Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Jan 1998; 148(1): 435–443.
PMCID: PMC1459770

Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice.


Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leriathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.

Full Text

The Full Text of this article is available as a PDF (648K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ahn S, Anderson JA, Sorrells ME, Tanksley SD. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet. 1993 Dec;241(5-6):483–490. [PubMed]
  • Bennetzen JL. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 1996 Sep;4(9):347–353. [PubMed]
  • Bennetzen JL, Freeling M. Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet. 1993 Aug;9(8):259–261. [PubMed]
  • Berg JM, Shi Y. The galvanization of biology: a growing appreciation for the roles of zinc. Science. 1996 Feb 23;271(5252):1081–1085. [PubMed]
  • Chen M, Bennetzen JL. Sequence composition and organization in the Sh2/A1-homologous region of rice. Plant Mol Biol. 1996 Dec;32(6):999–1001. [PubMed]
  • Chen M, SanMiguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA, Bennetzen JL. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):3431–3435. [PMC free article] [PubMed]
  • Civardi L, Xia Y, Edwards KJ, Schnable PS, Nikolau BJ. The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8268–8272. [PMC free article] [PubMed]
  • Cook WB, Walker JC. Identification of a maize nucleic acid-binding protein (NBP) belonging to a family of nuclear-encoded chloroplast proteins. Nucleic Acids Res. 1992 Jan 25;20(2):359–364. [PMC free article] [PubMed]
  • Das OP, Poliak E, Ward K, Messing J. A new allele of the duplicated 27kD zein locus of maize generated by homologous recombination. Nucleic Acids Res. 1991 Jun 25;19(12):3325–3330. [PMC free article] [PubMed]
  • Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. [PMC free article] [PubMed]
  • Elder JF, Jr, Turner BJ. Concerted evolution of repetitive DNA sequences in eukaryotes. Q Rev Biol. 1995 Sep;70(3):297–320. [PubMed]
  • Gaut BS, Doebley JF. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809–6814. [PMC free article] [PubMed]
  • Shaw JR, Hannah LC. Genomic Nucleotide Sequence of a Wild-Type Shrunken-2 Allele of Zea mays. Plant Physiol. 1992 Mar;98(3):1214–1216. [PMC free article] [PubMed]
  • Hulbert SH, Richter TE, Axtell JD, Bennetzen JL. Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4251–4255. [PMC free article] [PubMed]
  • Laughnan JR. The Action of Allelic Forms of the Gene A in Maize. IV. on the Compound Nature of A and the Occurrence and Action of Its A Derivatives. Genetics. 1952 Jul;37(4):375–395. [PMC free article] [PubMed]
  • Moore G, Devos KM, Wang Z, Gale MD. Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995 Jul 1;5(7):737–739. [PubMed]
  • Pelèse-Siebenbourg F, Caelles C, Kader JC, Delseny M, Puigdomènech P. A pair of genes coding for lipid-transfer proteins in Sorghum vulgare. Gene. 1994 Oct 21;148(2):305–308. [PubMed]
  • SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. [PubMed]
  • Schwarz-Sommer Z, Shepherd N, Tacke E, Gierl A, Rohde W, Leclercq L, Mattes M, Berndtgen R, Peterson PA, Saedler H. Influence of transposable elements on the structure and function of the A1 gene of Zea mays. EMBO J. 1987 Feb;6(2):287–294. [PMC free article] [PubMed]
  • Strathmann M, Hamilton BA, Mayeda CA, Simon MI, Meyerowitz EM, Palazzolo MJ. Transposon-facilitated DNA sequencing. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1247–1250. [PMC free article] [PubMed]
  • Whitkus R, Doebley J, Lee M. Comparative genome mapping of Sorghum and maize. Genetics. 1992 Dec;132(4):1119–1130. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Gene (nucleotide)
    Gene (nucleotide)
    Records in Gene identified from shared sequence links
  • MedGen
    Related information in MedGen
  • Nucleotide
    Published Nucleotide sequences
  • Protein
    Published protein sequences
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...