Skip to main content
SpringerLink
Log in

Molecular characterization of a genomic interval with highly uneven recombination distribution on maize chromosome 10 L

  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Homologous recombination in meiosis provides the evolutionary driving force in eukaryotic organisms by generating genetic variability. Meiotic recombination does not always occur evenly across the chromosome, and therefore genetic and physical distances are not consistently in proportion. We discovered a 278 kb interval on the long arm of chromosome 10 (10 L) through analyzed 13,933 descendants of backcross population. The recombinant events distributed unevenly in the interval. The ratio of genetic to physical distance in the interval fluctuated about 47-fold. With the assistance of molecular markers, the interval was divided into several subintervals for further characterization. In agreement with previous observations, high gene-density regions such as subinterval A and B were also genetic recombination hot subintervals, and repetitive sequence-riched region such as subinterval C was also found to be recombination inert at the detection level of the study. However, we found an unusual subinterval D, in which the 72-kb region contained 6 genes. The gene-density of subinterval D was 5.8 times that of the genome-wide average. The ratio of genetic to physical distance in subinterval D was 0.58 cM/Mb, only about 3/4 of the genome average. We carried out an analysis of sequence polymorphisms and methylation status in subinterval D, and the potential causes of recombination suppression were discussed. This study was another case of a detailed genetic analysis of an unusual recombination region in the maize genome.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Anderson LK, Lai A, Stack SM, Rizzon C, Gaut BS (2006) Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res 16:115–122

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Brown J, Sundaressan V (1991) A recombinational hotspot in the maize A1 intragenic region. Theor Appl Genet 81:185–188

    Article  Google Scholar 

  • Civardi L, Xia Y, Edwards K, Schnable P, Nikolau BJ (1994) The relation 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

    Article  PubMed  CAS  Google Scholar 

  • Davis GL, McMullen MD, Baysdorfer C, Musket T, Grant D, Staebell M et al (1999) A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152:1137–1172

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Dooner HK, Martinez-Ferez IM (1997) Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome. Plant Cell 9:1633–1646

    Article  PubMed  CAS  Google Scholar 

  • Dooner HK, Weck E, Adams S, Ralston E, Favreau M, English J (1985) A molecular genetic analysis of insertion mutations in the bronze locus in maize. Mol Gen Genet 200:240–246

    Article  CAS  Google Scholar 

  • Engler P, Weng A, Storb U (1993) Influence of CpG methylation and target spacing on V(D)J recombination in a transgenic substrate. Mol Cell Biol 13:571–577

    PubMed  CAS  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185

    PubMed  CAS  Google Scholar 

  • Freeling M, Bennett DC (1985) Maize Adh1. Annu Rev Genet 19:297–323

    Article  PubMed  CAS  Google Scholar 

  • Fu HH, Dooner HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci USA 99:9573–9578

    PubMed  CAS  Google Scholar 

  • Fu HH, Park WK, Yan XH, Zheng ZW, Shen BZ, 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

    Article  PubMed  CAS  Google Scholar 

  • Fu HH, Zheng ZW, 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

    PubMed  CAS  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202

    PubMed  CAS  Google Scholar 

  • Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwita BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117

    Article  PubMed  CAS  Google Scholar 

  • Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G et al (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624

    Article  PubMed  CAS  Google Scholar 

  • He LM, Dooner HK (2009) Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc Natl Acad Sci USA 106:8410–8416

    Article  PubMed  CAS  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

    PubMed  CAS  Google Scholar 

  • Li L, Santerre-Ayotte S, Boivin EB, Jean M, Belzile F (2004) A novel reporter for intrachromosomal homoeologous recombination in Arabidopsis thaliana. Plant J 40:1007–1015

    Article  PubMed  CAS  Google Scholar 

  • Li J, Hsia AP, Schnable PS (2007) Recent advances in plant recombination. Curr Opin Plant Biol 10:131–135

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Maloisel L, Rossignol JL (1998) Suppression of crossing-over by DNA methylation in Ascobolus. Genes Dev 12:1381–1389

    Article  PubMed  CAS  Google Scholar 

  • Mezard C (2006) Meiotic recombination hotspots in plants. Biochem Soc Trans 34:531–534

    Article  PubMed  CAS  Google Scholar 

  • Mezard C, Vignard J, Drouaud J, Mercier R (2007) The road to crossovers: plants have their say. Trends Genet 23:91–99

    Article  PubMed  CAS  Google Scholar 

  • Okagaki RJ, Weil CF (1997) Analysis of recombination sites within the maize waxy locus. Genetics 147:815–821

    PubMed  CAS  Google Scholar 

  • Petes TD (2001) Meiotic recombination hot spots and cold spots. Nat Rev Genet 2:360–369

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Schnable PS, Hsia AP, Nikolau BJ (1998) Genetic recombination in plants. Curr Opin Plant Biol 1:123–129

    Article  PubMed  CAS  Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Article  PubMed  CAS  Google Scholar 

  • Song R, Llaca V, Linton E, Messing J (2001) Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family. Genome Res 11:1817–1825

    PubMed  CAS  Google Scholar 

  • Thuriaux P (1977) Is recombination confined to structural genes on the eukaryotic genome? Nature 268:460–462

    Article  PubMed  CAS  Google Scholar 

  • Timmermans MC, Das OP, Bradeen JM, Messing J (1997) Region-specific cis- and trans-acting factors contribute to genetic variability in meiotic recombination in maize. Genetics 146:1101–1113

    PubMed  CAS  Google Scholar 

  • Yandeau-Nelson MD, Zhou Q, Yao H, Xu X, Nikolau BJ, Schnable PS (2005) MuDR transposase increases the frequency of meiotic crossovers in the vicinity of a Mu insertion in the maize a1 gene. Genetics 169:917–929

    Article  PubMed  CAS  Google Scholar 

  • Yandeau-Nelson MD, Nikolau BJ, Schnable PS (2006) Effects of trans-acting genetic modifiers on meiotic recombination across the a1-sh2 interval of maize. Genetics 174:101–112

    Article  PubMed  CAS  Google Scholar 

  • Yao H, Schnable PS (2005) Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common zea genetic background. Genetics 170:1929–1944

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Zhen YP, Subhash C, Yang XH, Zhou JQ, Li JS, Yan JB (2006) Method for detecting SNP based on PCR technique. J China Agricult Univ 11(3):51–55

    Google Scholar 

Download references

Acknowledgments

We would like to thank Binbin Huang for his technical support with DNA sequencing. This work was supported by NSFC (30700472 and 31171559), Ministry of Science and Technology of China (2006AA10Z148, 2006AA10A107, 2009CB118400).

Author information

Authors and Affiliations

  1. Shanghai Key Laboratory of Bio-Energy Crop, School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, People’s Republic of China

    Gang Wang, Jianping Xu, Yuanping Tang, Liangliang Zhou, Fei Wang, Zhengkai Xu & Rentao Song

Authors
  1. Gang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jianping Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yuanping Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Liangliang Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhengkai Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Rentao Song
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rentao Song.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 104 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, G., Xu, J., Tang, Y. et al. Molecular characterization of a genomic interval with highly uneven recombination distribution on maize chromosome 10 L. Genetica 139, 1109–1118 (2011). https://doi.org/10.1007/s10709-011-9613-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-011-9613-x

Keywords

Search

Navigation