Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853
Recently, we isolated and characterized four genome-type-specific repetitive
DNA sequences in rice. Characterization of these repetitive DNAs that are
unique in the AA, CC, EE or FF genome types is summarized in Table 1. There is
no cross hybridization among the four repetitive DNAs even under low-stringency
washing conditions (T\m\ -30degrees C). These genome-type-specific repetitive
sequences are useful as hybridization probes in classifying unknown species of
wild or domestic rice, and in studying genome evolution at the molecular level.
These sequences may also be used in monitoring crosses between different rice
genome types in plant breeding experiments. There are at least two advantages
in using repetitive DNAs rather than single-copy genes as hybridization probes.
First, since a specific repetitive DNA is present in thousands of copies in the
cell, the hybridization is much stronger than using a single-copy gene as a
probe. Second, since a given repetitive DNA sequence is usually located on a
number of chromosomes, it will serve as a more useful marker in monitoring
genetic crosses for plant breeders.
We used the AA genome-type-specific repetitive DNA sequence (pOs48) as a hybridization probe to determine the apparent copy number of this family of repetitive DNA among 31 rice entries of the AA genome type. The melting temperature (T\m\) of the homoduplex of pOs48 was shown to be 76 degrees C under specific conditions. Under a relatively low stringency condition (washing the filter at 21 degrees C below T\m\), the apparent copy number varies between 50 copies in O. glaberrima (Accession #103971) and 7,000 copies in O. meridionalis (Accession #101147). At a moderately high stringency condition (washing the filter at 6 degrees C below T\m\), the apparent copy number varies between zero (in five rice entries) and 3,700.
We noted that the apparent copy number and thermal stability of the pRC48-like sequence in the offspring of genetic crosses appears to follow a predictable pattern. For example, the cross between Belle Patna (female parent) and Dawn C1 gave rise to Labelle (Bollich et al. 1973). The apparent copy number and thermal stability of the pOs48-like sequences in Labelle follow those of Belle Patna more closely than those of Dawn C1. This information is consistent with the observation by Bollich et al. (1973) that Labelle is similar to Belle Patna in morphology and maturity time. In a second example, the female parents and grandparents of IR36 included IR1561 and Peta, and the male parents included CR9413. We noted that, again, the apparent copy number and thermal stability of pOs48-like sequences in IR36 follow those of its female parents more closely than those of its male parents. Obviously, more cases need to be studied before a firm conclusion can be drawn regarding the pattern of inheritance or the evolutionary changes of repetitive DNAs in rice.
This work is supported by research grant RF84066, Allocation No. 3, from the Rockefeller Foundation.
Table 1. Summary of the four genome-type specific rice repetitive DNAs
===============================================================================
Species IRRI Genome Name of Size of Copy
accession # type clone repeat unit number
===============================================================================
O. sativa var. Labelle AA pOs48 355 bp 2,000
O. officinalis 103286 CC pOo2 366 bp 170,000
O. australiensis 101467 EE pOa4 511 bp 80,000
O. brachyantha 101236 FF pOb1 159 bp 184,000
===============================================================================
Bollich, C.N., J.G. Atkins, J.E. Scott and B.D. Webb, 1973. Registration of Labelle rice. Crop Science 13: 773-774.