












Fig. 1

The karyotypes of B73, Ki3, CML277, and recombinant chromosomes. a Chromosomes are numbered one to ten from left to right. Short arms are oriented up. DNA is in blue, centromeres appear white, the knob 180-bp repeat is shown in turquoise, and TR-1 repeat is in red. b Recombinant chromosomes 4 (from Ki3 × B73 RILs) and 6 (from CML277 × B73 RILs). On chromosome 4, the mixed 4L1 knob from Ki3 often recombines with the TR-1 knob from B73. On chromosome 6, we found recombinants demonstrating that there are two different knobs in CML277, one of which is composed primarily of TR-1 and another that is composed primarily of the 180-bp repeat

Table 1 Positions of knobs mapped in this study. The primary repeat present in each knob is noted as “180” (primarily made up of the knob 180-bp repeat), “TR-1” (primarily the TR-1 repeat), or “mixed” (indicating both repeats are present). The interval sizes differ in the different RILs due to natural variation in recombination and SNP polymorphism


Knobs lie in gene-dense areas


Fig. 2

Knobs occur in gene-rich regions of the genome. Gene density plots are shown to the left of chromosome bars (turquoise). Knob 180 (blue) and TR-1 (red) BLAST hit counts are shown to the right. In seven knobs (2L, 3L, 4L1, 4L2, 5L, 8L, and 9S), four of which are B73-specific (4L2, 5L, 8L, and 9S) map to chromosome arms. Orange blocks mark centromere regions. Green bars represent the genetic map intervals where knobs were mapped, where the lengths of the bars are limited by the nearest SNPs and resolution of the mapping population


Knobs affect local recombination


Table 3 Recombination in regions including and flanking knobs on 2L, 3L, and 5L in NAM RIL populations. This table shows the mean cM/Mb values and the results of t tests (indicated by P value). See Supplementary Table 1 for the complete data set. All NAM lines were included unless appropriate SNPs in the selected regions could not be identified. Recombination is significantly reduced over the regions containing the 2L and 3L knobs when in the heterozygous condition, but not in flanking regions


Fig. 3

Graphical displays of merged maps from knobbed and knobless RILs. Cumulative SNP-based genetic map positions (cM) are plotted against the genomic coordinates for chromosomes 2, 3, and 5 (Mb). A steeper slope indicates higher recombination rates. SNPs are shown in blue, centromere domains in green, and knob map intervals in red. a Chromosome 2. Dotted lines delineate a region around the knob that includes 20 cM in the knobbed/knobless RILs, but which is nearly 30 cM in the knobless/knobless RILs. b Chromosome 3. As for chromosome 2 above, dotted lines delineate a region around the knob that includes 20 cM in knobbed/knobless RILs but nearly 30 cM in the knobless/knobless RILs. c Chromosome 5; comparing RILs that were heterozygous for large/small and small/small knobs. The regions around paired knobs show evidence of reduced recombination (flattening), even though most of the knob sequence is missing from the physical map. The effect would presumably be much more dramatic if the physical map were complete


Fig. 4

Linkage disequilibrium analyses. a LD plots for the three B73 knob regions mapped to B73 reference genome assembly. b LD plot for the entirety of chromosome 4 in five sections, short arm oriented to left. SNPs are indicated by vertical lines that connect to LD plots below. Dark gray and black areas in triangle plots indicate regions of high LD. The knob map intervals (based on genetic mapping in RILs) are show in green, TR-1 repeats in red, and 180-bp repeats in blue






Materials and methods

Knob mapping


Gene density comparisons


Graphical displays of recombination


Statistical comparison of recombination distances on knobbed and knobless chromosomes


$$ \mathbf{SNP1}-5\ \mathrm{to}\ 30\ \mathrm{cM}-\mathbf{SNP2}-0\ \mathrm{to}10\ \mathrm{cM}-(\mathrm{KNOB})-0\ \mathrm{to}10\ \mathrm{cM}-\mathbf{SNP3}-5\ \mathrm{to}\ 30\ \mathrm{cM}-\mathbf{SNP4} $$

Linkage disequilibrium analysis



  1. Albert PS, Gao Z, Danilova TV, Birchler JA (2010) Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 129:6–16

    PubMed  Article  CAS  Google Scholar 

  2. Ananiev EV, Phillips RL, Rines HW (1998) A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: are chromosome knobs megatransposons? Proc Nat Acad Sci USA 95:10785–10790

    PubMed  Article  CAS  Google Scholar 


    PubMed  Article  CAS  Google Scholar 

  4. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    PubMed  Article  CAS  Google Scholar 

  5. Buckler ES, Phelps-Durr TL, Buckler CSK, Dawe RK, Doebley JF, Holtsford TP (1999) Meiotic drive of chromosomal knobs reshaped the maize genome. Genet 153:415–426

    CAS  Google Scholar 

  6. Charlesworth B, Sniegowski P, Stephan W (1994) The evoluationary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220

    PubMed  Article  CAS  Google Scholar 

  7. Creighton HB, McClintock B (1931) A correlation of cytological and genetical crossing-over in Zea mays. Proc Natl Acad Sci USA 17:492–497

    PubMed  Article  CAS  Google Scholar 

  8. Dawe RK (2009) Maize centromeres and knobs (neocentromeres). In: Bennetzen JL, Hake S (eds) Handbook of maize: genetics and genomics. Springer, New York, pp 239–250

    Google Scholar 

  9. Dawe RK, Hiatt EN (2004) Plant neocentromeres: fast, focused, and driven. Chromosom Res 12:655–669

    Article  CAS  Google Scholar 

  10. Fu HH, Zheng ZW, Dooner HK (2002) Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc Nat Acad Sci USA 99:1082–1087

    PubMed  Article  CAS  Google Scholar 


  12. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117

    PubMed  Article  CAS  Google Scholar 

  13. Hiatt EN, Kentner EK, Dawe RK (2002) Independently regulated neocentromere activity of two classes of tandem repeat arrays. Plant Cell 14:407–420

    PubMed  Article  CAS  Google Scholar 

  14. Kato A, Lamb J, Birchler J (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Nat Acad Sci USA 101:13554–13559

    PubMed  Article  CAS  Google Scholar 

  15. Kato YTA (1976) Cytological studies of maize (Zea mays L.) and teosinte (Zea mexicana Shrader Kuntze) in relation to thier origin and evolution. Massachusettes Agric Exp Station Bull 635:1–185

    Google Scholar 

  16. Kikudome GY (1959) Studies on the phenomenon of preferential segregation in maize. Genet 44:815–831

    CAS  Google Scholar 

  17. Lawrence CJ, Seigfried TE, Bass HW, Anderson LK (2006) Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator. Genet 172:2007–2009

    Article  CAS  Google Scholar 

  18. McClintock B (1929) Chromosome morphology in Zea mays. Science 69:629

    PubMed  Article  CAS  Google Scholar 

  19. McClintock B (1987) Chromosome constitutions of Mexican and Guatemalan races of maize. In: Moore J (ed) Genes cells and organisms. Garland, New York, pp 395–406

    Google Scholar 

  20. McClintock B, Yamakake T, Blumenschein A (1981) Chromosome constitution of races of maize: its significance in the interpretation of relationships between races and varieties in the Americas. Colegio de Postgraduado pp, Chapingo, Mexico, p 521

    Google Scholar 

  21. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740

    PubMed  Article  CAS  Google Scholar 

  22. Peacock WJ, Dennis ES, Rhoades MM, Pryor AJ (1981) Highly repeated DNA sequence limited to knob heterochromatin in maize. Proc Nat Acad Sci USA 78:4490–4494

    PubMed  Article  CAS  Google Scholar 

  23. Plohl M, Luchetti A, Mestrovic N, Mantovani B (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409:72–82

    PubMed  Article  CAS  Google Scholar 

  24. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575

    PubMed  Article  CAS  Google Scholar 

  25. Rhoades M (1952) Preferential segreagation in maize. Iowa State College Press, Ames, pp 66–82

    Google Scholar 

  26. Rhoades M, Dempsey E (1985) Structural heterogeneity of chromosome 10 in races of maize and teosinte. Alan R. Liss, Inc, New York, pp 1–18

    Google Scholar 

  27. Rhoades MM, Dempsey E (1966) Effect of abnormal chromosome 10 on preferential segregation and crossing over in maize. Genet 53:989–1020

    CAS  Google Scholar 

  28. Sandler L, Novitski E (1957) Meiotic drive as an evolutionary force. Am Nat 91:105–110

    Article  Google Scholar 


  30. Wu Y, Close TJ, Lonardi S (2011) Accurate construction of consensus genetic maps via integer linear programming. Ieee-Acm Trans On Comput Biol And Bioinforma 8:381–394

    Article  Google Scholar 

  31. Yao H, Zhou Q, Li J, Smith H, Yandeau M et al (2002) Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize. Proc Nat Acad Sci USA 99:6157–6162

    PubMed  Article  CAS  Google Scholar 

Download references



Author information



Corresponding author

Correspondence to R. Kelly Dawe.

Additional information

Communicated by Peter Shaw

Electronic supplementary material

Below is the link to the electronic supplementary material.


(XLSX 22 kb)

Rights and permissions


Reprints and Permissions

About this article

Cite this article

Ghaffari, R., Cannon, E.K.S., Kanizay, L.B. et al. Maize chromosomal knobs are located in gene-dense areas and suppress local recombination. Chromosoma 122, 67–75 (2013).

Download citation


  • Recombinant Inbred Line
  • Genome Assembly
  • Recombinant Inbred Line Population
  • Meiotic Drive
  • Recombinant Inbred Population