Theoretical and Applied Genetics

, Volume 107, Issue 5, pp 931–939 | Cite as

Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum)

  • A. Cenci
  • N. Chantret
  • X. Kong
  • Y. Gu
  • O. D. Anderson
  • T. Fahima
  • A. Distelfeld
  • J. Dubcovsky
Article

Abstract.

Durum wheat (Triticum turgidum ssp. durum, 2n = 4x = 28, genomes AB) is an economically important cereal used as the raw material to make pasta and semolina. In this paper we present the construction and characterization of a bacterial artificial chromosome (BAC) library of tetraploid durum wheat cv. Langdon. This variety was selected because of the availability of substitution lines that facilitate the assignment of BACs to the A and B genome. The selected Langdon line has a 30-cM segment of chromosome 6BS from T. turgidum ssp. dicoccoides carrying a gene for high grain protein content, the target of a positional cloning effort in our laboratory. A total of 516,096 clones were organized in 1,344 384-well plates and blotted on 28 high-density filters. Ninety-eight percent of these clones had wheat DNA inserts (0.3% chloroplast DNA, 1.4% empty clones and 0.3% empty wells). The average insert size of 500 randomly selected BAC clones was 131 kb, resulting in a coverage of 5.1-fold genome equivalents for each of the two genomes, and a 99.4% probability of recovering any gene from each of the two genomes of durum wheat. Six known copy-number probes were used to validate this theoretical coverage and gave an estimated coverage of 5.8-fold genome equivalents. Screening of the library with 11 probes related to grain storage proteins and starch biosynthesis showed that the library contains several clones for each of these genes, confirming the value of the library in characterizing the organization of these important gene families. In addition, characterization of fingerprints from colinear BACs from the A and B genomes showed a large differentiation between the A and B genomes. This library will be a useful tool for evolutionary studies in one of the best characterized polyploid systems and a source of valuable genes for wheat. Clones and high-density filters can be requested at http://agronomy.ucdavis.edu/Dubcovsky/BAC-library/BAC_Langdon.htm

Keywords.

BAC Genomic library Wheat Polyploid Triticum durum 

References

  1. Anderson OD, Greene FC (1997) The alpha-gliadin gene family.II. DNA and protein sequence variation, subfamily structure, and origins of pseudogenes. Theor Appl Genet 95:59–65CrossRefGoogle Scholar
  2. Anderson OD, Greene FC, Yip RE, Halford NG, Shewry PR, Malpica-Romero J-M (1989) Nucleotide sequences of the two high-molecular-weight glutenin genes from the D genome of hexaploid wheat, Triticum aestivum L. cv. Cheyenne. Nucleic Acids Res 17:461–462PubMedGoogle Scholar
  3. Anderson OD, AbrahamPierce FA, Tam A (1998) Conservation in wheat high-molecular-weight glutenin gene promoter sequences: comparisons among loci and among alleles of the Glu-B1-1 locus. Theor Appl Genet 96:568–576Google Scholar
  4. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218Google Scholar
  5. Blanco A, Bellomo MP, Cenci A, DeGiovanni C, Dovidio R, Iacono E, Laddomada B, Pagnotta MA, Porceddu E, Sciancalepore A, Simeone R, Tanzarella OA (1998) A genetic linkage map of durum wheat. Theor Appl Genet 97:721–728CrossRefGoogle Scholar
  6. Burke DT, Carle GF, Olson MV (1987) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236:806–812PubMedGoogle Scholar
  7. Cassidy BG, Dvorak J (1991) Molecular characterization of a low-molecular-weight glutenin cDNA clone from Triticum durum. Theor Appl Genet 81:653–660Google Scholar
  8. Chen FQ, Foolad MR (1997) Molecular organization of a gene in barley which encodes a protein similar to aspartic protease and its specific expression in nucellar cells during degeneration. Plant Mol Biol 35:821–831PubMedGoogle Scholar
  9. Chen M, SanMiguel P, Oliveira ACd, Woo S-S, Zhang H, Wing RA, Bennetzen JL (1997) Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 94:3431–3435PubMedGoogle Scholar
  10. Choi S, Creelman RA, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13:124–128Google Scholar
  11. Clarke L, Carbon J (1976) A colony bank containing synthetic ColE1 hybrid plasmids representative of the entire E. coli genome. Cell 9:91–100PubMedGoogle Scholar
  12. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–1567PubMedGoogle Scholar
  13. Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928Google Scholar
  14. Dubcovsky J, Galvez AF, Dvorak J (1994) Comparison of the genetic organization of the early salt stress response gene system in salt-tolerant Lophopyrum elongatum and salt-sensitive wheat. Theor Appl Genet 87:957–964Google Scholar
  15. Dubcovsky J, Ramakrishna W, SanMiguel P, Busso C, Yan L, Shiloff B, Bennetzen J (2001) Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol 125:1342–1353PubMedGoogle Scholar
  16. Dvorak J, Zhang HB (1990) Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc Natl Acad Sci USA 87:9640–9644PubMedGoogle Scholar
  17. Dvorak J, McGuire PE, Cassidy B (1988) Apparent sources of the A genomes of wheats inferred from the polymorphism in abundance and restriction fragment length of repeated nucleotide sequences. Genome 30:680–689Google Scholar
  18. Dvorak J, di Terlizzi P, Zhang HB, Resta P (1993) The evolution of polyploid wheats: identification of the A genome donor species. Genome 36:21–31Google Scholar
  19. Forde BG, Heyworth A, Pywell J, Kreis M (1985) Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. Nucleic Acids Res 13:7327–7339PubMedGoogle Scholar
  20. Gale MD, Atkinson MD, Chinoy CN, Harcourt RL, Jia J, Li QY, Devos KM (1995) Genetic maps of hexaploid wheat. In: Li ZS, Xin ZY (eds) Proc 8th Int Wheat Genetic Symp. China Agricultural Scientech Press, Beijing, pp 29–40Google Scholar
  21. Gao M, Chibbar RN (2000) Isolation, characterization, and expression analysis of starch synthase IIa cDNA from wheat (Triticum aestivum L.). Genome 43:768–775CrossRefPubMedGoogle Scholar
  22. Huang S, Sirikhachornkit A, Su XJ, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99:8133–8138CrossRefPubMedGoogle Scholar
  23. Joppa LR, Williams ND (1988) Langdon durum disomic substitution lines and aneuploid analysis in tetraploid wheat. Genome 30:222–228Google Scholar
  24. Joppa LR, Du C, Hart GE, Hareland GA (1997) Mapping a QTL for grain protein in tetraploid wheat (Triticum turgidum L.) using a population of recombinant inbred chromosome lines. Crop Sci 37:1586–1589Google Scholar
  25. Khan IA, Procunier JD, Humphreys DG, Tranquilli G, Schlatter AR, Marcucci-Poltri S, Frohberg R, Dubcovsky J (2000) Development of PCR based markers for a high grain protein content gene from Triticum turgidum ssp. dicoccoides transferred to bread wheat. Crop Sci 40:518–524Google Scholar
  26. Kihara H (1944) Discovery of the DD-analyser, one of the ancestors of Triticum vulgare. Agric Hortic 19:13–14Google Scholar
  27. Li Z, Rahman S, Kosar-Hashemi B, Mouille G, Appels R, Morell MK (1999a) Cloning and characterization of a gene encoding wheat starch synthase I. Theor Appl Genet 98:1208–1216Google Scholar
  28. Li ZY, Chu XS, Mouille G, Yan LL, Kosar-Hashemi B, Hey S, Napier J, Shewry P, Clarke B, Appels R, Morell MK, Rahman S (1999b) The localization and expression of the class II starch synthases of wheat. Plant Physiol 120:1147–1155PubMedGoogle Scholar
  29. Lijavetzky D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J (1999) Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42:1176–1182CrossRefPubMedGoogle Scholar
  30. Liu YG, Nagaki K, Fujita M, Kawaura K, Uozumi M, Ogihara Y (2000) Development of an efficient maintenance and screening system for large-insert genomic DNA libraries of hexaploid wheat in a transformation-competent artificial chromosome (TAC) vector. Plant J 23:687–695PubMedGoogle Scholar
  31. Luo MZ, Wang YH, Frisch D, Joobeur T, Wing RA, Dean RA (2001) Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome 44:154–162CrossRefPubMedGoogle Scholar
  32. Ma Z, Weining S, Sharp PJ, Liu C (2000) Non-gridded library: a new approach for BAC (bacterial artificial chromosome) exploitation in hexaploid wheat (Triticum aestivum). Nucleic Acids Res 28:e106CrossRefPubMedGoogle Scholar
  33. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, LaHillier LW, McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072–1084PubMedGoogle Scholar
  34. Morell MK, Rahman S, Regina A, Appels R, Li Z (2001) Wheat starch biosynthesis. Euphytica 119:55–58CrossRefGoogle Scholar
  35. Moullet O, Zhang H-B, Lagudah ES (1999) Construction and characterization of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99:305–313CrossRefGoogle Scholar
  36. Nachit MM, Elouafi I, Pagnotta MA, El Saleh A, Iacono E, Labhilili M, Asbati A, Azrak M, Hazzam H, Benscher D, Khairallah M, Ribaut JM, Tanzarella OA, Porceddu E, Sorrells ME (2001) Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var. durum). Theor Appl Genet 102:177–186Google Scholar
  37. Nair RB, Baga M, Scoles GJ, Kartha KK, Chibbar RN (1997) Isolation, characterization and expression analysis of a starch branching enzyme II cDNA from wheat. Plant Sci 122:153–163CrossRefGoogle Scholar
  38. Ogihara Y, Tsunewaki K (2000) Chinese Spring wheat (Triticum aestivum L.) chloroplast genome: complete sequence and contig clones. Yokohama City University and Fukui Prefetural University, JapanGoogle Scholar
  39. Ozkan H, Levy AA, Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13:1735–1747PubMedGoogle Scholar
  40. Panstruga R, Buschges R, Piffanelli P, Schulze-Lefert P (1998) A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res 26:1056–1062PubMedGoogle Scholar
  41. Payne PI, Corfield KG, Holt LM, Blackman JA (1981) Correlations between the inheritance of certain high molecular weight subunits of glutenin and bread-making quality in progenies of six crosses of bread wheat. J Agric Sci 32:51–60Google Scholar
  42. Peng MS, Hucl P, Chibbar RN (2001) Isolation, characterization and expression analysis of starch synthase I from wheat (Triticum aestivum L.). Plant Sci 161:1055–1062CrossRefGoogle Scholar
  43. Rahman S, Abrahams S, Abbott D, Mukai Y, Samuel M, Morell M, Appels R (1997) A complex arrangement of genes at a starch branching enzyme I locus in the D-genome donor of wheat. Genome 40:465–474PubMedGoogle Scholar
  44. Rahman S, Li Z, Abrahams S, Abbott D, Appels R, Morell MK (1999) Characterisation of a gene encoding wheat endosperm starch branching enzyme-I. Theor Appl Genet 98:156–163Google Scholar
  45. Rahman S, Regina A, Li ZY, Mukai Y, Yamamoto M, Kosar-Hashemi B, Abrahams S, Morell MK (2001) Comparison of starch-branching enzyme genes reveals evolutionary relationships among isoforms. Characterization of a gene for starch-branching enzyme IIa from the wheat D genome donor Aegilops tauschii. Plant Physiol 125:1314–1324PubMedGoogle Scholar
  46. Sabelli PA, Shewry PR (1991) Characterization and organization of gene families at the Gli-1 loci of bread and durum wheats by restriction fragment analysis. Theor Appl Genet 83:209–216Google Scholar
  47. SanMiguel P, Ramakrishna W, Bennetzen JL, Busso CS, Dubcovsky J (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A. Functional Integrative Genomics 2:70–80CrossRefPubMedGoogle Scholar
  48. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–1759PubMedGoogle Scholar
  49. Shizuya H, Birren B, Kim U-J, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797PubMedGoogle Scholar
  50. Singh NK, Donovan GR, Carpenter HC, Skerritt JH, Langridge P (1993) Isolation and characterization of wheat triticin cDNA revealing a lysine-rich repetitive domain. Plant Mol Biol 22:227–237PubMedGoogle Scholar
  51. Soltis DE, Soltis PS (1995) The dynamic nature of polyploid genomes. Proc Natl Acad Sci USA 92:8089–8091PubMedGoogle Scholar
  52. Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68PubMedGoogle Scholar
  53. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z (1999) Colinearity and its exceptions in orthologous Adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409–7414PubMedGoogle Scholar
  54. Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA (1999) A bacterial artificial chromosome library for sugarcane. Theor Appl Genet 99:419–424CrossRefGoogle Scholar
  55. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249PubMedGoogle Scholar
  56. Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA (1994) Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22:4922–4931PubMedGoogle Scholar
  57. Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093–1099CrossRefGoogle Scholar
  58. Zhang H-B, Choi S, Woo SS, Li Z, Wing RA (1996) Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Mol Breed 2:11–24Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • A. Cenci
    • 1
    • 3
  • N. Chantret
    • 1
    • 4
  • X. Kong
    • 2
  • Y. Gu
    • 2
  • O. D. Anderson
    • 2
  • T. Fahima
    • 1
    • 5
  • A. Distelfeld
    • 1
    • 5
  • J. Dubcovsky
    • 1
  1. 1.Department of Agronomy and Range Science, University of California, One Shields Avenue, Davis, CA 95616-8515, USA
  2. 2.USDA Western Reg. Research Center, 800 Buchanan St, Albany, CA 94710, USA
  3. 3.Dip. Biologia e Chimica Agroforestale e Ambientale, Università degli Studi di Bari, Via G. Amendola 165/a, 70126 Bari, Italy
  4. 4.CIRAD-AMIS-Biotrop, av. Agropolis, TA 40/30, 34398 Montpellier Cedex 5, France
  5. 5.The Institute of Evolution, University of Haifa, Mt. Carmel, Haifa. Israel

Personalised recommendations