Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Parra González, Lorena B ^a   Aravena Abarzúa, Gabriela A ^a   Navarro Navarro, Cristell S ^a   Udall, Joshua ^b   Maughan, Jeff ^b   Peterson, Louis M ^b   Salvo Garrido, Haroldo E ^a,c   Maureira Butler, Iván J ^a  

^a Agri Aquaculture Nutritional Genomic Center (CGNA)   (Chile)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

^c INSTITUTO DE INVESTIGACIONES AGROPECUARIAS   (Chile)

Author keywords

EST SSR; Lupinus luteus; Microsynteny; Orphan crop

Indexed keywords

COMPLEMENTARY DNA; MOLECULAR MARKER; NUCLEOTIDE; PLANT DNA; TRANSCRIPTOME; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; BUD; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; FLOWER; GENE AMPLIFICATION; GENE CLUSTER; GENE SEQUENCE; GENETIC DISTANCE; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; GERMPLASM; GLYCINE (PLANT); LOTUS; LUPIN; LUPIN HISPANICUS; LUPIN LUTEUS; LUPIN MUTABILIS; MEDICAGO; NONHUMAN; PLANT LEAF; PLANT SEED; POPULATION GENETICS; PYROSEQUENCING; QUANTITATIVE TRAIT LOCUS; SEQUENCE HOMOLOGY; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

EXPRESSED SEQUENCE TAGS; GENE LIBRARY; LUPINUS; POLYMORPHISM, GENETIC; SYNTENY; TRANSCRIPTOME;

ARABIDOPSIS; LUPINUS LUTEUS; MEDICAGO;

EID: 84867642934     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-425     Document Type: Article

References (69)

1. Mace ES, Varshney RK, Mahalakshmi V, Seetha K, Gafoor A, Leeladevi Y, Crouch JH. 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 Sci 2008, 174:51-60.
2. Gladstones JS. Distribution, origin, taxonomy, history and importance. Lupins as crop plants: biology, production and utilization 1998, 1-37. CAB International, Cambridge, United Kingdom, Gladstones JS, Atkins CA, Hamblin J.
3. Múzquiz M, Burbano C, Gorospe MJ, Ródenas I. A chemical study of Lupinus hispanicus seed-toxic and antinutritional components. J Scie Food Agr 1989, 47:205-214.
4. Wolko B, Weeden NF. Estimation of Lupinus genome polyploidy on the basis of isozymic loci number. Genet Pol 1989, 30:165-170.
5. Naganowska B, Wolko B, Sliwinska E, Kaczmarek Z. Nuclear DNA content variation and species relationships in the genus Lupinus (Fabaceae). Ann Bot 2003, 92:349-355. 10.1093/aob/mcg145, 12853281.
6. Petterson DS. Composition and food uses of lupin. Lupins as a crop plants: biology, production and utilization 1998, 353-384. CAB International, Wallingford, UK, Gladstones JS, Atkins CA, Hamblin J.
7. Gladstones JS. Lupins of the Mediterranean Region and Africa. Technical Bulletin No. 26 1974, 43-48. Western Australian Department of Agriculture, Western Australia.
8. Glencross BD, Carter CG, Duijster N, Evans DR, Dods K, McCafferty P, Hawkins WE, Maas R, Sipsas S. A comparison of the digestibility of a range of lupin and soybean protein products when fed to either Atlantic salmon (Salmo salar) or rainbow trout (Oncorhynchus mykiss). Aquaculture 2004, 237:333-346.
9. Berville ABS, Heinanen J, Kartuzova LT, Bernatskaya ML, Chmeleva ZV. Diversity of lupin (Lupinus L.) based on biochemical composition. Plant Genet Res Newsletter 2003, 134:42-57.
10. Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR. Orphan legume crops enter the genomics era!. Curr Opin Plant Biol 2009, 12:202-210. 10.1016/j.pbi.2008.12.004, 19157958.
11. Kaur S, Cogan N, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 2011, 12:265. 10.1186/1471-2164-12-265, 3113791, 21609489.
12. Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 2011, 9:922-931. 10.1111/j.1467-7652.2011.00625.x, 3437486, 21615673.
13. Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD. Sequencing Medicago truncatula expressed tags using 454 Life Science technology. BMC Genomics 2006, 7:272. 10.1186/1471-2164-7-272, 1635983, 17062153.
14. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 2007, 144:32-42. 10.1104/pp.107.096677, 1913805, 17351049.
15. Yu JK, La Rota M, Kantety RV, Sorrells ME. EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 2004, 271:742-751.
16. Rexroad CE, Rodriguez MF, Coulibaly I, Gharbi K, Danzmann RG, DeKoning J, Phillips R, Palti Y. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 2005, 6:54. 10.1186/1471-2164-6-54, 1090573, 15836796.
17. Young ND, Udvardi M. Translating Medicago truncatula genomics to crop legumes. Curr Opin Plant Biol 2009, 12:193-201. 10.1016/j.pbi.2008.11.005, 19162532.
18. Aubert G, Morin J, Jacquin F, Loridon K, Quillet MC, Petit A, Rameau C, Lejeune-Henaut I, Huguet T, Bursting J. Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula. Theor Appl Genet 2006, 112:1024-1041. 10.1007/s00122-005-0205-y, 16416153.
19. Phan HT, Ellwood SR, Adhikari K, Nelson MN, Oliver RP, Phan HT, Ellwood SR, Adhikari K, Nelson MN, Oliver RP. The first genetic and comparative map of white lupin (Lupinus albus L.): Identification of QTLs for anthracnose resistance and flowering time, and a locus for alkaloid content. DNA Res 2007, 14:59-70. 10.1093/dnares/dsm009, 2779896, 17526914.
20. Nelson MN, Moolhuijzen PM, Boersma JG, Chudy M, Lesniewska K, Bellgard M, Oliver RP, Swiecicki W, Wolko B, Cowling WA, Ellwood SR. Aligning a New Reference Genetic Map of Lupinus angustifolius with the Genome Sequence of the Model Legume, Lotus japonicus. DNA Res 2010, 17:73-83. 10.1093/dnares/dsq001, 2853381, 20133394.
21. Nelson M, Huyen P, Ellwood S, Moolhuijzen P, Hane J, Williams A, O'Lone C, Fosu-Nyarko J, Scobie M, Cakir M, Jones M, Bellgard M, Ksiazkiewicz M, Wolko B, Barker S, Oliver R, Cowling W. The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theor Appl Genet 2006, 113:225-238. 10.1007/s00122-006-0288-0, 16791689.
22. Parra Gonzalez L, Straub S, Doyle J, Mora Ortega P, Salvo Garrido H, Maureira Butler I. Development of microsatellites inLupinus luteus(Fabaceae) and cross-species amplification in other lupine species. Am J Bot 2010, 97:e72-e74. 10.3732/ajb.1000170, 21616875.
23. Gao LL, Hane JK, Kamphuis LG, Foley R, Shi BJ, Atkins CA, Singh KB. Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing. BMC Genomics 2011, 12:521. 10.1186/1471-2164-12-521, 3206524, 22014081.
24. Gupta S, Prasad M. Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 2009, 52:761-771. 10.1139/G09-051, 19935924.
25. Kantety RM, Mathews DE, Sorrels ME. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 2002, 148:501-510.
26. La Rota RM, Kantety RV, Yu JK, Sorrells ME. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 2005, 6:23-35. 10.1186/1471-2164-6-23, 550658, 15720707.
27. Nicot N, Chiquet VB, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 2004, 109:800-805. 10.1007/s00122-004-1685-x, 15146317.
28. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106:411-422.
29. Domon E, Fuijita M, Ishikawa N. The insertion/deletion polymorphisms in the waxy gene of barley genetic resources from East Asia. Theor Appl Genet 2002, 104:132-138. 10.1007/s001220200016, 12579438.
30. Blair M, McCouch SR. Microsatellite and sequence-tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa-5. Theor Appl Genet 1997, 95:174-184.
31. Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD. Microsatellites and a single nucleotide polymorphism differenciate apparent amylase classes in an extended pedigree of US rice germplasm. Theor Appl Genet 1997, 94:773-781.
32. Prathepha P. Characterization of Waxy microsatellite classes that are closely linked to the rice Waxy gene and amylose content in Thai rice germplasm Songklanakarin. J Sci Technol 2003, 25:1-8.
33. Selvaraj I, Nagarajan P, Thiyagarajan K, Bharathi M, Rabindran R. Identification of Microsatellite (SSR) and RAPD Markers Linked to Rice Blast Disease Resistance gene in Rice (Oryza sativa L.). African J Biotechnol 2011, 10:3301-3321.
34. Zhou WC, Kolb FL, Bai GH, Domier LL, Boze LK, Smith NJ. Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat. Plant Breeding 2003, 122:40-46.
35. Abdurakhmonov IY, Abdullaev AA, Saha S, Buriev ZT, Arslanov D, Kuryazov Z, Mavlonov GT, Rizaeva SM, Reddy UK, Jenkins JN, Abdullaev A, Abdukarimov A. Simple Sequence Repeat Marker Associated with a Natural Leaf Defoliation Trait in Tetraploid Cotton. J Hered 2005, 96:644-653. 10.1093/jhered/esi097, 16159909.
36. Zeng L, Meredith WR, Gutiérrez OA, Boykin DL. Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among Gossypium tetraploid species. Theor Appl Genet 2009, 119:93-103. 10.1007/s00122-009-1020-7, 19360391.
37. Li X, Yang H, Buirchell B, Yan G. Development of a DNA marker tightly linked to low-alkaloid gene iucundus in narrow-leafed lupin (Lupinus angustifolius L.) for marker-assisted selection. Crop and Pasture Sci 2011, 62:218-224.
38. Logeman J, Schell J, Willmitzer L. Improved method for the isolation of RNA from plant tissues. Anal Biochem 1987, 163:16-20. 10.1016/0003-2697(87)90086-8, 2441623.
39. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
40. Podicheti R, Gollapudi R, Dong Q. WebGBrowse: a web server for GBrowse. Bioinformatics 2009, 25:1550-1551. 10.1093/bioinformatics/btp239, 19357095.
41. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 1978, 19:11-15.
42. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativaL.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res 2001, 11:1441-1452. 10.1101/gr.184001, 311097, 11483586.
43. Edwards D, Batley J. Plant genome sequencing: applications for crop improvement. Plant Biotech J 2010, 8:2-9.
44. Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol 2009, 12:107-118. 10.1016/j.pbi.2008.11.004, 2723731, 19157957.
45. Zhang L, Kasif S, Cantor CR, Broude NE. GC_AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci 2004, 101:16855-16860. 10.1073/pnas.0407821101, 534751, 15548610.
46. Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C. UTRdb and UTRsite: specialized database of sequences and functional elements of 5' and 3' unstranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res 2002, 30:335-340. 10.1093/nar/30.1.335, 99102, 11752330.
47. Diaz I, Vicente-Carbajosa J, Abraham Z, Martinez M, Isabel-La Moneda I, Carbonero P. The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. Plant J 2002, 29:453-464. 10.1046/j.0960-7412.2001.01230.x, 11846878.
48. Koornneff M, Bentsink L, Hilhorst H. Seed dormancy and germination. Curr Opin Plant Biol 2002, 5:33-36. 10.1016/S1369-5266(01)00219-9, 11788305.
49. Tillett RL, Ergül A, Albion RL, Schlauch KA, Cramer GR, Cushman JC. Identification of tissue-specific, abiotic stress responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets. BMC Plant Biology 2011, 11:86. 10.1186/1471-2229-11-86, 3224124, 21592389.
50. Covitz PA, Smith LS, Long SR. Expressed Sequence Tags from a Root-Hair-Enriched Medicago truncatula cDNA Library. Plant Physiol 1998, 117:1325-1332. 10.1104/pp.117.4.1325, 34896, 9701588.
51. Yamada S, Katsuhara M, Kelly WB, Michalowski CB, Bohnert HJ. A family of transcripts encoding water channel proteins: Tissue-specific expression in the common ice plant. Plant Cell 1995, 7:1129-1142. 160939, 7549476.
52. Bertioli DJ, Moretzsohn MC, Madsen LH, Sandal N, Leal-Bertioli S, Guimarães PM, Hougaard BK, Fredslund J, Schauser L, Nielsen AM, Sato S, Tabata S, Cannon SB, Stougaard J. An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 2009, 10:45. 10.1186/1471-2164-10-45, 2656529, 19166586.
53. Wojciechowski MF, Lavin M, Sanderson MJ. A phylogeny of legumes (leguminosae) based on analysis of the plastid MATK gene resolves many well-supported subclades within the family. Am J Bot 2004, 91:1846-1862. 10.3732/ajb.91.11.1846, 21652332.
54. Cardle I, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 2000, 156:847-854. 1461288, 11014830.
55. Varshney RK, Thiel T, Stein N, Langridge P, Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereals species. Cell Mol Biol Lett 2002, 7:537-546.
56. Varshney RK, Graner A, Sorrels ME. Genic microsatellite markers in plants: features an applications. Trends Biotechnol 2005, 23:48-55. 10.1016/j.tibtech.2004.11.005, 15629858.
57. Gao L, Tang J, Li H, Jia J. Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breeding 2003, 12:245-261.
58. Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits expansion in coding DNA. Genome Res 2000, 10:72-80. 310501, 10645952.
59. Jung S, Abbott A, Jesudurai C, Tomkins J, Main D. Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 2005, 5:136-143. 10.1007/s10142-005-0139-0, 15761705.
60. Beckett P, Bancroft I, Trick M. Computational tools for Brassica-Arabidopsis comparative genomics. Comp Funct Genom 2005, 6:147-152.
61. Shoemaker RC, Schlueter J, Doyle JJ. Paleopolyploidy and gene duplication in soybean and other legumes. Curr Opin Plant Biol 2006, 9:104-109. 10.1016/j.pbi.2006.01.007, 16458041.
62. Mudge J, Cannon SB, Kalo P, Oldroyd GED, Roe BA, Town CD, Young ND. Highly syntenic regions in the genomes of soybean,Medicago truncatula, andArabidopsis thaliana. BMC Plant Biology 2005, 5:15. 10.1186/1471-2229-5-15, 1201151, 16102170.
63. Grover CE, Wendel JF. Recent insights into mechanisms of genome size change in plants. J Botany 2010 2010, Article ID 382732:1-8.
64. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer FX, Messing J. Uneven chromosome contraction and expansion in the maize genome. Genome Res 2006, 16:1241-1251. 10.1101/gr.5338906, 1581433, 16902087.
65. Ainouche AK, Bayer R. Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. Am J Bot 1999, 86:590-607. 10.2307/2656820, 10205079.
66. Swiecicki W, Swiecicki WK, Nijaki T. Lupinus x hispanicoluteus - An interspecific hybrid of Old world lupins. Acta Soc Bot Pol 1999, 68:217-220.
67. Drummond CS. Diversification of Lupinus (Leguminosae) in the western New World: Derived evolution of perennial life history and colonization of montane habitats. Mol Phylogenet Evol 2008, 48:408-421. 10.1016/j.ympev.2008.03.009, 18534869.
68. Callow JA, Ford-Lloyd BV, Newbury HJ. Biotechnology and plant genetic resources: conservation and use 1997, 49-76. CAB International, Wallingford, UK.
69. Swanson T. Global values of Biological diversity: the public interest in the conservation of plant genetic resources for agriculture. Plant Genet Res Newsletter 1996, 105:1-3.