Peanut (Arachis hypogaea) expressed sequence tag project: Progress and application

Comparative and Functional Genomics

Volumn 2012, Issue , 2012, Pages

  Feng, Suping ^a,b   Wang, Xingjun ^c   Zhang, Xinyou ^d   Dang, Phat M ^e   Holbrook, C Corley ^f   Culbreath, Albert K ^a   Wu, Yaoting ^b   Guo, Baozhu ^a,f  

^a UNIVERSITY OF GEORGIA   (United States)

^b Qiongzhou University   (Macao)

^c SHANDONG PEANUT RESEARCH INSTITUTE   (China)

^d INSTITUTE OF PLANT PROTECTION   (China)

^e NATIONAL PEANUT RESEARCH LABORATORY   (United States)

^f AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; BARLEY; DNA LIBRARY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; MAIZE; MARKER GENE; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; PEANUT; PLANT GENETICS; POTATO; PRIORITY JOURNAL; REVIEW; RICE; SORGHUM; SOYBEAN; WHEAT;

ARACHIS HYPOGAEA;

EID: 84863692072     PISSN: 15316912     EISSN: 15326268     Source Type: Journal    
DOI: 10.1155/2012/373768     Document Type: Review

References (80)

1. Doyle J. J., Brenner S., Miller J. H., Leguminosae Encyclopedia of Genetics 2001 San Diego, Calif, USA Academic Press 1081 1085
2. Guo B. Z., Chen C. Y., Chu Y., Holbrook C. C., Ozias-Akins P., Stalker H. T., Benkeblia N., Advances in genetics and genomics for sustainable peanut production Sustainable Agriculture and New Biotechnologies 2012 Boca Raton, Fla, USA CRC Press 341 367
3. Wilson R. F., Stalker H. T., Brummer E. C., Legume Crop Genomics 2004 Champaign, Ill, USA AOCS Press
4. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F., Kerlavage A. R., McCombie W. R., Venter J. C., Complementary DNA sequencing: expressed sequence tags and human genome project Science 1991 252 5013 1651 1656 (Pubitemid 21917081)
5. Luo M., Dang P., Guo B. Z., He G., Holbrook C. C., Bausher M. G., Lee R. D., Generation of expressed sequence tags (ESTS) for gene discovery and marker development in cultivated peanut Crop Science 2005 45 1 346 353 (Pubitemid 40118408)
6. Proite K., Leal-Bertioli S. C. M., Bertioli D. J., Moretzsohn M. C., Da Silva F. R., Martins N. F., Guimares P. M., ESTs from a wild Arachis species for gene discovery and marker development BMC Plant Biology 2007 7, article 7
7. Guo B. Z., Chen X. P., Dang P., Scully B. T., Liang X. Q., Holbrook C. C., Yu J., Culbreath A. K., Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection BMC Developmental Biology 2008 8, article 12
8. Guo B. Z., Chen X. P., Hong Y. B., Liang X. Q., Dang P., Brenneman T., Holbrook C., Culbreath A., Analysis of gene expression profiles in leaf tissues of cultivated peanuts and development of EST-SSR markers and gene discovery International Journal of Plant Genomics 2009 2009 14
9. Haegeman A., Jacob J., Vanholme B., Kyndt T., Mitreva M., Gheysen G., Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: the first transcriptome analysis of an Anguinid nematode Molecular and Biochemical Parasitology 2009 167 1 32 40
10. Bi Y. P., Liu W., Xia H., Su L., Zhao C. Z., Wan S. B., Wang X. J., EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea L) Genome 2010 53 10 832 839
11. Song G. Q., Li M. J., Xiao H., Wang X. J., Tang R. H., Xia H., Zhao C. Z., Bi Y. P., EST sequencing and SSR marker development from cultivated peanut (Arachis hypogaea L) Electronic Journal of Biotechnology 2010 13 3 1 9
12. Tirumalaraju S. V., Jain M., Gallo M., Differential gene expression in roots of nematode-resistant and -susceptible peanut (Arachis hypogaea) cultivars in response to early stages of peanut root-knot nematode (Meloidogyne arenaria) parasitization Journal of Plant Physiology 2011 168 5 481 492
13. Holbrook C. C., Culbreath A. K., Registration of Tifrunner peanut Journal of Plant Registrations 2007 1, article 124
14. Alves D. M. T., Pereira R. W., Leal-Bertioli S. C. M., Moretzsohn M. C., Guimares P. M., Bertioli D. J., Development and use of single nucleotide polymorphism markers for candidate resistance genes in wild peanuts (Arachis spp) Genetics and Molecular Research 2008 7 3 631 642
15. Koilkonda P., Sato S., Tabata S., Shirasawa K., Hirakawa H., Sakai H., Sasamoto S., Watanabe A., Wada T., Kishida Y., Tsuruoka H., Fujishiro T., Yamada M., Kohara M., Suzuki S., Hasegawa M., Kiyoshima H., Isobe S., Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Molecular Breeding 2012 30 1 125 138
16. Yan Y. S., Lin X. D., Zhang Y. S., Wang L., Wu K., Huang S. Z., Isolation of peanut genes encoding arachins and conglutins by expressed sequence tags Plant Science 2005 169 2 439 445 (Pubitemid 40912395)
17. Wang L., Yan Y. S., Liao B., Lin X. D., Huang S. Z., The cDNA cloning of conarachin gene and its expression in developing peanut seeds Journal of Plant Physiology and Molecular Biology 2005 31 1 107 110
18. Wang X. J., Su L., Quan X. Q., Shan L., Zhang H. T., Bi Y. P., Peanut (Arachis hypogaea L) EST sequencing, gene cloning and Agrobacteria-mediated transformation Proceedings of the International Groundnut Conference on Groundnut Aflatoxin and Genomics November, 2006 Guangzhou, China 59 60
19. Wang J. Y., Pan L. J., Yang Q. L., Yu S. L., Development and characterization of EST-SSR makers from NCBI and cDNA library in cultivated peanut (Arachis hypogaea L) Molecular Plant Breeding 2009 7 4 806 810
20. Wang J. Y., Pan L. J., Yang Q. L., Yu S. L., Development and characterization of EST-SSR markers from NCBI and cDNA library in cultivated peanut (Arachis hypogaea L) Legume Genomics and Genetics 2010 1 6 30 33
21. Huang J. Q., Yan L. Y., Lei Y., Jiang H. F., Liao B. S., Peanut cDNA library construction and EST sequence analysis Chinese Journal of Oil Crop Sciences 2008 10 121 125
22. Xiao Y., Liao B. S., Yan L. Y., Huang J. Q., Ren X. P., Lei Y., Jiang H. F., Development and utilization of EST-SSR primers in peanut(Arachis hypogaea L) Hubei Agricultural Sciences 2010 49 11 2625 2628
23. Li M. J., Xia H., Zhao C. Z., Li A. Q., Li C. S., Bi Y. P., Wan S. B., Wang X. J., Isolation and characterization of putative Acetyl-CoA carboxylases in Arachis hypogaea L. Plant Molecular Biology Reporter 2009 28 1 58 68
24. Li M. J., Li A. Q., Xia H., Zhao C. Z., Li C. S., Wan S. B., Bi Y. P., Wang X. J., Cloning and sequence analysis of putative type II fatty acid synthase genes from Arachis hypogaea L. Journal of Biosciences 2009 34 2 227 238
25. Li M. J., Wang X. J., Su L., Bi Y. P., Wan S. B., Characterization of five putative acyl carrier protein (ACP) isoforms from developing seeds of Arachis hypogaea L. Plant Molecular Biology Reporter 2010 28 3 365 372
26. Siloto R. M. P., Findlay K., Lopez-Villalobos A., Yeung E. C., Nykiforuk C. L., Moloney M. M., The accumulation of oleosins determines the size of seed oilbodies in Arabidopsis Plant Cell 2006 18 8 1961 1974 (Pubitemid 44260190)
27. Wang X. J., Xia H., Li C. S., Zhao C. Z., Li A. Q., Peanut Allergens: Gene Cloning and RNAi Interference. Sino-Dutch Symposium on Multedisciplinary Allergy Research Hangzhou, China
28. Su L., Zhao C. Z., Bi Y. P., Wan S. B., Xia H., Wang X. J., Cloning and expression analysis of peanut LEA protein genes Journal of Biosciences 2011 36 2 223 228
29. Shao F. X., Liu Z. J., Wei L. Q., Cao M., Bi Y. P., Cloning and sequence analysis of a novel NAC-like gene AhNAC1 in Peanut (Arachis hypogaea) Acta Botanica Boreali-Occidentalia Sinica 2008 10 1929 1934
30. Zhang M., Liu W., Bi Y. P., Wang Z. Z., Isolation and identification of PNDREB1: a new DREB transcription factor from peanut (Arachis hypogaea L) Acta Agronomica Sinica 2009 35 11 1973 1980
31. Zhang G. L., Shi X. G., Cai N. B., Zhao Y. L., Zhuang W. J., Molecular cloning and expression of pericarp and testaspecific expression gene AhPSG13 Chinese Journal of Oil Crop Sciences 2010 32 1 035 040
32. Li W. F., Liu H. Y., Zhong N., Liang X. Q., Cloning and prokaryotic expression of defensin gene from peanut (Arachis hypogaea L) Genomics and Applied Biology 2009 28 4 645 650
33. Xie C. Z., Liang X. Q., Li L., Liu H. Y., Cloning and prokaryotic expression of AhPR10 gene with resistance to aspergillus flavus in peanut Genomics and Applied Biology 2009 28 2 237 244
34. Zhao C. Z., Li A. Q., Wang X. J., Xia H., Su L., Li C. S., Cloning and expression analysis of lipid transfer protein family genes in Arachis hypogaea L. Journal of Peanut Science 2009 38 4 15 20
35. Luo M., Dang P., Bausher M. G., Holbrook C. C., Lee R. D., Lynch R. E., Guo B. Z., Identification of transcripts involved in resistance responses to leaf spot disease caused by Cercosporidium personatum in peanut (Arachis hypogaea) Phytopathology 2005 95 4 381 387 (Pubitemid 40398899)
36. Luo M., Liang X., Dang P., Holbrook C. C., Bausher M. G., Lee R. D., Guo B. Z., Microarray-based screening of differentially expressed genes in peanut in response to Aspergillus parasiticus infection and drought stress Plant Science 2005 169 4 695 703 (Pubitemid 41097197)
37. Payton P., Kottapalli K. R., Rowland D., Faircloth W., Guo B. Z., Burow M., Puppala N., Gallo M., Gene expression profiling in peanut using high density oligonucleotide microarrays BMC Genomics 2009 10, article 265
38. Guo B. Z., Fedorova N. D., Chen X. P., Wan C. H., Wang W., Nierman W. C., Deepak B., Yu J., Gene expression profiling and identification of resistance genes to Aspergillus flavus infection in peanut through EST and microarray strategies Toxins 2011 3 7 737 753
39. Zhuang W. J., Chen H., Nancy P. K., Jiang B. J., Zeng J. B., Zhang C., Chen X. Y., Deng Y., Cai T. C., Isolation and characterization of important genes toward improvement peanut resistance to Aspergillus flavus Proceedings of the 5th International Conference of the Peanut Research Community on Advances in Arachis Through Genomics and Biotechnology June, 2011 Brasillia, Brazil 28
40. Liang X. Q., Chen X. P., Hong Y. B., Liu H., Zhou G., Li S., Guo B. Z., Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L) and Arachis wild species BMC Plant Biology 2009 9, article 35
41. Qin H., Feng S., Chen C., Guo Y., Knapp S., Culbreath,G. He A., Wang M., Zhang X., Holbrook C., Ozias-Akins P., Guo B. Z., An Integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations Theoretical and Applied Genetics 2012 124 653 664
42. Liang X. Q., Hong Y. B., Chen X. P., Liu H. Y., Zhou G. Y., Li S. X., Wen S.J., Characterization and application of EST-SSRs in peanut (Arachis hypogaea L.) Acta Agronomica Sinica 2009 35 2 246 254
43. Thiel T., Michalek W., Varshney R. K., Graner A., Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) Theoretical and Applied Genetics 2003 106 3 411 422 (Pubitemid 36599853)
44. Liewlaksaneeyanawin C., Ritland C. E., El-Kassaby Y. A., Ritland K., Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs Theoretical and Applied Genetics 2004 109 2 361 369 (Pubitemid 39059548)
45. Varshney R. K., Sigmund R., Brner A., Korzun V., Stein N., Sorrells M. E., Langridge P., Graner A., Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice Plant Science 2005 168 1 195 202 (Pubitemid 39464780)
46. Feng S. P., Li W. G., Huang H. S., Wang J. Y., Wu Y. T., Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) Molecular Breeding 2009 23 1 85 97
47. Bushman B. S., Larson S. R., Tuna M., West M. S., Hernandez A. G., Vullaganti D., Gong G., Robins J. G., Jensen K. B., Thimmapuram J., Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability Theoretical and Applied Genetics 2011 123 1 119 129
48. Choudhary S., Sethy N. K., Shokeen B., Bhatia S., Development of chickpea EST-SSR markers and analysis of allelic variation across related species Theoretical and Applied Genetics 2009 118 3 591 608
49. Koppolu R., Upadhyaya H. D., Dwivedi S. L., Hoisington D. A., Varshney R. K., Genetic relationships among seven sections of genus Arachis studied by using SSR markers BMC Plant Biology 2010 10, article 15
50. Mace E. S., Varshney R. K., Mahalakshmi V., Seetha K., Gafoor A., Leeladevi Y., Crouch J. H., In silico development of simple sequence repeat markers within the aeschynomenoid/dalbergoid and genistoid clades of the Leguminosae family and their transferability to Arachis hypogaea, groundnut Plant Science 2008 174 1 51 60 (Pubitemid 350086730)
51. Varshney R. K., Bertioli D. J., Moretzsohn M. C., Vadez V., Krishnamurthy L., Aruna R., Nigam S. N., Moss B. J., Seetha K., Ravi K., He G., Knapp S. J., Hoisington D. A., The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.) Theoretical and Applied Genetics 2009 118 4 729 739
52. Moretzsohn M. C., Leoi L., Proite K., Guimares P. M., Leal-Bertioli S. C. M., Gimenes M. A., Martins W. S., Valls J. F. M., Grattapaglia D., Bertioli D. J., A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae) Theoretical and Applied Genetics 2005 111 6 1060 1071 (Pubitemid 41434116)
53. Moretzsohn M. C., Barbosa A. V. G., Alves-Freitas D. M. T., Teixeira C., Leal-Bertioli S. C. M., Guimares P. M., Pereira R. W., Lopes C. R., Cavallari M. M., Valls J. F. M., Bertioli D. J., Gimenes M. A., A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome BMC Plant Biology 2009 9, article 40
54. Foncéka D., Hodo-Abalo T., Rivallan R., Faye I., Sall M. N., Ndoye O., Fvero A. P., Bertioli D. J., Glaszmann J. C., Courtois B., Rami J. F., Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid BMC Plant Biology 2009 9, article 103
55. Leal-Bertioli S. C. M., José A. C. V. F., Alves-Freitas D. M. T., Moretzsohn M. C., Guimares P. M., Nielen S., Vidigal B. S., Pereira R. W., Pike J., Fvero A. P., Parniske M., Varshney R. K., Bertioli D. J., Identification of candidate genome regions controlling disease resistance in Arachis BMC Plant Biology 2009 9, article 112
56. Ravi K., Vadez V., Isobe S., Mir R. R., Guo Y., Nigam S. N., Gowda M. V. C., Radhakrishnan T., Bertioli D. J., Knapp S. J., Varshney R. K., Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.) Theoretical and Applied Genetics 2011 122 6 1119 1132
57. Hong Y. B., Chen X. P., Liang X. Q., Liu H., Zhou G., Li S., Wen S., Holbrook C. C., Guo B. Z., A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome BMC Plant Biology 2010 10, article 17
58. Mondal S., Badigannavar A. M., DSouza S. F., Molecular tagging of a rust resistance gene in cultivated groundnut (Arachis hypogaea L.) introgressed from Arachis cardenasii Molecular Breeding 2012 29 2 467 476
59. Knauft D. A., Gorbet D. W., SunOleic 97R Florida Agricultural Experiment Stations Circular 1997 400 1 7
60. Gorbet D. W., Knauft D. A., Registration of SunOleic 95R peanut Crop Science 1997 4, article 1932
61. Norden A. J., Gorbet D. W., Knauft D. A., Registration of Sunrunner peanut Crop Science 1985 25, article 1126
62. Culbreath A. K., Gorbet D. W., Martinez-Ochoa N., Holbrook C. C., Todd J. W., Isleib T. G., Tillman B., High levels of field resistance to tomato spotted wilt virus in peanut breeding lines derived from hypogaea and hirsuta botanical varieties Peanut Science 2005 32 20 24
63. Chu Y., Ramos L., Holbrook C. C., Ozias-Akins P., Frequency of a loss-of-function mutation in oleoyl-PC desaturase (ahFAD2A) in the mini-core of the U.S. peanut germplasm collection Crop Science 2007 47 6 2372 2378 (Pubitemid 351267938)
64. Chu Y., Holbrook C. C., Ozias-Akins P., Two alleles of ahFAD2B control the high oleic acid trait in cultivated peanut Crop Science 2009 49 6 2029 2036
65. Kochert G., Halward T., Branch W. D., Simpson C. E., RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species Theoretical and Applied Genetics 1991 81 5 565 570
66. He G., Prakash C., Evaluation of genetic relationships among botanical varieties of cultivated peanut (Arachis hypogaea L.) using AFLP markers Genetic Resources and Crop Evolution 2001 48 4 347 352 (Pubitemid 33119087)
67. Halward T., Stalker H. T., Kochert G., Development of an RFLP linkage map in diploid peanut species Theoretical and Applied Genetics 1993 87 3 379 384 (Pubitemid 2013676)
68. 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 2 823 837 (Pubitemid 33035123)
69. Stalker H. T., Moss J. P., Speciation, Cytogenetics, and Utilization of Arachis Species Advances in Agronomy 1987 41 C 1 40
70. 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) American Journal of Botany 1996 83 10 1282 1291 (Pubitemid 27011972)
71. Young N. D., Weeden N. F., Kochert G., Paterson A. H., Genome mapping in legumes (Fam. Fabaceae) Genome Mapping in Plants 1996 Austin, Tex, USA Landes Bioscience Press 211 227
72. Goff S. A., Ricke D., Lan T. H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., Hadley D., Hutchison D., Martin C., Katagiri F., Lange B. M., Moughamer T., Xia Y., Budworth P., Zhong J., Miguel T., Paszkowski U., Zhang S., Colbert M., Sun W. L., Chen L., Cooper B., Park S., Wood T. C., Mao L., Quail P., Wing R., Deans R., Yu Y., Zharkikh A., Shen R., Sahasrabudhe S., Thomas A., Cannings R., Gutin A., Pruss D., Reid J., Tavtigian S., Mitchell J., Eldredge G., Scholl T., Miller R. M., Bhatnagar S., Adey N., Rubano T., Tusneem N., Robinson R., Feldhaus J., Macalma T., Oliphant A., Briggs S., A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 2002 296 5565 92 100 (Pubitemid 34280065)
73. Yu J., Hu S., Wang J., Wong G. K., Li S., Liu B., A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 2002 296 5565 79 92 (Pubitemid 34280064)
74. Tian A. G., Wang J., Cui P., Han Y. J., Xu H., Cong L. J., Huang X. G., Wang X. L., Jiao Y. Z., Wang B. J., Wang Y. J., Zhang J. S., Chen S. Y., Characterization of soybean genomic features by analysis of its expressed sequence tags Theoretical and Applied Genetics 2004 108 5 903 913 (Pubitemid 38463854)
75. Thudi M., Li Y., Jackson S. A., May G. D., Varshney R. K., Current state-of-art of sequencing technologies for plant genomics research Briefings in Functional Genomics 2012 11 3 11
76. Hillier L. D., Lennon G., Becker M., Bonaldo M. F., Chiapelli B., Chissoe S., Dietrich N., DuBuque T., Favello A., Gish W., Hawkins M., Hultman M., Kucaba T., Lacy M., Le M., Le N., Mardis E., Moore B., Morris M., Parsons J., Prange C., Rifkin L., Rohlfing T., Schellenberg K., Soares M. B., Tan F., Thierry-Meg J., Trevaskis E., Underwood K., Wohldman P., Waterston R., Wilson R., Marra M., Generation and analysis of 280,000 human expressed sequence tags Genome Research 1996 6 9 807 828 (Pubitemid 26385363)
77. Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K., Functional annotation of a full-length Arabidopsis cDNA collection Science 2002 296 5565 141 145 (Pubitemid 34280073)
78. Brent M. R., Steady progress and recent breakthroughs in the accuracy of automated genome annotation Nature Reviews Genetics 2008 9 1 62 73 (Pubitemid 350277298)
79. Zhao C. Z., Wang X. J., Li A. Q., Li C. S., De novo characterization of peanut transcriptome during gynophore development Proceedings of the 5th International Conference of the Peanut Research Community on Advances in Arachis Through Genomics and Biotechnology June, 2011 Brasillia, Brazil 48
80. Emrich S. J., Barbazuk W. B., Li L., Schnable P. S., Gene discovery and annotation using LCM-454 transcriptome sequencing Genome Research 2007 17 1 69 73 (Pubitemid 46041667)