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PMID: 15659640 Published · ppublish English Comparative Study Journal Article

Evolution of DNA sequence nonhomologies among maize inbreds.

The Plant cell ·Vol. 17 ·No. 2 ·2005-02-00 ·Pages 343-60

Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A

Abstract

Allelic chromosomal regions totaling more than 2.8 Mb and located on maize (Zea mays) chromosomes 1L, 2S, 7L, and 9S have been sequenced and compared over distances of 100 to 350 kb between the two maize inbred lines Mo17 and B73. The alleles contain extended regions of nonhomology. On average, more than 50% of the compared sequence is noncolinear, mainly because of the insertion of large numbers of long terminal repeat (LTR)-retrotransposons. Only 27 LTR-retroelements are shared between alleles, whereas 62 are allele specific. The insertion of LTR-retrotransposons into the maize genome is statistically more recent for nonshared than shared ones. Most surprisingly, more than one-third of the genes (27/72) are absent in one of the inbreds at the loci examined. Such nonshared genes usually appear to be truncated and form clusters in which they are oriented in the same direction. However, the nonshared genome segments are gene-poor, relative to regions shared by both inbreds, with up to 12-fold difference in gene density. By contrast, miniature inverted terminal repeats (MITEs) occur at a similar frequency in the shared and nonshared fractions. Many times, MITES are present in an identical position in both LTRs of a retroelement, indicating that their insertion occurred before the replication of the retroelement in question. Maize ESTs and/or maize massively parallel signature sequencing tags were identified for the majority of the nonshared genes or homologs of them. In contrast with shared genes, which are usually conserved in gene order and location relative to rice (Oryza sativa), nonshared genes violate the maize colinearity with rice. Based on this, insertion by a yet unknown mechanism, rather than deletion events, seems to be the origin of the nonshared genes. The intergenic space between conserved genes is enlarged up to sixfold in maize compared with rice. Frequently, retroelement insertions create a different sequence environment adjacent to conserved genes.

MeSH Terms
Alleles Breeding Chromosome Mapping Chromosomes, Artificial, Bacterial Chromosomes, Plant/genetics DNA, Plant/chemistry,genetics Evolution, Molecular Genome, Plant Molecular Sequence Data Multigene Family Oryza/genetics Plant Proteins/genetics Retroelements/genetics Sequence Analysis, DNA Terminal Repeat Sequences/genetics Zea mays/genetics
Chemicals
DNA, Plant Plant Proteins Retroelements BZ2 protein, Zea mays
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Brunner Stephan
DuPont Crop Genetics Research, Wilmington, Delaware 19880, USA. stephan.brunner@cgr.dupont.com
Fengler Kevin
Morgante Michele
Tingey Scott
Rafalski Antoni
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.104.025627
Email
stephan.brunner@cgr.dupont.com
Published
2005-02-00
Epub
2005-00-19
Pages
343-60
Language
English
Region
England
NLM ID
9208688
PMCID
PMC548811
Subset
IM
Databases
GENBANK
AY664413, AY664414, AY664415, AY664416, AY664417, AY664418, AY664419, AY691949
External Links
PubMed source DOI: 10.1105/tpc.104.025627 PMC Full Text View journal details
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