandey, M.K., Wang, H., Feng, S., Qiao, L., Culbreath, A.K., Kale, S. et al. (2016). Mapping quantitative trait loci of resistance to tomato spotted wilt virus and leaf spots in a recombinant inbred line population of peanut (Arachis hypogaea L.) from SunOleic 97R and NC94022. PLoS One. 11: e0158452. doi.org/10.1371/journal.pone.0158452
  30. Knoll, J.E., Ramos, M.L., Zeng, Y., Holbrook, C.C., Chow, M., Chen, S., Maleki, S., Bhattacharya, A., Ozias-Akins, P. (2011). TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol. 11:81.
  31. Kochert, G., Halward, T., Branch, W.D., Simpson, C.E. (1991). RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor. Appl. Genet. 81:565-570.
  32. Kolekar, R.M., Sujay, V., Shirasawa, K., Sukruth, M., Khedikar, Y.P., Gowdan, M.V.C. (2016). QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.). Euphytica. 209:147-156.
  33. Kooke, R., Johannes, F., Wardenaar, R., Becker, F., Etcheverry, M., Colot, V., Vreugdenhil, D., Keurentjes, J.J. (2015). Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. Plant Cell. 27:337-348.
  34. Krishna, G., Singh, B.K., Kim, E.K., Morya, V.K., Ramteke, P.W. (2015). Progress in genetic engineering of peanut (Arachis hypogaea L.) - A review. Plant Biotechnol. J. 13:147-162. 
  35. Leal-Bertioli, S.C.M., Cavalcante, U., Gouvea, E.G., Ballén-Taborda, C., Shirasawa, K., Guimarães, P.M., Jackson, S.A. et al. (2015). Identification of QTLs for rust resistance in the peanut wild species Arachis magna and the development of KASP markers for marker-assisted selection. G3: Genes, Genomes, Genet. 5:1403-1413.
  36. Leal-Bertioli, S.C.M., José, A.C., Alves-Freitas, D.M., Moretzsohn, M.C., Guimarães, P.M., Nielen, S., Vidigal, B.S. et al. (2009). Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biol. 9:112.
  37. Leal-Bertioli, S.C.M., Moretzsohn, M.C., Roberts, P.A., Ballén-Taborda, C., Borba, T.C., Valdisser, P.A., Vianello, R.P. et al. (2016). Genetic mapping of resistance to Meloidogyne arenaria in Arachis stenosperma: a new source of nematode resistance for peanut. G3: Genes, Genomes, Genet. 6:377-390.
  38. Liu, S., Yeh, C.T., Tang, H.M., Nettleton, D., Schnable, P.S. (2012). Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One.7: e36406. doi.org/10.1371/journal.pone.0036406
  39. Milla, S.R., Isleib, T.G., Stalker, H.T. (2005).Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers. Genome. 48:1-11.
  40. Mishra, G.P., Radhakrishnan, T., Kumar, A., Thirumalaisamy, P.P., Kumar,N., Bosamia, T.C., Nawade, B., Dobaria, J.R. (2015). Advancements in molecular marker development and their applications in the management of biotic stresses in peanuts. Crop Prot. 77:74-86.
  41. Mondal, S., Badigannavar, A.M., D’Souza S.F. (2012a). Molecular tagging of a rust resistance gene in cultivated groundnut (Arachis hypogaea L.) introgressed from Arachis cardenasii. Mol. Breed. 29:467-476.
  42. Mondal, S., Badigannavar, A.M., D’Souza, S.F. (2012b). Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Euphytica. 188:163-173. 
  43. Nagy, E.D., Guo, Y., Tang, S. Bowers, J.E., Okashah, R.A., C.A., Taylor, Zhang, D., Khanal, S.A., Heesacker, F., Khalilian, N., Farmer, A.D. (2012). A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics.13:469. 
  44. Nelson, S.C., Simpson, C.E., Starr, J.L. (1990). Expression of resistance to Meloidogyne arenaria in Arachis batizocoi and A. cardenasii. J. Nematol. 22:242-244.
  45. Nugrahaeni, N. and Rahayu, M. (2017). Peanut introduced germplasm response against Ralstonia bacterial wilt disease. Nusantara Biosci. 9:138-140.
  46. Pandey, M.K., Wang, H., Khera, P., Vishwakarma, M.K., Kale, S., Culbreath, A.K., Holbrook, C.C. et al. (2017a). Genetic dissection of novel QTLs for resistance to leaf spots and tomato spotted wilt virus in peanut (Arachis hypogaea L). Front. Plant Sci. 8:25.
  47. Pandey, M.K., Khan, A.W., Singh, V.K., Vishwakarma, M.K., Shasidhar, Y., Kumar, V., Garg, V. et al. (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. 
  48. Pandey, M.K., Agarwal, G., Kale, S.M., Clevenger, J., Nayak, S.N., Sriswathi, M., Chitikineni, A. et al. (2017c). Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut. Sci. Rep. 7: 40577. doi: 10.1038/srep40577.
  49. Pandey, M.K., Monyo, E., Ozias-Akins, P., Liang, X., Guimarães, P., Nigam, S.N., Upadhyaya, H.D. et al. (2012). Advances in Arachis genomics for peanut improvement. Biotechnol. Adv. 30:639-651.
  50. Pandey, M.K., Roorkiwal, M., Singh, V.K., Ramalingam, A., Kudapa, H., Thudi, M., Chitikineni, A. et al. (2016). Emerging genomic tools for legume breeding: current status and future prospects. Front. Plant Sci. 7:455.
  51. Proite, K., Leal-Bertioli, S.C.M., Bertioli, D.J., Moretzsohn, M.C., da Silva, F.R., Martins, N.F., Guimarães, P.M. (2007). ESTs from a wild Arachis species for gene discovery and marker development. BMC Plant Biol. 7:7. doi.org/10.1186/1471-2229-7-7.
  52. Qin, H., Feng, S., Chen, C., Guo, Y., Knapp, S., Culbreath, A., He, G. et al. (2012). An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. Theor. Appl. Genet. 124:653-664.
  53. Sarkar, T., Radhakrishnan, T., Kumar, A., Mishra, G.P., Dobaria, J.R. (2014). Heterologous expression of the AtDREB1A gene in transgenic peanut-conferred tolerance to drought and salinity stresses. PLoS One. 9:e110507. doi.org/10.1371/journal.pone.    0110507.
  54. Simpson, C.E. (1991). Pathways for introgression of pest resistance into Arachis hypogaea L. Peanut Sci. 18:22-26.
  55. Simpson, C.E. and Starr, J.L. (2001). Registration of COAN peanut. Crop Sci. 41:918.
  56. Simpson, C.E., Nelson, S.C. Starr, J.L., Woodard, K.E., Smith, O.D. (1993). Registration of TxAG-6 and TxAG-7 peanut germplasm lines. Crop Sci. 33:1418-1418.
  57. Simpson, C.E., Starr, J.L., Baring, M.R., Burow, M.D., Cason, J.M., Wilson, J.N. (2013). Registration of ‘Webb’ peanut. J Plant Regist.7:265-268.
  58. Simpson, C.E., Starr, J.L., Church, G.T., Burow, M.D., Paterson, A.H. (2003). Registration of ‘NemaTAM’ peanut. (Registrations of Cultivars). Crop Sci. 43:1561-1562.
  59. Stalker, H.T., Beute, M.K., Shew, B.B., Barker, K.R. (2002). Registration of two root-knot nematode-resistant peanut germplasm lines. (Registrations of Germplasm). Crop Sci. 42:312-314.
  60. Sujay, V., Gowda, M.V.C., Pandey, M.K., Bhat, R.S., Khedikar, Y.P., Nadaf, H.L., Gautami, B. et al. (2012). QTL analysis and construction of consensus genetic map for foliar diseases resistance based on two RIL populations in cultivated groundnut (Arachis hypogaea L.). Mol. Breed. 32:773-788. 
  61. Sumarno. (2007). Toward plant germplasm management equitable and useful. Zuriat. 18:63-68.
  62. Tseng, Y.C., Tillman, B.L., Peng, Z., Wang, J. (2016). Identification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar Florida-EP TM ‘113’. BMC Genet. 17:128.
  63. Upadhyaya, H.D., Bramel, P.J., Ortiz, R., Singh, S. (2002). Developing a mini core of peanut for utilization of genetic resources. Crop Sci. 42:2150-2156.
  64. Upadhyaya, H.D., Ortiz, R., Bramel, P.J., Singh, S. (2003). Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genet. Resour. Crop Evol. 50: 139-148.
  65. Varshney, R.K., Pandey, M.K., Janila, P., Nigam, S.N., Sudini, H., Gowda, M.V.C., Sriswathi, M. et al. (2014). 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. 127:1771-1781.
  66. Wang, H., Pandey, M.K., Qiao, L., Qin, H., Culbreath, A.K., He, G., Varshney, R.K. et al. (2013). Genetic mapping and quantitative trait loci analysis for disease resistance using F and F Generation–based Genetic Maps Derived from ‘Tifrunner’בGT–C20’ in peanut. The Plant Genome.6. doi: 10.3835/plantgenome2013.05.0018.
  67. Yu, J., Holland, J.B., McMullen, M.D., Buckler, E.S. (2008). Genetic design and statistical power of nested association mapping in maize. Genet. 178:539-551. 

Global Footprints