Single nucleotide polymorphism-based genetic diversity in the reference set of peanut (Arachis spp.) by developing and applying cost-effective kompetitive allele specific polymerase chain reaction genotyping assays

Plant Genome

Volumn 6, Issue 3, 2013, Pages 10-

  Khera, Pawan ^a   Upadhyaya, Hari D ^a   Pandey, Manish K ^a   Roorkiwal, Manish ^a   Sriswathi, Manda ^a   Janila, Pasupuleti ^a   Guo, Yufang ^b,c   McKain, Michael R ^b   Nagy, Ervin D ^b   Knapp, Steven J ^b   Leebens Mack, James ^b   Conner, Joann A ^c   Ozias Akins, Peggy ^c   Varshney, Rajeev K ^a,d  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d NONE   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890768974     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2013.06.0019     Document Type: Article

References (44)

1. Alves, D.M.T., R.W. Pereira, S.C. Leal-Bertioli, M.C. Moretzsohn, P.M. Guimarães, and D.J. Bertioli. 2008. Development and use of single nucleotide polymorphism markers for candidate resistance genes in wild peanuts (Arachis spp). Genet. Mol. Res. 7:631-642. doi:10.4238/vol7-3gmr453.
2. Bravo, J.P., A.A. Hoshino, C. Angelici, C.R. Lopes, and M.A. Gimenes. 2006. Transferability and use of microsatellite markers for the genetic analysis of the germplasm of some Arachis section species of the genus Arachis. Genet. Mol. Biol. 29:516-524. doi:10.1590/S1415-47572006000300021.
3. Chen, X., W. Zhu, S. Azam, H. Li, F. Zhu, H. Li, Y. Hong, H. Liu, E. Zhang, H. Wu, S. Yu, G. Zhou, S. Li, N. Zhong, S. Wen, X. Li, S.J. Knapp, P. Ozias-Akins, R.K. Varshney, and X. Liang. 2013. Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotech. J. 11: 115-127.
4. Cuc, L.M., E.S. Mace, J.H. Crouch, V.D. Quang, T.D. Long, and R.K. Varshney. 2008. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea L.). BMC Plant Biol. 8:55. doi:10.1186/1471-2229-8-55.
5. Dwivedi, S.L., S. Gurtu, S. Chandra, W. Yuejin, and S.N. Nigam. 2001. Assessment of genetic diversity among selected groundnut germplasm I: RAPD analysis. Plant Breed. 120:345-349. doi:10.1046/j.1439-0523.2001.00613.x.
6. Gautami, B., K. Ravi, M. LakshimiNarasu, D.A. Hoisington, and R.K. Varshney. 2009. Novel set of groundnut SSR markers for germplasm analysis and interspecific transferability. Int. J. Integr. Biol. 7:100-106.
7. Guo, Y., S. Khanal, S. Tang, J.E. Bowers, A.F. Heesacker, N. Khalilian, E.D. Nagy, D. Zhang, C.A. Taylor, H.T. Stalker, P. Ozias-Akins, and S.J. Knapp. 2012. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A-and B-genome diploid species of peanut. BMC Genomics 13:608. doi:10.1186/1471-2164-13-608.
8. Gupta, P.K., and R.K. Varshney. 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163-185. doi:10.1023/A:1003910819967.
9. He, G., and S.H. Prakash. 2001. Evaluation of genetic relationship among botanical varieties of cultivated peanut (Arachis hypogaea L.) using AFLP markers. Genet. Resour. Crop Evol. 48:347-352. doi:10.1023/A:1012019600318.
10. Herselman, L. 2003. Genetic variation among southern African cultivated peanut (Arachis hypogaea L.) genotypes as revealed by AFLP analysis. Euphytica 133:319-327. doi:10.1023/A:1025769212187.
11. Hilu, K.W., and H.T. Stalker. 1995. Genetic relationship between peanuts and wild species of Arachis section Arachis: Evidence from RAPD. Plant Syst. Evol. 198:167-178. doi:10.1007/BF00984735.
12. Hiremath, P.J., A. Kumar, R.V. Penmetsa, A. Farmer, J.A. Schlueter, K. Siva, A.M. Whaley, N. Carrasquilla-Garcia, P.M. Gaur, H.D. Upadhyaya, P.B.K. Kishor, T.M. Shah, D.R. Cook, and R.K. Varshney. 2012. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol. J. 10:716-732. doi:10.1111/j.1467-7652.2012.00710.x.
13. Holbrook, C.C., and H.T. Stalker. 2003. Peanut breeding and genetic resources. Plant Breed. Rev. 22:297-356.
14. Huson, D.H., D.C. Richter, C. Rausch, T. Dezulian, M. Franz, and R. Rupp. 2007. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinf. 8:460. doi:10.1186/1471-2105-8-460.
15. Kochert, G., H.T. Stalker, M. Gimenes, L. Galgaro, and K. Moore. 1996. RFLP and cytogenetic evidence for the progenitor species of allotetraploid cultivated peanut (Arachis hypogaea L.). Am. J. Bot. 83:1282-1291. doi:10.2307/2446112.
16. Koppolu, R., U. Hari, D. Sangam, H. David, and R.K. Varshney. 2010. Genetic relationships among seven sections of genus Arachis studied by using SSR markers. BMC Plant Biol. 10:15. doi:10.1186/1471-2229-10-15.
17. Kottapalli, K.R., M.D. Burow, G. Burow, J. Burke, and N. Puppala. 2007. Molecular characterization of the U.S. peanut mini core collection using microsatellite markers. Crop Sci. 47:1718-1727. doi:10.2135/cropsci2006.06.0407.
18. LGC Genomics. 2013. SNPviewer. SNPviewer. LGC Limited, Teddington, UK. http://www.lgcgenomics.com/services/instruments-andsoftware/software/?id=78 (accessed 3 Mar. 2013).
19. Liu, K., and S. V. Muse. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129. doi:10.1093/bioinformatics/bti282.
20. Mallikarjuna, N., S. Senthilvel, and D. Hoisington. 2011. Development of new sources of tetraploid Arachis to broaden the genetic base of cultivated groundnut (Arachis hypogaea L.). Genet. Resour. Crop Evol. 58:889-907. doi:10.1007/s10722-010-9627-8.
21. Mammadov, J., W. Chen, J. Mingus, S. Thompson, and S. Kumpatla. 2011. Development of versatile gene based SNP assays in maize (Zea mays L.). Mol. Breed. 3:779-790.
22. Mir, R.R., P.J. Hiremath, O. Riera-Lizarazu, and R.K. Varshney. 2013. Evolving molecular marker technologies in plants: From RFLPs to GBS. In: T. Lübberstedt and R.K. Varshney, editors, Diagnostics in plant breeding. Springer, Dordrecht, Netherlands. p. 229-247.
23. Moretzsohn, M.C., E.G. Gouves, P.W. Inglis, S.C.M. Leal-Bertioli, J.F.M. Valls, and D.J. Bertioli. 2013. A study of the relationships of cultivated peanut (Arachis hypogaea L.) and its most closely related wild species using intron sequences and microsatellite markers. Ann. Bot. (London) 111:113-126. doi:10.1093/aob/mcs237.
24. Moretzsohn, M.C., M.S. Hopkins, S.E. Mitchell, S. Kresovich, J.F.M. Valls, and M.E. Ferreira. 2004. Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hyper variable regions of the genome. BMC Plant Biol. 4:11. doi:10.1186/1471-2229-4-11.
25. Nagy, E.D., Y. Guo, S. Tang, J.E. Bowers, R.A. Okashah, C.A. Taylor, D. Zhang, S. Khanal, A.F. Heesacker, N. Khalilian, A.D. Farmer, N. Carrasquilla-Garcia, R.V. Penmetsa, D. Cook, H.T. Stalker, N. Nielsen, P. Ozias-Akins, and S.J. Knapp. 2012. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics 13:469. doi:10.1186/1471-2164-13-469.
26. Neelam, K., G. Brown-Guedira, and L. Huang. 2013. Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21. Mol. Breed. 31:233-237. doi:10.1007/s11032-012-9773-0.
27. Pandey, M.K., E.S. Monyo, P. Ozias-Akins, X. Liang, P. Guimarães, S.N. Nigam, H.D. Upadhyaya, P. Janila, X. Zhang, B. Guo, D.R. Cook, D.J. Bertioli, R. Michelmore, and R.K. Varshney. 2012. Advances in Arachis genomics for peanut improvement. J. Biotechnol. Adv. 30:639-651. doi:10.1016/j.biotechadv.2011.11.001.
28. Perrier, X., and J.P. Jacquemoud-Collet. 2006. DARwin software. Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Paris, France. http://darwin.cirad.fr/(accessed 17 Apr. 2013).
29. Podder, M., J. Ruan, B.W. Tripp, Z.E. Chu, and S.J. Tebbutt. 2008. Robust SNP genotyping by multiplex PCR and arrayed primer extension. BMC Med. Genet. 1:5.
30. Ragoussis, J. 2009. Genotyping technologies for genetic research. Annu. Rev. Genomics Hum. Genet. 10:117-133. doi:10.1146/annurevgenom-082908-150116.
31. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
32. Sauer, S., D. Lechner, K. Berlin, C. Plançon, A. Heuermann, and H. Lehrach. 2000. Full flexibility genotyping of single nucleotide polymorphisms by the good assay. Nucleic Acids Res. 28:E100. doi:10.1093/nar/28.23.e100.
33. Saxena, R.K., R.V. Penmetsa, H.D. Upadhyaya, A. Kumar, N.C. Garcia, J.A. Schlueter, A. Farmer, A.M. Whaley, B.K. Sarma, G.D. May, D.R. Cook, and R.K. Varshney. 2012. Large-scale development of costeffective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res. 19:449-461. doi:10.1093/dnares/dss025.
34. Semagn, K., R. Babu, S. Hearne, and M. Olsen. 2013. Single nucleotide polymorphism genotyping using Kompetitive allele specific PCR (KASP): Overview of the technology and its application in crop improvement. Mol. Bred. doi:10.1007/s11032-013-9917-x.
35. Subramanian, V., S. Gurtu, R.C. Nageswara Rao, and S.N. Nigam. 2000. Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome 43:656-660. doi:10.1139/g00-034.
36. Thudi, M., A. Bohra, S.N. Nayak, N. Varghese, T.M. Shah, R.V. Penmetsa, N. Thirunavukkarasu, S. Gudipati, P.M. Gaur, P.L. Kulwal, H.D. Upadhyaya, P.B.K. Kishor, P. Winter, G. Kahl, C.D. Town, A. Kilian, D.R. Cook, and R.K. Varshney. 2011. Novel SSR markers from BAC-End sequences, DArT arrays and a comprehensive genetic map with 1291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6:e27275. doi:10.1371/journal.pone.0027275.
37. Upadhyaya, H.D., P.J. Bramel, R. Ortiz, and S. Singh. 2002. Developing a mini core of peanut for utilization of genetic resources. Crop Sci. 42:2150-2156. doi:10.2135/cropsci2002.2150.
38. Upadhyaya, H.D., R. Ortiz, P.J. Bramel, and S. Singh. 2003. Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genet. Resour. Crop Evol. 50:139-148. doi:10.1023/A:1022945715628.
39. Upadhyaya, H.D., D. Yadav, N. Dronavalli, C.L.L. Gowda, and S. Singh. 2010. Mini core germplasm collections for infusing genetic diversity in plant breeding programs. Electron. J. Plant Breed. 1:1294-1309.
40. Varshney, R.K., H. Kudapa, M. Roorkiwal, M. Thudi, M.K. Pandey, R.K. Saxena, S.K. Chamarthi, S. Murali Mohan, N. Mallikarjun, H.D. Upadhyaya, P.M. Gaur, L. Krishnamurthy, K.B. Saxena, S.N. Nigam, and S. Pande. 2012. Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J. Biosci. 37:811-820. doi:10.1007/s12038-012-9228-0.
41. Varshney, R.K., T. Mahendar, R. Aruna, S.N. Nigam, K. Neelima, and V. Vadez. 2009a. High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers. Plant Breed. 128:486-494. doi:10.1111/j.1439-0523.2009.01638.x.
42. Varshney, R.K., S. Murali Mohan, P.M. Gaur, N.V.P.R. Gangarao, M.K. Pandey, A. Bohra, S.L. Sawargaonkar, A. Chitikineni, P.K. Kimurto, P. Janila, K.B. Saxena, A. Fikre, M. Sharma, A. Rathore, A. Pratap, S. Tripathi, S. Datta, S.K. Chaturvedi, N. Mallikarjuna, G. Anuradha, A. Babbar, A.K. Choudhary, M.B. Mhase, Ch. Bharadwaj, D.M. Mannur, P.N. Harer, B. Guo, X. Liang, N. Nadarajan, and C.L.L. Gowda. 2013. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol. Adv. doi:10.1016/j.biotechadv.2013.01.001.
43. Varshney, R.K., S.N. Nayak, G.D. May, and S.A. Jackson. 2009b. Nextgeneration sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27:522-530. doi:10.1016/j. tibtech.2009.05.006.
44. Yang, S.Y., R.K. Saxena, P.L. Kulwal, G.J. Ash, A. Dubey, J.D.I. Harper, H.D. Upadhaya, R. Gothalwal, A. Kilian, and R.K. Varshney. 2011. The first genetic map of pigeonpea based on diversity arrays technology (DArT) markers. J. Genet. 90:103-109. doi:10.1007/s12041-011-0050-5.