Table 3.
Sequence Analysis of DMRs
| DMRa | Selective Primer Combinationb | Inbredc | Lengthd | ESTe | DNA or Protein Homologye |
|---|---|---|---|---|---|
| MMP4 | ACA/CGAA | W23 | 757 | None | CC933496 |
| MMP5* | As above | W23 | 546 | BM339610 | AF078917 (centromeric retrotransposon-like repeat CentA) |
| MMM7* | ACA/AATT | W64 | 344 | BU093060 | BAB12027 (hypothetical ring finger protein, Oryza sativa) |
| MMP8 | ACA/CGAA | A69Y | 351 | None | None |
| MMP9* | As above | A69Y | 583 | BM080498 | NP_563889 (expressed protein, A. thaliana) |
| MMP11* | AGA/CGAA | W23 | 197 | AW172080 | NP_921858 (En/Spm-like transposon, O. sativa) |
| MMP21* | ACC/TAGC | W64 | 326 | CF056235 | NP_908521 (transposon Tip100, O. sativa) |
| MMP22* | AGT/TAGC | A69Y | 540 | None | None |
| MMP26* | AGA/TCCA | A69Y | 509 | None | BZ368936 |
| PMP2* | AGA/CGAA | W64 | 985 | CF041957 | AAB84331 (putative N-acetylglucosaminephosphotransferse, A. thaliana) |
| MMP43* | AGT/AATT | W64 | 665 | CD976902 | NP_190991 (RNA recognition motif containing protein, A. thaliana) |
| MPM53* | ACA/CGTT | W64 | 292 | None | BZ539615 |
| MMPa3 | ACA/AATT | B73 | 443 | CD526326 | AF479697 (putative target of liguless3/4); NP_922450 (putative gypsy-type retrotransposon) |
| MMPa4 | As above | B73 | 344 | As MMP7 | As MMP7 |
| MMPa5 | As above | Mo17 | 317 | None | CG383037 |
| MMPa6 | As above | B73 | 188 | None | BH869432 |
| MMPe3 | AGA/CGTT | Mo17 | 305 | CF049215 | X15406 (3′ noncoding region of GpaI pseudogene; NP_198800 (putative RNA-like helicase, O. sativa) |
| MMPe4 | As above | B73 | 330 | None | BZ317541 (methylation-filtered genomic sequence) |
| MMPf1 | ACC/CGTT | B73 | 227 | None | None |
| MMPh5 | AGA/CGAA | Mo17 | 294 | CA275440 (Saccharum officinarum) | CAE05494 (putative protein, O. sativa) |
| MMPh7 | As above | B73 | 162 | None | BH783657 |
| MMPi2 | ACC/CGAA | B73 | 506 | None | BH870119 |
| MMPi3 | As above | Mo17 | 494 | None | As MMPi2 |
| MMPi6 | As above | Mo17 | 268 | CF037288 | NP_914980 (putative protein, O. sativa) |
| MMPi7 | As above | Mo17 | 258 | None | NP_922823 (putative transposase, O. sativa) |
| MMPm1 | ACA/CGTT | B73 | 595 | CA399229 | None |
| MMPm2 | As above | Mo17 | 552 | CF674952 | S29330 (hypothetical En-1 transposon protein) |
| MMPn4.1 | AGA/TAGC | B73 | 313 | None | BH777106 |
| MMPn4.2 | As above | B73 | 313 | CB927767 (Sorghum bicolor) | NP_912742 (unnamed protein, O. sativa) |
| MMPn5 | As above | B73 | 233 | BG104058 (S. propinquum) | NP_908906 (putative Ser/Thr protein phosphatase, O. sativa) |
| MMPn6 | As above | B73 | 226 | CA140644 (S. officinarum) | NP_916752 (putative protein, O. sativa) |
| MMPp3 | AGT/TAGC | B73 | 554 | CD227645 (S. bicolor) | NP_199332 (cyclin family, A. thaliana) |
An MSAP fragment that showed an MMP or a PMP was excised after acrylamide gel electrophoresis, reamplified using the appropriate primer combinations, cloned, and subjected to DNA sequencing. Only fragments exhibiting identical sequences of three independent clones were included.
Nucleotide extensions of EcoRI-00 and HpaII-00 primers (see Methods) used in the selective amplification reaction.
The inbred line that exhibited an MMP or a PMP.
Length of the fragment analyzed.
BlastN (Basic Local Alignment Search Tool) and BlastX similarity scores were considered significant for E values <0.00001. Unless indicated, EST and genomic clones were from Z. mays; the BlastX hits indicated of MMP9, PMP2, MMPa3, MMPi6, and MMPn6 were specific to the EST sequence, and the others were common to both the EST and DMR.
Refers to an MMP or a PMP analyzed by DNA gel blotting.
GpaI, glyceraldehyde-3-phosphate dehyrogenase subunit A.