Table 2.
Selected candidate genes present in the ± 50 kb regions flanking markers with significantly different allele frequencies in early versus late elongating pools of red clover
| Candidate gene(s) | Locus | Putative pathway/process | Putative function |
|---|---|---|---|
| Frigida-like protein (FRL) | 1_1.16 | Vernalization | Transcription factor |
| Antagonist of like heterochromatin protein 1 (ALP1) | 4_17.77 | Vernalization/autonomous | Inhibition of PRC2-mediated silencing of FT-like genes |
| B3 domain-containing REM protein |
1_10.40 (3) 1_24.28 (2) |
Vernalization/meristem identity/organogenesis | Transcription factors |
| RNA-directed DNA methylation |
1_0.76 7_14.52 |
Regulating timing of reproductive development | Transcriptional gene silencing |
| Dicer-like 2 (DCL2) | 3_30.48 | Regulating development | Transcriptional and post-transcriptional gene silencing |
| DExH-box ATP-dependent RNA helicases | 1_12.58 | Regulating timing of reproductive development |
Post-transcriptional gene silencing RNA processing |
| Ribosome production factor 1 | 1_7.60 | Regulating timing of reproductive development | RNA processing |
| Receptor-like kinases similar to FERONIA | 6_21.88 (2) |
Vernalization/autonomous Photoperiod Cell elongation |
Alternative splicing Interaction with circadian clock |
| Gibberellin insensitive 1 (GID1) | 1_12.58 | Gibberellin signaling | Gibberellin receptor, interaction with DELLAs |
| Indeterminate domain (IDD) | 7_14.52 |
Gibberellin signaling Auxin signaling |
Interaction with DELLAs Auxin synthesis and transport |
| Ovate family protein (OFP) | 1_1.16 | Organogenesis | Transcriptional repressor |
| Cyclin-dependent kinase (CdK) inhibitor | 3_30.48 (2) | Cell cycle control | Binds and inhibits CdK |
| Auxin response factor (ARF) | 7_14.52 |
Auxin signaling Stem growth Organ polarity |
Transcriptional activator |
| Pectate lyase | 1_0.76 |
Auxin response Loosening of cell walls and cell elongation |
Pectin degradation |
|
Cobra (COB) Cobra-like 4 (COB4) |
6_21.88 | Anisotropic cell elongation | Regulator of cellulose biogenesis and microfibril orientation |
| Fasciclin-like arabinoglucan proteins | 7_14.52 (3) | Cell wall functioning | |
| Beta-fructofuranosidase | 1_10.40 | Cell wall formation | Provide hexoses for cellulose synthesis |
| UDP-arabinopyranose mutase 1 | 6_21.88 | Cell wall formation | Provide UDP-arabinose for synthesis of pectin and hemicellulose |
| Sec14-like phosphatidylinositol transfer protein (SEC14L-PITP) | 7_14.52 |
Auxin signaling Cellular trafficking |
Phospholipid transfer between membranes |
| Pleiotropic drug resistance protein 1 | 6_10.41 (6) |
Strigolactone signaling Cell to cell transport |
Transporter protein |
| Sorting nexin | 1_10.40 | Cellular trafficking | |
| Actin-related protein (ARP) | 3_5.42 | Cellular trafficking | Actin filament assembly and branching |
| Actin-depolymerizing factor (ADF) | 3_8.10 | Cellular trafficking | Actin cytoskeleton remodeling |
| Formin-like protein | 4_17.77 | Cellular trafficking |
More details are given in Table 1 and Supplementary Files 3 and 4