Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives.
We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences of TRIM elements, Br1 and Br2. TRIM display using genomic DNA produced 50-70 bands ranging from 100 to 700 bp in all the species of the family Brassicaceae. TRIM display using B. rapa cDNA produced about 20 bands. Sequences of 11 randomly selected bands, 7 from genomic DNA and 4 from cDNA, begin with about 104 bp of the terminal repeat sequences of TRIM elements Br1 or Br2 and end with unique sequences indicating that all bands are derived from unique insertion sites of TRIM elements. Furthermore, 7 of the 11 unique sequences showed significant similarity with expressed gene. Most of the TRIM display bands were polymorphic between genera and about 55% (132 of 239 bands) are polymorphic among 19 commercial F1 hybrid cultivars. Analysis of phylogenetic relationships shows clear-cut lineage among the 19 cultivars. Furthermore, a combination of 11 polymorphic bands derived from only one primer combination can clearly distinguish one cultivar from the others. TRIM display bands were reproducible and inheritable through successive generations that is revealed by genetic mapping of 6 out of 27 polymorphic TRIM markers on the genetic map of Brassica napus. Collective data provide evidence that TRIM display can provide useful DNA markers in Brassica relatives because these markers are distributed in gene-rich regions, and are sometimes involved in the restructuring of genes.
Kwon
Soo-Jin
SJ
Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon, 441-707, South Korea.
Kim
Dong-Hyun
DH
Lim
Myung-Ho
MH
Long
Yan
Y
Meng
Jin-Ling
JL
Lim
Ki-Byung
KB
Kim
Jin-A
JA
Kim
Jung Sun
JS
Jin
Mina
M
Kim
Ho-Il
HI
Ahn
Sang-Nag
SN
Wessler
Susan R
SR
Yang
Tae-Jin
TJ
Park
Beom-Seok
BS
D001483:Base Sequence; D001937:Brassica / Q000145:classification / Q000235:genetics*; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000032:analysis* / Q000502:physiology; D005819:Genetic Markers / Q000502:physiology; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000502:physiology; D010802:Phylogeny; D011110:Polymorphism, Genetic; D018626:Retroelements / Q000502:physiology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D020079:Terminal Repeat Sequences
D018744:DNA, Plant; D005819:Genetic Markers; D018626:Retroelements
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