A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Zhang, Xiaojun ^a,f   Scheuring, Chantel F ^a   Zhang, Meiping ^a,b   Dong, Jennifer J ^a   Zhang, Yang ^a   Huang, James J ^a   Lee, Mi Kyung ^a   Abbo, Shahal ^c   Sherman, Amir ^d   Shtienberg, Dani ^d   Chen, Weidong ^e   Muehlbauer, Fred ^e   Zhang, Hong Bin ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b JILIN AGRICULTURAL UNIVERSITY   (China)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^d VOLCANI CENTER   (Israel)

^e WASHINGTON STATE UNIVERSITY   (United States)

^f INSTITUTE OF OCEANOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL CHROMOSOME; BACTERIAL ARTIFICIAL CHROMOSOME; CHICKPEA; CONTIG MAPPING; CULTIVAR; DNA FINGERPRINTING; FLOWER; GENE CONSTRUCT; GENE LIBRARY; GENE MAPPING; MOLECULAR CLONING; NONHUMAN; PLANT GENOME; PLANT TRANSFORMATION COMPETENT BINARY BACTERIAL ARTIFICIAL CHROMOSOME; QUANTITATIVE TRAIT LOCUS; CHROMOSOME MAP; GENETICS; METHODOLOGY; VARIABLE NUMBER OF TANDEM REPEAT;

CICER ARIETINUM; GLYCINE MAX; MEDICAGO; MYCOSPHAERELLA RABIEI;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CICER; CONTIG MAPPING; DNA FINGERPRINTING; GENE LIBRARY; GENOME, PLANT; MINISATELLITE REPEATS; PHYSICAL CHROMOSOME MAPPING; QUANTITATIVE TRAIT LOCI;

EID: 77958511375     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-501     Document Type: Article

References (55)

1. Ladizinsky G. Chickpea. Evolution of Crop Plants 1995, 258-261. London Longman, Smartt J, Simmonds NW.
2. FAO Production Data Base. 2005, FAO., http://www.fao.org
3. Singh KB, Reddy MV. Improving chickpea yield by incorporating response to Ascochyta blight. Theor Appl Genet 1996, 92:509-515.
4. Santra DK, Tekeoglu M, Ratnaparkhe ML, Kaiser WJ, Muehlbauer FJ. Identification and mapping of QTLs conferring resistance to Ascochyta blight in chickpea. Crop Sci 2000, 40:1606-1612.
5. Vir S, Grewal JS, Gupta VP. Inheritance of resistance to Ascochyta blight in chickpea. Euphytica 1975, 24:209-211.
6. Or E, Hovav R, Abbo S. A major gene for flowering time in chickpea. Crop Sci 1999, 39:315-322.
7. Kumar J, Abbo S. Genetics of flowering time in chickpea and its bearing on productivity in semi-arid environments. Adv Agron 2001, 72:107-138.
8. Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G. Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 1999, 262:90-101. 10.1007/s004380051063, 10503540.
9. Winter P, Benko-Iseppon AM, Huttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant VJ, Rajesh PN, Kahl G, Muehlbauer FJ. A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum X C. reticulatum cross: Localization of resistance genes for fusarium wilt races 4 and 5. Theor Appl Genet 2000, 101:1155-1163.
10. Tekeoglu M, Rajesh PN, Muehlbauer FJ. Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 2002, 105:847-854. 10.1007/s00122-002-0993-2, 12582909.
11. Flandez-Galvez H, Ford R, Pang ECK, Taylor PWJ. An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theor Appl Genet 2003, 106:1447-1456.
12. Pfaff T, Kahl G. Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Mol Gen Genomics 2003, 269:243-251.
13. Lichtenzveig J. Genetic and epidemiological aspects of D. rabiei resistance in chickpea. 2004, Ph.D. thesis, the Hebrew University of Jerusalem. Rehovot, Israel.
14. Flandez-Galvez H, Ades PK, Ford R, Pang ECK, Taylor PWJ. QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (Cicer arietinum L.). Theor Appl Genet 2003, 107:1257-1256. 10.1007/s00122-003-1371-4, 12928777.
15. Udupa SM, Baum M. Genetic dissection of pathotype-specific resistance to ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theor Appl Genet 2003, 106:1196-1202.
16. Cho S, Chen W, Muehlbauer FJ. Pathotype-specific genetic factors in chickpea (Cicer arietinum L.) for quantitative resistance to ascochyta blight. Theor Appl Genet 2004, 109:733-739. 10.1007/s00122-004-1693-x, 15146319.
17. Abbo S, Molina C, Jungmann R, Grusak MA, Berkovitch Z, Reifen R, Kahl G, Winter P, Reifen R. Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.). Theor Appl Genet 2005, 111:185-195. 10.1007/s00122-005-1930-y, 15918010.
18. Lichtenzveig J, Bonfil DJ, Zhang HB, Shtienberg D, Abbo S. Mapping quantitative trait loci in chickpea associated with time to flowering and resistance to Didymella rabiei the causal agent of Ascochyta blight. Theor Appl Genet 2006, 113:1357-1369. 10.1007/s00122-006-0390-3, 17016689.
19. Anbessa Y, Taran B, Warkentin TD, Tullu A, Vandenberg A. Genetic analyses and conservation of QTL for ascochyta blight resistance in chickpea (Cicer arietinum L.). Theor Appl Genet 2009, 119:757-765. 10.1007/s00122-009-1086-2, 19517090.
20. Rajesh PN, Coyne C, Meksem K, DerSharma K, Gupta V, Muehlbauer FJ. Construction of a Hind III bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 2004, 108:663-669. 10.1007/s00122-003-1464-0, 14564396.
21. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB. Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 2005, 110:492-510. 10.1007/s00122-004-1857-8, 15712010.
22. Buhariwalla HK, Jayashree BK, Eshwar K, Crouch JH. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biology 2005, 5:16. 10.1186/1471-2229-5-16, 1215491, 16107212.
23. Coram TE, Pang ECK. Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library. 2005, 66:192-200. Physiol Mol Plant Pathol.
24. Choudhary S, Sethy NK, Shokeen B, Bhatia S. Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 2009, 118:591-608. 10.1007/s00122-008-0923-z, 19020854.
25. Wu C, Sun S, Lee MK, Xu Z, Ren C, Santos TS, Zhang HB. Whole-genome Physical Mapping: An Overview on Methods for DNA Fingerprinting. The Handbook of Plant Genome Mapping: Genetic and Physical Mapping 2005, 257-284. Weinheim: Wiley-VCH Verlag GmbH, Meksem K, Kahl G.
26. Zhang H-B. Map-based cloning of genes and quantitative trait loci. Principles and Practices of Plant Genomics, Vol. 1: Genome Mapping 2007, 29-267. New Hampshire: Science Publishers, Kole C, Abbott AG.
27. Zhang H-B, Wu C. BACs as tools for genome sequencing. Plant Physiol Biochem 2001, 39:195-209.
28. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CMB, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, Maclean DJ, McDonald WH, Medina M, Meijer HJG, Morris PF, Nordberg EK, Ospina-Giraldo MD, Phuntumart V, Putnam NH, Rash S, Rose JKC, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BWS, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang HB, Grigoriev IV, Rokhsar DS, Boore JL. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 2006, 313:1261-1266. 10.1126/science.1128796, 16946064.
29. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S. Genome structure of the legume, Lotus japonicus. DNA Res 2008, 15:227-239. 10.1093/dnares/dsn008, 2575887, 18511435.
30. Medicago truncatula Sequence Resources. , http://www.medicago.org/genome/
31. Miyakogusa.jp. , http://www.kazusa.or.jp/lotus/
32. Phytozome. , http://www.phytozome.net/soybean
33. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Rep 1991, 9:208-218.
34. Cheng RIJ, Grant WF. Species relationships in the Lotus corniculatus group as determined by karyotype and cytophotometric analyses. Can J Genet Cytol 1973, 15:101-115.
35. Ren C, Xu ZY, Sun S, Lee MK, Wu C, Scheuring C, Santos TS, Zhang HB. Genomic DNA Libraries and Physical Mapping. The Handbook of Plant Genome Mapping: Genetic and Physical Mapping 2005, 173-213. Weinheim: Wiley-VCH Verlag GmbH, Meksem K, Kahl G.
36. Xu Z, van den Berg M, Scheuring C, Covaleda L, Lu H, Santos FA, Uhm T, Lee MK, Wu C, Liu S, Zhang HB. Genome-wide physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: A robust physical map of Penicillium chrysogenum. Nucleic Acids Res 2005, 33:e50. 10.1093/nar/gni037, 1065262, 15767275.
37. Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, Tian SK, Arredond F, Lee MK, Santos FA, Zhang HB, Tyler BM. An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 2006, 19:1302-1310. 10.1094/MPMI-19-1302, 17153914.
38. Xu Z, Sun S, Covaleda L, Ding K, Zhang A, Scheuring C, Zhang HB. Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage and contig map quality. Genomics 2004, 84:941-951. 10.1016/j.ygeno.2004.08.014, 15533711.
39. FPC. , http://www.agcol.arizona.edu/software/fpc/
40. Wu C, Sun S, Padmavathi N, Santos FA, Springman R, Meksem K, Lightfoot D, Zhang HB. A BAC and BIBAC-based physical map of the soybean genome. Genome Res 2004, 14:319-326. 10.1101/gr.1405004, 327108, 14718376.
41. Chang YL, Tao Q, Scheuring C, Meksem K, Zhang HB. An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 2001, 159:1231-1242. 1461882, 11729165.
42. Tao QZ, Chang YL, Wang J, Chen H, Schuering C, Islam-Faridi MN, Wang B, Stelly DM, Zhang HB. Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 2005, 158:1711-1724.
43. Ren C, Lee MK, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang HB. A BAC-based physical map of the chicken genome. Genome Res 2003, 13:2754-2758. 10.1101/gr.1499303, 403818, 14656976.
44. Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, Zhang HB. Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet 2004, 109:1041-1050. 10.1007/s00122-004-1712-y, 15164176.
45. The International Human Genome Mapping Consortium A physical map of the human genome. Nature 2001, 409:934-941. 10.1038/35057157, 11237014, The International Human Genome Mapping Consortium.
46. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor JF, Tellam R, Van Tassell1 CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol 2007, 8:R165. 10.1186/gb-2007-8-8-r165, 2374996, 17697342.
47. Wu Y, Tulsieram L, Tao Q, Zhang HB, Rothstein SJ. A binary vector-based large insert library for Brassica napus and identification of clones linked to a fertility restorer locus for Ogura cytoplasmic male sterility (CMS). Genome 2000, 43:102-109. 10.1139/gen-43-1-102, 10701119.
48. Ercolano MR, Ballvora A, Paal J, Steinbiss HH, Salamini F, Gebhardt C. Functional complementation analysis in potato via biolistic transformation with BAC large DNA fragments. Mol Breed 2004, 13:15-22.
49. Men AE, Meksem K, Kassem MA, Lohar D, Stiller J, Lightfoot D, Gresshoff PM. A bacterial artificial chromosome library of lotus japonicus constructed in an Agrobacterium tumefaciens- transformable vector. Mol Plant-Microbe Interact 2001, 14:422-425. 10.1094/MPMI.2001.14.3.422, 11277441.
50. Zhang HB. Construction and manipulation of large-insert bacterial clone libraries-manual. 2000, Texas A&M University, Texas., http://hbz7.tamu.edu
51. He L, Du C, Li Y, Scheuring C, Zhang HB. Large-insert bacterial clone libraries and their applications. Aquaculture Genome Technologies 2007, 215-244. Ames, Iowa: Blackwell Publishing, Liu Z.
52. Zhang MP, Li Y, Zhang HB. Isolation of megabase-sized DNA fragments from plants. Handbook of Nucleic Acid Purification 2008, 513-524. Florida, Taylor & Francis Group, LLC, Liu D.
53. Sambrook J, Russell DW. Molecular cloning: a laboratory manual (3rd ed.). 2001, 1-68. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, pp1..
54. ABI-ExportTabularData. , http://www.chromosomelab.dk/mlpa/download_ABI-ExportTabularData.html
55. Lee MK, Ren CW, Yan B, Cox B, Zhang HB, Romanov M, Sizemore FG, Suchyta SP, Peters E, Dodgson JB. Construction and characterization of three complementary BAC libraries for analysis of the chicken genome. Animal Genet 2003, 34:151-152. 10.1046/j.1365-2052.2003.00965_5.x, 12648103.