Analysis of genome organization, composition and microsynteny using 500 kb BAC sequences in chickpea

Theoretical and Applied Genetics

Volumn 117, Issue 3, 2008, Pages 449-458

  Rajesh, P N ^a   O'Bleness, Majesta ^b   Roe, Bruce A ^b   Muehlbauer, Fred J ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANNING; FOOD PRESERVATION; HEALTH; LIFE CYCLE; MAPS;

ASCOCHYTA BLIGHT RESISTANCE; CHICKPEA GENOME; CICER ARIETINUM; ECONOMIC IMPORTANCE; GENE DENSITY; GENETIC LINKAGE MAPS; GENOME ORGANIZATION; GENOME SIZES; GENOMIC REGIONS; GENOMIC RESEARCH; GENOMIC SEQUENCING; GENOMIC TOOLS; GENOMICS; MEDICAGO TRUNCATULA; MICROSYNTENY; PROTEIN LENGTHS; SPRINGER (CO); SYNTENY;

ECONOMIC ANALYSIS;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BASE PAIRING; CELL CLONE; CHICKPEA; GENETICS; GENOME; NUCLEOTIDE SEQUENCE; QUANTITATIVE TRAIT LOCUS; RETROPOSON; SYNTENY;

BASE PAIRING; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CICER; CLONE CELLS; GENOME, PLANT; QUANTITATIVE TRAIT LOCI; RETROELEMENTS; SYNTENY;

ASCOCHYTA; CICER ARIETINUM; MEDICAGO TRUNCATULA;

EID: 47249151337     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-008-0789-0     Document Type: Article

References (44)

1. Bodenteich A, Chissoe S, Wang YF, Roe BA (1993) Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. In: Venter JC (ed) Automated DNA sequencing and analysis techniques. Academic Press, London, pp 42-50
2. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 17(5):16
3. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78-94
4. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103:14959-14964
5. Chissoe SL, Bodenteich A, Wang YF, Wang YP, Burian Dennis CSW, Crabtree J, Freeman A, Iyer K, Jian L, Ma Y, McLaury HJ, Pan HQ, Sharan O, Toth S, Wong Z, Zhang G, Heisterkamp N, Groffen J, Roe BA (1995) Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia chromosomal translocation. Genomics 27:67-82
6. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci 101:15289-15294
7. Corum T, Pang ECK (2005) Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library. Physiol Mol Plant Pathol 66:192-200
8. Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M, Nelson JR, Chapman J, Lou Y, Rokhsar D, Hawkins TL, Richardson PM (2002) Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 80:691-698
9. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small amount of fresh leaf tissue. Phytochem Bull 19:11-15
10. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of collinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342-1353
11. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194
12. Ewing B, Hillier L, Wendl M, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185
13. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X et al (2002) Sequence and analysis of rice chromosome 4. Nature 420:316-320
14. Gill KS, Gill BS, Endo TR, Taylor T (1996) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144:1883-1891
15. Goff SA et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100
16. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195-202
17. Jeandet P, Douillet-Breuil AC, Bessis R, Debord S, Sbaghi M, Adrian M (2002) Phytoalexins from the Vitaceae: biosynthesis, phytoalexins gene expression in transgenic plants, antifungal activity and metabolism. J Agric Food Chem 50:2731-2741
18. Jurka J (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16:418-420
19. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172-175
20. Kato T, Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (2003) Structural analysis of a Lotus japonicus genome: V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 Mb regions of the genome. DNA Res 10:277-285
21. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
22. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) 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 110:492-510
23. Manly KF (1998) User's manual for map manager classic and map manager QT
24. Nelson JC (1997) QGENE: software for maker-based genomic analysis and breeding. Mol Breed 3:239-245
25. Neumann P, Koblížková A, Navrátilová A, Macas JI (2006) Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics 173:1047-1056
26. Pan HQ, Wang YP, Chissoe SL, Bodenteich A, Wang Z, Iyer K, Clifton SW, Crabtree JS, Roe BA (1994) The complete nucleotide sequence of the SacBII domain of the P1 pAD10-SacBII cloning vector and three cosmid cloning vectors: pTCF, svPHEP, and LAWRIST16. Genetic Anal Techniques Appl 11:181-186
27. Rajesh PN, Muehlbauer FJ (2008) Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.). Euphytica (in press)
28. Rajesh PN, Coyne C, Meksem K, Sharma KD, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663-669
29. Rajesh PN, McPhee K, Muehlbauer FJ (2005) Detection of polymorphism using CAPS and dCAPS markers in two chickpea genotypes. Int Chickpea Pigeonpea Newsl 12:4-6
30. Rakshit S, Winter P, Tekeoglu M, Juarez Muñoz J, Pfaff T, Benko-Iseppon AM, Muehlbauer FJ, Kahl G (2003) DAF marker tightly linked to a major locus for Ascochyta blight resistance in chickpea (Cicer arietinum L.). Euphytica 132:23-30
31. Roe BA (2004) Shotgun library construction for DNA sequencing in methods in molecular biology, vol 255: Bacterial artificial chromosomes, vol 1: Library construction, physical mapping and sequencing. Human Press, Totowa, pp 171-187
32. Roe B, Crabtree J, Khan A (1996) In: Rickwood D (eds) DNA isolation and sequencing: essential techniques series. Wiley, New York
33. Salamov AA, Solovyev VV (2000) Ab initio gene finding in drosophila genomic DNA. Genome Res 10:516-522
34. Sandhu D, Gill KS (2002) Gene-containing regions of wheat and the other grass genomes. Plant Physiol 128:803-811
35. Santra DK, Tekeoglu M, Ratnaparkhe MB, Gupta VS, Ranjekar PK, Muehlbauer FJ (2000) Identification and mapping of QTLs conferring resistance to ascochyta blight in chickpea. Crop Sci 40:1606-1612
36. Sanyal I, Singh AK, Kaushik M, Amla DV (2005) Agrobacterium-mediated transformation of chickpea (Cicer arietinum L.) with Bacillus thuringiensis cry-IAc gene for resistance against pod borer insect Helicoverpa armigera. Plant Sci 168:1135-1146
37. Sarmah BK, Moore A, Tate W, Molvig L, Morton RL, Rees DP, Chiaiese P, Chrispeels MJ, Tabe LM, Higgins TJV (2004) Transgenic chickpea seeds expressing high levels of a bean α-amylase inhibitor. Mol Breeding 14:73-82
38. Stein L et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599-1610
39. Tekeoglu M, Rajesh PN, Muehlbauer FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 105:847-854
40. Ware D, Stein L (2003) Comparison of genes among cereals. Curr Opin Plant Biol 6:121-127
41. Wheeler DL et al (2005) Plant genome resources at the National Center for Biotechnology Information. Plant Physiol 138:1280-1288
42. Yu O et al (2002) A draft sequence of the rice genome. Science 296:79-91
43. Yu O, Shi J, Hession AO, Maxwell CA, McGonigle B, Odell JT (2003) Metabolic engineering to increase isoflavone biosynthesis in soybean seed. Phytochemistry 63:753-763
44. Zhang J, Madden T (1997) PowerBLAST: a new network BLAST application for interactive and automated sequence analysis and annotation. Genome Res 7:649-656