Skip to main content
Log in

Distribution of genes and recombination in wheat and other eukaryotes

  • Review of Plant Biotechnology and Applied Genetics
  • Published:
Plant Cell, Tissue and Organ Culture Aims and scope Submit manuscript

Abstract

The genome sizes of eukaryotes may differ as much as 10,400-fold. A part of these differences may be attributed to polyploidy, and increase in gene number and size. Most of the genome size disparity is due to non-transcribed repeated DNA including retrotransposons and pseudogenes. Only a small fraction of the larger genomes such as those of many crop plants, contain genes. Genes are distributed unevenly along the chromosomes, often organized in clusters of varying sizes and gene-densities (gene-rich regions). The regions corresponding to gene-clusters in smaller genome plants such as rice may be divided into many ‘mini’ gene-clusters in the related larger genomes. The range of gene-density within the ‘mini2019; gene-clusters is about the same among plants with varying genome sizes. Recombination per chromosome is similar among eukaryotes, and thus is considerably independent of DNA content and chromosome size. Relatively little recombination occurs outside the gene-rich regions. Recombination varies dramatically among various gene regions, and is highly uneven within gene regions as well. Consequently, a significant number of genes may be inaccessible to recombination-based manipulations such as map-based cloning.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Adams MD et al. (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185–2195

    Article  PubMed  Google Scholar 

  • Arumuganathan K & Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208–218

    Google Scholar 

  • Barakat A, Carels N & Bernardi G (1997) The distribution of genes in the genomes of Gramineae. Proc. Natl. Acad. Sci. USA 94: 6857–6861

    Google Scholar 

  • Bennett MD & Smith JB (1991) Nuclear DNA amounts in angiosperms. Philos. Trans. Roy. Soc. Lond. B 334: 309–345

    Google Scholar 

  • Bollag RJ, Waldman AS & Liskay RM (1989) Homologous recombination in mammalian cells. Annu. Rev. Genet. 23: 199–225

    Google Scholar 

  • Bondareva SN (2000) Extent of Recombination and Its Detection Using F2 vs. Backcross Population. Department of Agronomy, University of Nebraska-Lincoln, USA

    Google Scholar 

  • Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B & Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc. Natl. Acad. Sci. USA 99: 9328–9333

    Google Scholar 

  • Bussey H et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387: 103–105

    Google Scholar 

  • Cao L, Alani E & Kleckner N (1990) A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell 61: 1089–1101

    Google Scholar 

  • Chen M, SanMiguel P & Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435–443

    Google Scholar 

  • Civardi L, Xia Y, Edwards KJ, Schnable PS & Nikolau BJ (1994) The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc. Natl. Acad. Sci. USA 91: 8268–8272

    Google Scholar 

  • Cook KR & Karpen GH (1994) A rosy future for heterochromatin. Proc. Natl. Acad. Sci. USA 91: 5219–5221

    Google Scholar 

  • CSHL/WUGSC/PEB Arabidopsis Sequencing Consortium (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100: 377–386

    Google Scholar 

  • Curtis CA & Lukaszewski AJ (1991) Genetic linkage between C-bands and storage protein genes in chromosome 1B of tetraploid wheat. Theor. Appl. Genet. 81: 245–252

    Google Scholar 

  • Dimitri P & Junakovic N (1999) Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin. Trends Genet. 15: 123–124

    Google Scholar 

  • Dooner HK (1986) Genetic fine structure of bronze locus in maize. Genetics 113: 1021–1036

    Google Scholar 

  • Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA & Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol. 125: 1342–1353

    Google Scholar 

  • Dujon B et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature 387: 98–102

    Google Scholar 

  • Dvorak J & Chen KC (1984) Phylogenetic relationships between chromosomes of wheat and chromosome 2E of Elytrigia elongata. Can. J. Genet. Cytol. 26: 128–132

    Google Scholar 

  • Endo TR & Gill BS (1996) The deletion stocks of common wheat. J. Hered. 87: 295–307

    Google Scholar 

  • Ernest K, Kumar A, Kriseleit D, Kloos DU, Phillips MS & Ganal MW (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J. 31: 127–136

    Google Scholar 

  • Feuillet C & Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. USA 96: 8265–8270

    Google Scholar 

  • Finnegan D (1992) Transposable elements. Curr. Opin. Genet. Dev. 4: 838–844

    Google Scholar 

  • Flavell AJ, Pearce S & Kumar A (1994) Plant transposable elements and the genome. Curr. Opin. Genet. Dev. 4: 838–844

    Google Scholar 

  • Fu H, Park W, Yan X, Zheng Z, Shen B & Dooner HK (2001) The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome. Proc. Natl. Acad. Sci. USA 98: 8903–8908

    Google Scholar 

  • Fu H, Zheng Z & Dooner HK (2002) Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99: 1082–1087

    Google Scholar 

  • Gill BS, Friebe B & Endo TR (1991) Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome 34: 830–839

    Google Scholar 

  • Gill KS, Gill BS & Endo TR (1993) A chromosome region-specific mapping strategy reveals gene rich telomeric ends in wheat. Chromosoma 102: 374–381

    Article  CAS  Google Scholar 

  • Gill KS, Gill BS, Endo TR & Boyko E (1996a) Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143: 1001–1012

    CAS  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR & Taylor T (1996b) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144: 1883–1891

    CAS  PubMed  Google Scholar 

  • Goff SA et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100

    Article  CAS  PubMed  Google Scholar 

  • Grandbastien M (1992) Retroelements in higher plants. Trends Genet. 8: 103–108

    Google Scholar 

  • Grewal SI, Bonaduce MJ & Klar AJ (1998) Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics 150: 563–576

    Google Scholar 

  • Henikoff S, Greene AE, Pietrokovski S, Bork P, Attwood TK & Hood L (1997) Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609–614

    Google Scholar 

  • Hey J & Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595–608

    CAS  PubMed  Google Scholar 

  • Hubert R, MacDonald M, Gusella J & Arnheim N (1994) High resolution localization of recombination hot spots using sperm typing. Nat. Genet. 7: 420–424

    Google Scholar 

  • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921

    Google Scholar 

  • Inukai T, Sako A, Hirano HY & Sano Y (2000) Analysis of intragenic recombination at wx in rice: correlation between the molecular and genetic maps within the locus. Genome 43: 589–596

    Google Scholar 

  • Kihara H (1944) Discovery of the DD-analyser, one of the ancestors of vulgare wheats. Agric. Hortic. 19: 889–890

    Google Scholar 

  • Kimber G (1970) The relationships of single alien chromosomes to the homoeologous groups of Triticum aestivum. In: Finlay KW & Shephard KW (eds) Proceedings of the 3rd International Wheat Genetics Symposium (pp. 62–68), New York, NY

  • Klein S, Zenvirth D, Dror V, Barton AB, Kaback DB & Simchen G (1996) Patterns of meiotic double-strand breakage on native and artificial yeast chromosomes. Chromosoma 105: 276–284

    Google Scholar 

  • Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR & Stefansson K (2002) A high-resolution recombination map of the human genome. Nat. Genet. 31: 241–247

    Google Scholar 

  • Kubis S, Schmidt T & Heslop-Harrison J (1998) Repetitive DNA elements as a major component of plant genomes. Ann. Bot. 82: 45–55

    Google Scholar 

  • Kumar A & Bennetzen JL (1999) Plant retrotransposons. Annu. Rev. Genet. 33: 479–532

    Google Scholar 

  • Kunzel G, Korzum L & Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154: 397–412

    PubMed  Google Scholar 

  • Lahaye T, Shirasu K & Schulze-Lefert P (1998) Chromosome landing at the barley Rar1 locus. Mol. Gen. Genet. 260: 92–101

    Google Scholar 

  • Lambie EJ & Roeder GS (1986) Repression of meiotic crossing over by a centromere (CEN3) in Sacchromyces cerevisiae. Genetics 114: 769–789

    Google Scholar 

  • Lambie EJ & Roeder GS (1988) A yeast centromere acts in cis to inhibit meiotic gene conversion of adjacent sequences. Cell 52: 863–873

    Google Scholar 

  • Laurent AM, Puechberty J, Prades C & Roizes G (1998) Informative genetic polymorphic markers within the centromeric regions of human chromosome 17 (D17S2205) and 11 (D11S4975). Genomics 52: 166–172

    Google Scholar 

  • Laurie DA & Hulten MA (1985) Further studies on bivalent chiasma frequency in human males with normal karyotypes. Ann. Hum. Genet. 49: 189–201

    Google Scholar 

  • Lichten M & Goldman ASH (1995) Meiotic recombination hotspots. Annu. Rev. Genet. 29: 423–444

    Google Scholar 

  • Llaca V & Messing J (1998) Amplicons of maize zein genes are conserved within genic but expanded and constricted in intergenic regions. Plant J. 15: 211–220

    Google Scholar 

  • McFadden ES & Sears ER (1946) The origin of Triticum spelta and its free-threshing hexaploid relatives. J. Hered. 37: 81–89

    Google Scholar 

  • Mckee BD, Lumsden SE & Das S (1993) The distribution of male meiotic pairing sites on chromosome 2 of Drosophila melanogaster: meiotic pairing and segregation of 2-Y transpositions. Chromosoma 102: 180–194

    Google Scholar 

  • Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfeiffer F & Zollner A (1997) Overview of the yeast genome. Nature 387 suppl.: 7–8

    Google Scholar 

  • Meyers BC, Tingey SV & Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11: 1660–1676

    Google Scholar 

  • Meyers BC, Kozik A, Griego A, Kuang H & Michelmore RW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809–834

    Article  CAS  PubMed  Google Scholar 

  • Nicolas A, Treco D, Svostak S & Svostak JW (1989) An initiation site for meiotic gene conversion in the yeast Saccharomyces cerevisiae. Nature 338: 35–39

    Google Scholar 

  • Noel L, Moores TL, van Der Biezen EA, Parniske M, Daniels MJ, Parker JE & Jones JD (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11: 2099–2112

    Article  CAS  PubMed  Google Scholar 

  • Ozkan H, Levy A & Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735–1747

    Article  CAS  PubMed  Google Scholar 

  • 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: 1056–1062

    Google Scholar 

  • Pimpinelli S, Berloco M, Fanti L, Dimitri P, Bonaccorsi S, Marchetti E, Caizzi R, Caggese C & Gatti M (1995) Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92: 3804–3808

    Google Scholar 

  • Puechberty J, Laurent AM, Gimenez S, Billault A, Laurent MEB, Calenda A, Marcais B, Prades C, Loannou P, Yurov Y & Roizes G (1999) Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across 5cen. Genomics 56: 274–287

    Google Scholar 

  • 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: 465–474

    Google Scholar 

  • Ross L, Maxfield R & Dawson D (1996) Exchanges are not equally able to enhance meiotic chromosome segregation in yeast. Proc. Natl. Acad. Sci. USA 93: 4979–4983

    Google Scholar 

  • Rostoks N, Park YJ, Ramakrishna W, Ma J, Druka A, Shiloff BA, SanMiguel PJ, Jiang Z, Brueggeman R, Sandhu D, Gill K, Bennetzen JL & Kleinhofs A (2002) Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct. Integr. Genomics 2: 51–59

    Google Scholar 

  • Rubin et al. (2000) Comparative genomics of the eukaryotes. Science 287: 2204–2215

    Article  CAS  PubMed  Google Scholar 

  • Sandhu D & Gill KS (2002a) Gene-containing regions of wheat and the other grass genomes. Plant Physiol. 128: 803–811

    Google Scholar 

  • Sandhu D & Gill KS (2002b) Structural and functional organization of the ‘1S0.8 gene-rich region’ in the Triticeae. Plant Mol. Biol. 48: 791–804

    Google Scholar 

  • Sandhu D, Champoux JA, Bondareva SN & Gill KS (2001) Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes. Genetics 157: 1735–1747

    Google Scholar 

  • Sandhu D, Erayman M, Dilbirligi M, Sidhu D & Gill KS (2003) The gene-rich regions of the wheat genome. In: Proceedings of the 10th International Wheat Genetics Symposium 1: 308–312

    Google Scholar 

  • SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z & Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768

    Google Scholar 

  • Shaked H, Kashkush K, Ozkan H, Feldman M & Levy A (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749–1759

    Google Scholar 

  • Shirasu K, Schulman AH, Lahaye T & Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908–915

    Google Scholar 

  • Spring J (1997) Vertebrate evolution by interspecific hybridization- are we polyploid? FEBS Lett. 400: 2–8

    Google Scholar 

  • Stein N, Feuillet C, Wicker T, Schlagenhauf E & Keller B (2000) Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc. Natl. Acad. Sci. USA 97: 13436–13441

    Google Scholar 

  • Su Y, Barton AB & Kaback DB (2000) Decreased meiotic reciprocal recombination in subtelomeric regions in Saccharomyces cerevisiae. Chromosoma 109: 467–475

    Google Scholar 

  • Sumner AT, Torre JDL & Stuppia L (1993) The distribution of genes on chromosomes: a cytological approach. J. Mol. Evol. 37: 117–122

    Google Scholar 

  • Tanksley SD et al. (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141–1160

    CAS  PubMed  Google Scholar 

  • Tarchini R, Biddle P, Wineland R, Tingey S & Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1–Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381–391

    Article  CAS  PubMed  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815

    Google Scholar 

  • The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2018–2018

    Google Scholar 

  • 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: 7409–7414

    Google Scholar 

  • Tranquilli G, Lijavetzky D, Muzzi G & Dubcovsky J (1999) Genetic and physical characterization of grain texture-related loci in diploid wheat. Mol. Gen. Genet. 262: 846–850

    Google Scholar 

  • Venter JC et al. (2001) The sequence of the human genome. Science 291: 1304–1351

    Article  CAS  PubMed  Google Scholar 

  • Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing RA, Leister D, Schulze-Lefert P & Wise RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153: 1929–1948

    CAS  PubMed  Google Scholar 

  • Wei F, Wing RA & Wise RP (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14: 1903–1917

    Google Scholar 

  • White MA, Dominska M & Petes TD (1993) Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 90: 6621–6625

    Google Scholar 

  • Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E & Keller B (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26: 307–316

    Google Scholar 

  • Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T & Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525–535

    Article  Google Scholar 

  • Wu TC & Lichten M (1994) Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263: 515–518

    Google Scholar 

  • Yao H, Zhou Q, Li J, Smith H, Yandeau M, Nikolau BJ & Schnable PS (2002) Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize. Proc. Natl. Acad. Sci. USA 99: 6157–6162

    Google Scholar 

  • Yu J et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kulvinder S. Gill.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sidhu, D., Gill, K.S. Distribution of genes and recombination in wheat and other eukaryotes. Plant Cell Tiss Organ Cult 79, 257–270 (2005). https://doi.org/10.1007/s11240-005-2487-9

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11240-005-2487-9

Key words

Navigation