The Peanut Genome: The History of the Consortium and the Structure of the Genome of Cultivated Peanut and Its Diploid Ancestors

Peanuts: Genetics, Processing, and Utilization

Volumn , Issue , 2016, Pages 147-161

  Bertioli, David J ^a,b   Leal Bertioli, Soraya C ^b,c   Thomas Stalker, H ^d  

^a UNIVERSITY OF BRASILIA   (Brazil)

^b UNIVERSITY OF GEORGIA   (United States)

^c EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^d NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

Evolution; Genomes; Peanut consortium; Sequencing; Species

Indexed keywords

EID: 84966783564     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-1-63067-038-2.00005-8     Document Type: Chapter

References (77)

1. Adams K.L., Wendel J.F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 2005, 8:135-141.
2. Bertioli D.J., Araujo A.C.G., Nielen S., Heslop-Harrison P., Guimarães P.M., Schwarzacher T., Isobe S., Shirasawa K., Leal-Bertioli S.C.M. An overview of peanut genome structure. Genetics, Genomics and Breeding of Peanuts 2014, 266p. CRC Press, Boca Raton, FL, USA. N. Mallikarjuna, R.K. Varshney (Eds.).
3. Bertioli D.J., Ozias-Akins P., Chu Y., Dantas K.M., Santos S.P., Gouvea E., Guimarães P.M., Leal-Bertioli S.C.M., Knapp S.J., Moretzsohn M.C. The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 Genes Genomes Genet. 2014, 4:89-96.
4. Bertioli D.J., Vidigal B., Nielen S., Ratnaparkhe M.B., Lee T.H., Leal-Bertioli S.C.M., Kim C., Guimarães P.M., Seijo G., Schwarzacher T., Paterson A.H., et al. The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. Ann. Bot. 2013, 112:545-559.
5. Boerma H.R., St John J., Molen J.Y. U.S. Legume Crops Genomics Workshop 2001, July 30-31,2011, White Paper, Hunt Valley, MD, 29 pp.
6. Burow M.D., Simpson C.E., Starr J.L., Paterson A.H. Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). Broadening the gene pool of a monophyletic polyploid species. Genetics 2001, 159:823-837.
7. Cannon E., Dash S., Kalberer S., Weeks N., Huang W., Farmer A., Cannon S., Dickerson J. PeanutBase: The genomic data portal for Arachis. 7th International Conference on Legume Genetics and Genomics, Saskatoon, Canada July 6-11, 2014.
8. Cermeno M.C., Orellana J., Santos J.L., Lacadena J.R. Nucleolar activity and competition (Amphiplasty) in the genus Aegilops. Heredity 1984, 53:603-611.
9. Charrier B., Foucher F., Kondorosi E., D'Aubenton-Carafa Y., Thermes C., Kondorosi A., Ratet P. Bigfoot: A new family of MITE elements characterized from the Medicago genus. Plant J. 1999, 18:431-441.
10. Cuc L.M., Mace E.S., Crouch J.H., Quang V.D., Long T.D., Varshney R.K. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea L.). BMC Plant Biol. 2008, 8:55.
11. Dash S., Cannon E.K.S., Kalberer S., Huang W., Weeks N., Dickerson J., Farmer A., Cannon S. PeanutBase: a community resource to help improve peanut varieties by integrating genetic, genomic, and trait information. AAGB 2014: Advances in Arachis through Genomics & Biotechnology, Savannah, GA November 10-14, 2014, (abstract). http://www.peanutbioscience.com.
12. Devos K.M., Brown J.K.M., Bennetzen J.L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 2002, 12:1075-1079.
13. Fávero A.P., Simpson C.E., Valls F.M.J., Velo N.A. Study of evolution of cultivated peanut through crossability studies among Arachis ipaënsis, A. duranensis and A. hypogaea. Crop Sci. 2006, 46:1546-1552.
14. Fernández A., Krapovickas A. Cromosomas y Evolucion en Arachis (Leguminosae). Bonplandia 1994, 8:187-200.
15. Feschotte C., Jiang N., Wessler S.R. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 2002, 3:329-341.
16. Foncéka D., Tossim H.-A., Rivallan R., Vignes H., Faye I., Ndoye O., Moretzsohn M.C., Bertioli D.J., Glaszmann J.C., Courtois B., et al. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biol. 2012, 12:26.
17. Foncéka D., Hodo-Abalo T., Rivallan R., Faye I., Sall M., Ndoye O., Fávero A., Bertioli D.J., Glaszmann J.-C., Courtois B. Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biol. 2009, 9:103.
18. Freitas F.O. Ampliação da Área de Ocorrência da Espécie. Arachis villosulicarpa Embrapa Comunicado Técnico- Embrapa, Brasilia, Brazil 2004.
19. Gautami B., Foncéka D., Pandey M.K., Moretzsohn M.R.C., Sujay V., Qin H., Hong Y., Faye I., Chen X., BhanuPrakash A., et al. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 2012, 7:e41213.
20. Gepts P., Beavis W.D., Brummer E.C., Shoemaker R.C., Stalker H.T., Weeden N.F., Young N.D. Legumes as a model plant family. Genomics for food and feed: report of the cross-legume advances through genomics conference. Plant Physiol. 2005, 137:1228-1235.
21. Gowda M., Bhat R., Sujay V., Kusuma P., Varshakumari V., Bhat S., Varshney R. Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.). Plant Syst. Evol. 2011, 291:153-158.
22. Gowda M.V.C., Bhat R.S., Motagi B.N., Sujay V., Kumari V., Sujatha B. Association of high-frequency origin of late leaf spot resistant mutants with AhMITE1 transposition in peanut. Plant Breed. 2010, 129:567-569.
23. Grabiele M., Chalup L., Robledo G., Seijo G. Genetic and geographic origin of domesticated peanut as evidenced by 5S rDNA and chloroplast DNA sequences. Plant Syst. Evol. 2012, 298:1151-1165.
24. Gregory M.P., Gregory W.C. Exotic germplasm of Arachis L. interspecific hybrids. J. Hered. 1979, 70:185-193.
25. Gregory W.C., Gregory M.P. Groundnut. Evolution of Crop Plants 1976, 151-154. Longman, London. N. Simmonds (Ed.).
26. Guimarães P., Garsmeur O., Proite K., Leal-Bertioli S., Seijo G., Chaine C., Bertioli D., D'Hont A. BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut. BMC Plant Biol. 2008, 8:14.
27. Halward T., Stalker T., LaRue E., Kochert G. Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol. Biol. 1992, 18:315-325.
28. Halward T.M., Stalker H.T., LaRue E.A., Kochert G. Genetic variation detectable with molecular markers among unadapted germ-plasm resources of cultivated peanut and related wild species. Genome 1991, 34:1013-1020.
29. Hong Y.B., Chen X.P., Liang X.Q., Liu H.Y., Zhou G.Y., Li S.X., Wen S.J., Holbrook C.C., Guo B.Z. A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC Plant Biol. 2010, 10:1-13.
30. Husted L. Cytological studies on the peanut. Arachis. II - chromosome number, morphology and behavior, and their application to the problem of the origin of the cultivated forms. Cytologia 1936, 7:396-423.
31. Kochert G., Stalker H.T., Gimenes M., Galgaro L., Lopes C.R., Moore K. RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am. J. Bot. 1996, 83:1282-1291.
32. Krapovickas A. The origin, variability and spread of the groundnut (Arachis hypogaea). The Domestication and Exploration of Plants and Animals 1969, 427-441. Duckworth Publishers, London. P.J. Ucko, G.W. Dimbleby (Eds.).
33. Krapovickas A., Gregory W.C. Taxonomia del Genero Arachis (Leguminosae). Bonplandia 1994, 8:1-186.
34. Krapovickas A., Gregory W.C. Taxonomy of the genus Arachis (Leguminosae). Bonplandia 2007, 16 (Suppl.):1-205.
35. Leal-Bertioli S., Shirasawa K., Abernathy B., Moretzsohn M., Chavarro C., Clevenger J., Ozias-Akins P., Jackson S., Bertioli D. Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 2015, 199:1093-1105.
36. Leal-Bertioli S.C., Santos S.P., Dantas K.M., Inglis P.W., Nielen S., Araujo A.C., Silva J.P., Cavalcante U., Guimarães P.M., Brasileiro A.C. Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. Ann. Bot. 2014, 115:237-249.
37. McClintock B. The significance of responses of the genome to challenge. Science 1984, 226:792-801.
38. Ma J., Devos K.M., Bennetzen J.L. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 2004, 14:860-869.
39. Magallon S., Sanderson M. Absolute diversification rates in angiosperm clades. Evolution 2001, 55:1762-1780.
40. Mallikarjuna N., Senthilvel S., Hoisington D. Development of new sources of tetraploid Arachis to broaden the genetic base of cultivated groundnut (Arachis hypogaea L.). Genet. Res. Crop Evol. 2011, 58:889-907.
41. Michael T.P., Jackson S. The first 50 plant genomes. Plant Genome 2013, 6:1-7.
42. Moretzsohn M.C., Gouvea E.G., Inglis P.W., Leal-Bertioli S.C.M., Valls J.F.M., Bertioli D.J. A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann. Bot. 2013, 11:113-126.
43. Nielen S., Campos-Fonseca F., Leal-Bertioli S., Guimarães P., Seijo G., Town C., Arrial R., Bertioli D. FIDEL - a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosome Res. 2010, 18:227-246.
44. Nielen S., Vidigal B.S., Leal-Bertioli S.C., Ratnaparkhe M., Paterson A.H., Garsmeur O., D'Hont A., Guimaraes P.M., Bertioli D.J. Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol. Genet. Genomics 2012, 287:21-38.
45. Patel M., Jung S., Moore K., Powell G., Ainsworth C., Abbott A. High-oleate peanut mutants result from a MITE insertion into the FAD2 gene. Theor. Appl. Genet. 2004, 108:1492-1502.
46. Pereira V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 2004, 5:R79.
47. Preuss S., Pikaard C.S. rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. Biochem. Biophys. Acta 2007, 1769:383-392.
48. Qin H., Feng S., Chen C., Guo Y., Knapp S., Culbreath A., He G., Wang M.L., Zhang X., Holbrook C.C., et al. An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. Theor. Appl. Genet. 2012, 124:653-664.
49. Ramos M.L., Fleming G., Chu Y., Akiyama Y., Gallo M., Ozias-Akins P. Chromosomal and phylogenetic context for conglutin genes in Arachis based on genomic sequence. Mol. Genet. Genomics 2006, 275:578-592.
50. Robledo G., Seijo G. Species relationships among the wild B genome of Arachis species (section Arachis) based on FISH mapping of rDNA loci and heterochromatin detection: a new proposal for genome arrangement. Theor. Appl. Genet. 2010, 121:1033-1046.
51. Samoluk S.S., Robledo G., Podio M., Chalup L., Robledo G., Ortiz J.P.A., Pessino S.C., Seijo J.G. First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species. Genetica 2015, 143:113-125.
52. Samoluk S.S., Chalup L., Robledo G., Seijo J.G. Genome sizes in diploid and allopolyploid Arachis L. species (section Arachis). Genet. Res. Crop Evol. 2014, 61:1-17. 10.1007/s10722-014-0193-3.
53. Seijo G., Lavia G.I., Fernández A., Krapovickas A., Ducasse D.A., Bertioli D.J., Moscone E.A. Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am. J. Bot. 2007, 94:1963-1971.
54. Seijo J.G., Lavia G.I., Fernández A., Krapovickas A., Ducasse D., Moscone E.A. Physical mapping of the 5S and 18S-25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaënsis are the wild diploid progenitors of A. hypogaea (Leguminosae). Am. J. Bot. 2004, 91:1294-1303.
55. Shirasawa K., Bertioli D.J., Varshney R.K., Moretzsohn M.C., Leal-Bertioli S.C., Thudi M., Pandey M.K., Rami J.F., Foncéka D., Gowda M.V., et al. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res. 2013, 20:173-184.
56. Shirasawa K., Hirakawa H., Tabata S., Hasegawa M., Kiyoshima H., Suzuki S., Sasamoto S., Watanabe A., Fujishiro T., Isobe S. Characterization of active miniature inverted-repeat transposable elements in the peanut genome. Theor. Appl. Genet. 2012, 124:1429-1438.
57. Singh A.K., Moss J.P. Utilization of wild relatives in genetic improvement of Arachis hypogaea L. II. Chromosome complements of species in section Arachis. Theor. Appl. Genet. 1982, 61:305-314.
58. Singh A.K., Smartt J. The genome donors of the groundnut/peanut (Arachis hypogaea L.) revisited. Genet. Res. Crop Evol. 1998, 45:113-118.
59. Smartt J., Gregory W., Gregory M. The genomes of Arachis hypogaea. 1. Cytogenetic studies of putative genome donors. Euphytica 1978, 27:665-675.
60. Stalker H.T., Dalmacio R.D. Karyotype relations and analysis among varieties of Arachis hypogaea L. Cytologia 1986, 58:617-629.
61. Stalker H.T., Dhesi J.S., Parry D.C., Hahn J.H. Cytological and interfertility relationships of Arachis section Arachis. Am. J. Bot. 1991, 78:238-246.
62. Stebbins G.L. Types of polyploids: their classification and significance. Adv. Genet. 1947, 1:403-429.
63. Stebbins G.L. Variation and Evolution in Plants 1950, Columbia University Press, New York, NY.
64. Sujay V., Gowda M.V., Pandey M.K., Bhat R.S., Khedikar Y.P., Nadaf H.L., Gautami B., Sarvamangala C., Lingaraju S., Radhakrishan T., et al. 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. 2012, 32:773-788.
65. Temsch E.M., Greilhuber J. Genome size variation in Arachis hypogaea and A. monticola re-evaluated. Genome 2000, 43:449-451.
66. Temsch E.M., Greilhuber J. Genome size in Arachis duranensis: A critical study. Genome 2001, 44:826-830.
67. Valentine H., Grabau E., Ozias-Akins P., Nwosu V., Wilson R., Gallo M., Chenault K., Stalker H.T., Weissinger A.W., Donahue P., et al. Biotech Peanut White Paper: Benefits and Issues 2006, American Peanut Council, Alexandria, VA, 14 pp.
68. Varshney R.K., Bertioli D.J., Moretzsohn M.C., Vadez V., Krishnamurty L., Aruna R., Nigam S.N., Ravi K., He G., Knapp S.J., et al. The first SSR based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 2009, 118:729-739.
69. Vicient C.M., Suoniemi A., Anamthawat-Jansson K., Tanskanen J., Beharav A., Nevo E., Schulman A.H. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell Online 1999, 11:1769-1784.
70. Wang H., Penmetsa R.V., Yuan M., Gong L., Zhao Y., Guo B., Farmer A.D., Rosen B.D., Gao J., Isobe S., et al. Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). BMC Plant Biol. 2012, 12:10.
71. Wendel J.F. Genome evolution in polyploids. Plant Mol. Biol. 2000, 42:225-249.
72. Wilson R.F., Stalker H.T., Brummer E.C. Legume Crop Genomics 2004, AOCS Press, Champaign, IL.
73. Wilson R.F. National Strategic Plan for the Peanut Genome Initiative 2004-2008 2006, Version 2.4, USDA, Beltsville, MD, 19 pp. http://www.peanutbioscience.com.
74. Wilson R.F. National Program Action Plan for the Peanut Genome Initiative: Application of Plant Genomics to Mitigate Peanut Allergy 2006, Version 2.4, USDA, Beltsville, MD, 25 pp. http://www.peanutbioscience.com.
75. Wilson R.F. International Peanut Genomic Research Initiative Strategic Plan for 2012 to 2016 Characterization of the Peanut Genome September 2011 2012, Version 4.3. http://www.peanutbioscience.com.
76. Wynne J.C., Halward T. Genetics and cytogenetics of Arachis. Crit. Rev. Plant Sci. 1989, 8:189-220.
77. Wynne J.C., Coffelt T.A. Genetics of Arachis hypogaea L. Peanut Science and Technology 1982, 50-94. American Peanut Research and Education Society, Inc., Yoakum, TX. H.E. Pattee, C.T. Young (Eds.).