Advances in lentil genomics

Legumes in the Omic Era

Volumn , Issue , 2014, Pages 111-130

  Kumar, Shiv ^a   Hamwieh, Aladdin ^a   Manickavelu, Alagu ^a   Kumar, Jitendra ^b   Sharma, Tilak Raj ^c   Baum, Michael ^a  

^a INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS ICARDA   (Syrian Arab Republic)

^b INDIAN INSTITUTE OF PULSES RESEARCH   (India)

^c CSK HIMACHAL PRADESH AGRICULTURAL UNIVERSITY   (India)

Author keywords

Genomic resources; Lens culinaris; Lentil; Marker assisted breeding; Molecular marker

Indexed keywords

EID: 84923228383     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-8370-0_6     Document Type: Chapter

References (85)

1. Abo-el-Wafa A, Murai K, Shimada T (1995) Intra-and inter-specific variations in Lens revealed by RAPD markers. Theor Appl Genet 90:335-340
2. Ahmad M, McNeil DL (1996) Comparison of crossability, RAPD, SDS-PAGE and morphological markers for revealing genetic relationships within and among Lens species. Theor Appl Genet 93:788-793
3. Ahmad M, Fautrer AG, McNeil V, Hill GD, Burritt DJ (1997) In vitro propagation of Lens species and their F 1 interspecific hybrids. Plant Cell Tiss Org Cult 47:169-176
4. Akcay UC, Mahmoudian M, Kamci H, Yucel M, Oktem HA (2009) Agrobacterium tumefaciens-mediated genetic transformation of a recalcitrant grain legume, lentil (Lens culinaris Medik). Plant Cell Rep 28:407-417
5. Alo F, Furman BJ, Akhunov E, Dvorak J, Gepts P (2011) Leveraging genomic resources of model species for the assessment of diversity and phylogeny in wild and domesticated lentil. J Hered 102:315-329
6. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218
7. Bajaj YPS, Dhanju MS (1979) Regeneration of plants from apical meristem tips of some legumes. Curr Sci 48:906-907
8. Barton J, Klyne A, Tennakon D, Francis C, Hamblin J (1997) Development of a system for gene transfer to lentils. In: Proceedings of international food legume research conference III, Adelaide, South Australia, Kluwer Academic Publishers, Dordrecht, The Netherlands, p 85
9. Chagne D, Carlisle CM, Blond C, Volz RK, Whitworth CJ, Oraguzie NC, Crowhurst RN, Allan AC, Espley RV, Hellens RP, Gardiner SE (2007) Mapping a candidate gene (MdMYB10) for red fl esh and foliage colour in apple. BMC Genomics 8:212
10. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis TNH, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289-15294
11. Choudhary S, Sethy NK, Shokeen B, Bhatia S (2008) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591-608
12. Chowdhury M, Andrahennadi CP, Slinkard AE, Vandenberg A (2001) RAPD and SCAR markers for resistance to ascochyta blight in lentil. Euphytica 118:331-337
13. Chowrira GM, Akella VF, Fuerst PE, Lurquin PF (1996) Transgenic grain legumes obtained by in planta electroporation-mediated gene transfer. Mol Biotechnol 5:85-86
14. Datta S, Tiwari S, Kaashyap M, Gupta PP, Choudhary PR, Kumari J, Kumar S (2011) Genetic similarity analysis of lentil (Lens culinaris Medik. Subsp. Culinaris) using cross genera legume STMS markers. Crop Sci 51:2412-2422
15. Duran Y, Fratini R, Garcia P, De La Vega MP (2004) An intersubspecific genetic map of Lens. Theor Appl Genet 108:1265-1273
16. Erskine W, Sarker A, Kumar S (2011) Crops that feed the world 3. Investing in lentil improvement toward a food secure world. Food Secur 3:127-139
17. Eujayl I, Baum M, Powell W, Erskine W, Pehu E (1998a) A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines. Theor Appl Genet 97:83-89
18. Eujayl I, Erskine W, Bayaa B, Baum M, Pehu E (1998b) Fusarium vascular wilt in lentil: inheritance and identification of DNA markers for resistance. Plant Breed 117:497-499
19. Eujayl I, Erskine W, Baum M, Pehu E (1999) Inheritance and linkage analysis of frost injury in lentil. Crop Sci 39:639-642
20. Ford R, Pang ECK, Taylor PWJ (1997) Diversity analysis and species identification in Lens using PCR generated markers. Euphytica 96:247-255
21. Ford R, Pang ECK, Taylor PWJ (1999) Genetics of resistance to ascochyta blight (Ascochyta lentis) of lentil and the identification of closely linked RAPD markers. Theor Appl Genet 98:93-98
22. Ford R, Viret L, Pang ECK, Taylor PWJ, Materne M, Mustafa B (2007) Defense responses in lentil to Ascochyta lentis. In: Proceedings of the Australian plant pathology conference, Australian Plant Pathology Society, Adelaide, South Australia, p 64
23. Fratini R, Ruiz ML (2003) A rooting procedure for lentil (Lens culinaris Medik.) and other hypogeous legumes (pea, chickpea and lathyrus) based on explant polarity. Plant Cell Rep 21:726-732
24. Fratini R, Duran Y, Garcia P, Perezdela Vega M (2007) Identification of quantitative trait loci (QTL) for plant structure, growth habit and yield in lentil. Spanish J Ag Res 5:348-356
25. Furman BJ (2006) Methodology to establish a composite collection: case study in lentil. Plant Genet Resour 4:2-12
26. Gulati A, Schryer P, McHughen A (2002) Production of fertile transgenic lentil (Lens culinaris Medik) plants using particle bombardment. In Vitro Cell Dev Biol 38:316-324
27. Gupta PK, Singh J (1981) Standard karyotype in lentil var. Plant L-639. Lentil Exp News Serv 8:23
28. Gupta D, Taylor PWJ, Inder P, Phan HTT, Ellwood SR, Mathur PN, Sarker A, Ford R (2012a) Integration of EST-SSR markers of Medicago truncatula into intraspecific linkage map of lentil and identification of QTL conferring resistance to ascochyta blight at seedling and pod stages. Mol Breed 30:429-439
29. Gupta M, Verma B, Kumar N, Chahota RK, Rathour R, Sharma SK, Bhatia S, Sharma TR (2012b) Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. J Genet 91(3):279-287
30. Hamwieh A, Udupa SM, Choumane W, Sarker A, Dreyer F, Jung C, Baum M (2005) A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance. Theor Appl Genet 110:669-677
31. Hamwieh A, Udupa SM, Sarker A, Jung C, Baum M (2009) Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breed Sci 59:77-86
32. Havey MJ, Muehlbauer FJ (1989) Linkage between restriction fragment length, isozyme and morphological markers. Theor Appl Genet 77:395-401
33. Kahraman A, Kusmenoglu I, Aydin N, Aydogan A, Erskine W, Muehlbauer FJ (2004) QTL mapping of winter hardness genes in lentil. Crop Sci 44:13-22
34. Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T (2002) Discovery and assay of singlenucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol Biol 48:529-537
35. Kaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW (2011) Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 12:265
36. Khatib F, Koudsieh S, Ghazal B, Barton JE, Tsujimoto H, Baum M (2007) Developing herbicide resistant lentil (Lens culinaris Medikus subsp. culinaris) through Agrobacterium mediated transformation. Arab J Plant Prot 25:185-192
37. Khatib F, Makris A, Yamaguchi-Shinozakic K, Kumar S, Sarker A, Erskine W, Baum M (2011) Expression of DREB1A gene in lentil (lens culinaris Medik. culinaris) transformed with the Agrobacterium system. Crop Pasture Sci 62:488-495
38. Khawar KM, Özcan S (2002) Effect of indole-3-butyric acid on in vitro root development in lentil (Lens culinaris Medik.). Turk J Bot 26:109-111
39. Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145-151
40. Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 270:224-233
41. Kumar J, Pratap A, Solanki RK, Gupta DS, Goyal A, Chaturvedi SK, Nadarajan N, Kumar S (2011) Advances in genomics resources for improving food legume crops. J Agric Sci 150:289-318
42. Lurquin PF, Cai Z, Stiff CM, Fuerst P (1998) Half embryo cocultivation technique for estimating the susceptibility of pea (Pisum sativum L.) and lentil (Lens culinaris Medik) cultivars to Agrobacterium tumefaciens. Mol Biotechnol 9:175-179
43. Mahmoudian M, Yücel M, Öktem HA (2002) Transformation of lentil (Lens culinaris M.) cotyledonary nodes by vacuum infiltration of Agrobacterium tumefaciens. Plant Mol Biol Rep 20:251-257
44. Mohamed MF, Read PE, Coyne DP (1992) Plant regeneration from in vitro culture of embryonic axis explants in common and tepary beans. J Am Soc Hort Sci 117:332-336
45. Muehlbauer FJ, Cho S, Sarker A, Ford R (2006) Application of modern technologies in lentil breeding for biotic and abiotic stress resistance. Euphytica 147:149-165
46. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufi-pogon) and establishment of SNP markers. DNA Res 9:163-171
47. Newell C, Growns D, McComb J (2006) Aeration is more important than shoot orientation when rooting lentil (Lens culinaris medik.) cv. digger microcuttings In vitro. In vitro Cell Dev Biol Plant 42:197-200
48. Nguyen TT, Taylor PWJ, Brouwer JB, Pang ECK, Ford R (2001) A novel source of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight caused by Ascochyta lentis. Aust J Plant Pathol 30:211-215
49. Öktem HA, Mahmoudian M, Eyidooan F, Yücel M (1999) GUS gene delivery and expression in lentil cotyledonary nodes using particle bombardment. Lens Newsl 26:3-6
50. Pandian A, Ford R, Taylor PWJ (2000) Transferability of sequence tagged microsatellite site (STMS) primers across four major pulses. Plant Mol Biol Rep 18:395a-395h
51. Phan HTT, Ellwood SR, Hane JK, Ford R, Materne M, Oliver RP (2007) Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris. Theor Appl Genet 114:549-558
52. Polanco MC, Ruiz ML (2001) Factors that affect plant regeneration from in vitro culture of immature seeds in four lentil (Lens culinaris Medik.) cultivars. Plant Cell Tiss Org Cult 66:133-139
53. Polanco MC, Pelaez MI, Ruiz ML (1988) Factors affecting callus and shoot formation from in vitro cultures of Lens culinaris Medik. Plant Cell Tiss Org Cult 15:175-182
54. Rahman MM, Sarker A, Kumar S, Ali A, Yadav NK, Rahman ML (2009) Breeding for short season environments. In: Erskine W, Muehlbauer FJ, Sarker A, Sharma B (eds) The lentil: botany, production and use. CAB International, Wallingford, UK, pp 121-136
55. Reddy MRK, Rathour R, Kumar N, Katoch P, Sharma TR (2009) Cross-genera legume SSR markers for analysis of genetic diversity in Lens species. Plant Breed 129(5):514-518
56. Rubeena A, Ford R, Taylor PWJ (2003) Construction of an intraspecific linkage map of lentil (Lens culinaris ssp. culinaris). Theor Appl Genet 107:920-926
57. Rubeena A, Taylor PWJ, Ades PK, Ford R (2006) QTL mapping of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight (Ascochyta lentis). Plant Breed 125:506-512
58. Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 87:321-329
59. Saha GC, Sarker A, Chen W, Vandemark GJ, Muehlbauer FJ (2010a) Inheritance and linkage map positions of genes conferring resistance to Stemphylium blight in lentil. Crop Sci 50:1831-1839
60. Saha GC, Sarker A, Chen W, Vandemark GJ, Muehlbauer FJ (2010b) Identification of markers associated with genes for rust resistance in Lens culinaris Medik. Euphytica 175:261-265
61. Sarker RH, Biswas A, Mustafa BM, Mahbub S, Hoque MI (2003a) Agrobacterium-mediated transformation of lentil (Lens culinaris Medik.). Plant Tiss Cult 13:1-12
62. Sarker RH, Mustafa BM, Biswas A, Mahbub S, Nahar SMM, Mahbub S, Hashem R, Hoque MI (2003b) In vitro regeneration in lentil (Lens culinaris Medik.). Plant Tiss Cult 13:155-163
63. Schmutz J, Cannon SB, Schlueter J, Jianxin M, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Dong X, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Jane GX, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178-183
64. Sharma SK, Dawson IK, Wauge R (1995) Relationship among cultivated and wild Lentil revealed by RAPD analysis. Theor Appl Genet 91:647-651
65. Sharma SK, Knox MR, Ellis TNH (1996) AFLP analysis of the diversity and phylogeny of Lens and its comparison with RAPD analysis. Theor Appl Genet 93:751-758
66. Simon CJ, Muehlbauer FJ (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. J Hered 88:115-119
67. Singh RK, Raghuvanshi SS (1989) Plantlet regeneration from nodal segment and shoot tip derived explants of lentil. Lens Newsl 16:33-35
68. Solanki RK, Singh S, Kumar J (2010) Molecular marker assisted testing of hybridity of F 1 plants in lentil. J Food Legumes 23:21-24
69. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46:431-437
70. Tadmor Y, Zamir D, Ladizinsky G (1987) Genetic mapping of an ancient translocation in the genus Lens. Theor Appl Genet 73:883-892
71. Taran B, Buchwaldt L, Tullu A, Banniza S, Warkentin TD, Vandenberg A (2003) Using molecular markers to pyramid genes for resistance to ascochyta blight and anthracnose in lentil (Lens culinaris Medik.). Euphytica 134:223-230
72. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc Natl Acad Sci USA 98:9161-9166
73. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
74. Tullu A, Buchwaldt L, Warkentin T, Taran B, Vandenberg A (2003) Genetics of resistance to anthracnose and identification of AFLP and RAPD markers linked to the resistance gene in PI320937 germplasm of lentil (Lens culinaris Medikus). Theor Appl Genet 106:428-434
75. Tullu A, Taran B, Warkentin T, Vandenberg A (2008) Construction of an intraspecific linkage map and QTL analysis for earliness and plant height in lentil. Crop Sci 48:2254-2264
76. Vaillancourt RE, Slinkard AE (1993) Linkage of morphological and isozyme loci in lentil. Can J Plant Sci 73:917-926
77. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48-55
78. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA (2011) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83-89
79. Warkentin TD, McHughen A (1992) Agrobacterium tutumefaciens-mediated beta-glucuronidase (GUS) gene expression in lentil (Lens culinaris Medik.) tissues. Plant Cell Rep 11:274-278
80. Weber JL (1990) Informativeness of human (dC-dA)n (dG-dT)n polymorphisms. Genomics 7:524-530
81. Weeden NF, Muehlbauer FJ, Ladizinsky G (1992) Extensive conservation of linkage relationships between pea and lentil genetic maps. J Hered 83:123-129
82. Williams DJ, McHughen A (1986) Plant regeneration of the legume Lens culinaris Medik (lentil) in vitro. Plant Cell Tiss Org Cult 7:149
83. Zamir D, Ladizinsky D (1984) Genetics of allozyme variants and linkage groups in lentil. Euphytica 33:329-336
84. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single nucleotide polymorphisms (SNPs) in soybean. Genetics 163:1123-1134
85. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005) Bridging model and crop legumes through comparative genomics. Plant Physiol 137:1189-1196