Table 3.
Summary of candidate gene selection at fs8.1 locus
AO, RNA-Seq dataset of anthesis-stage ovaries of fs8.1 backcrossed lines (from this study). Upstream indicates that SNPs or small indels are located upstream of the transcriptional start.
| Candidate gene | Expressed | Differentially expressed in AO (average of log2fold change, fs8.1/WT) | SNPs or small indels (compared with WT) | Selected only by putative function (annotation of encoding protein) |
|---|---|---|---|---|
| Solyc08g061560 | Yes | No | No | Yes (a putative orthologue of AtERECTA) |
| Solyc08g061650 | Yes | Yes (0.60) | Non-coding, upstreama | No |
| Solyc08g061820 | Yes | No | No | Yes (a putative orthologue of AtSLOMO) |
| Solyc08g061850 | Yes | No | Coding, N253D | No |
| Solyc08g061910 | Yes | No | Coding, premature stop codon | No |
| Solyc08g061930 | Yes | No | Non-coding, upstream | Yes (cytokinin oxidase) |
| Solyc08g062200 | Yes | No | Coding, +109aa | No |
| Solyc08g062340 | Yes | Yes (–1.26) | Non-coding, upstreamb | No |
| Solyc08g062370 | Yes | Yes (–1.89) | Non-coding, upstream | No |
| Solyc08g062450 | Yes | Yes (–1.53) | No | No |
| Solyc08g062580 | Yes | Yes (–4.11) | No | No |
| Solyc08g062630 | Yes | No | Non-coding, upstream | Yes (aminopeptidase M1-like protein) |
a A gap was found in the reference genome sequence between the coding region and the SNPs.
b SNPs that were not found in both M82 and Yellow Pear genome sequence datasets (Lin et al., 2014; E. van der Knaap, unpublished).