Table 2. Causative deletion candidates identified by BSREx-seq.
| BSR-seqa | Exome-seqb | Causative Deletion Candidates | Description | |
|---|---|---|---|---|
| 1039_o2 | chr7:12.5 Mb | chr7:10,800,211-10,800,237 | GRMZM2G015534 (chr7:10,798,621-10,801,375) | Chr7: 25 bp deletion in OPAQUE-2 gene |
| 916 | chr5:59.3 Mb | NA | GRMZM2G017081 (chr5:59,835,738-59,840,942)c | Chr5: Cyclin-A2 in a ∼8.6 kb deletion |
| 1554 | chr10:130.2 Mb | None overlappedd | GRMZM2G139797 (chr10: 130,166,275-130,168,20)c | Chr10: ZmCLO2b, a caleosin family member |
| 146 | NA | chr4:41,397,178-41,401,983 | GRMZM2G138060 (chr4:41,396,390-41,405,179) | Chr4: 10 exons deleted in SUGARY-1 gene, ∼4.8 kb |
| 1115 | chr3:137.7 Mb | chr3:125,369,536-127,035,245 | >86 exons in 26 genes | Chr3: 1.7-Mb deletion |
| 937 | chr4:174.9 Mb | chr4:176,912,920-176,919,560 | GRMZM2G449909 (chr4:176,900,008-176,926,797) | Chr4: Six exons deleted in OPAQUE-1 gene, 6203 bp |
| 883 | chr8:13.2 Mb | None overlappedd | Possible regulatory elements | Chr8: beyond coding regions |
a
In BSR-seq, linkage peak was plotted across the whole genome, and its genome coordinate was shown (chrosome#:coordinate, Mb).
b
In exome-seq, the deletion overlapped with the linkage peak was used as causative deletion candidate.
c
Mutants 916 and 1554 were with a causative gene candidate based on BSR-seq gene expression difference.
d
Exome-seq analysis showed that no gene/exon showed a deletion in the linkage peak region of mutants 883 and 1554. And a deletion in the regulatory region might be beyond coding regions.