Table 2.
GWAS sites stable over the two years
| QTL name | Trait | Chrom | Panel | Segment position (bp) | Sig. SNPs_ nb | Colocated genes | Colocated miRNA loci | ||
|---|---|---|---|---|---|---|---|---|---|
| Locus_id | Gene_symbol_Annotation | Locus_id | Annotation | ||||||
| QTL_1 | PBN | 1 | ind | 577,906–792,359 | 10 | MI0008222 | osa-MIR531b | ||
| QTL_2 | SpN | 1 | FP | 5,730,221–5,768,520 | 1 | ||||
| QTL_3 | PBintL | 1 | FP | 7,051,706–7,151,706 | 1 | ||||
| QTL_4 | SpN | 1 | ind | 8,812,823–8,951,604 | 3 | LOC_Os01g15900* | RDD1 | ||
| QTL_5 | PBN | 1 | FP & jap | 22,974,971–23,332,164 | 7 | LOC_Os01g40630* | LOG | ||
| QTL_6 | PBN & SpN | 1 | FP | 23,846,573–23,946,573 | 1 | LOC_Os01g42260 | LEUNIG putative homologue | ||
| QTL_7 | SpN | 1 | ind | 33,190,668–33,732,800 | 2 | LOC_Os01g54620* | OsCesA4/BC7 | ||
| QTL_8 | PBintL | 1 | FP_jap | 34,237,359–34,435,745 | 1 | ||||
| QTL_9 | SBN & SpN | 2 | FP | 16,621,984–17,305,751 | 9 | MI0001688 | osa-MIR437 | ||
| QTL_10 | PBN | 2 | FP & ind | 23,998,460–24,128,723 | 3 | LOC_Os02g39710* | OsCOL4 | MI0000661 | osa-MIR156i |
| QTL_11 | PBN | 3 | FP | 16,258,723–16,383,959 | 3 | ||||
| QTL_12 | SBL | 3 | FP | 17,703,587–18,076,496 | 1 | ||||
| QTL_13 | SpN | 3 | ind | 32,504,412–32,645,583 | 1 | MI0000666 | osa-MIR160d | ||
| QTL_14 | RL & PBintL | 4 | ind | 15,160,289–15,260,289 | 1 | ||||
| QTL_15 | RL | 4 | ind | 24,257,299–24,356,022 | 4 | MI0001102 | osa-MIR162b | ||
| QTL_16 | PBintL | 4 | FP | 32,699,641–32,843,112 | 2 | LOC_Os04g54900* | ILI1 | ||
| LOC_Os04g55070 | OsGA20ox2 putative homologue | ||||||||
| QTL_17 | PBintL | 6 | FP | 4,596,235–4,763,792 | 3 | ||||
| QTL_18 | PBintL | 7 | FP | 18,924,787–19,100,034 | 1 | LOC_Os07g32170* | OsSPL13 | ||
| QTL_19 | PBN & PBL | 8 | FP & jap | 5,221,963–5,450,178 | 1 | LOC_Os08g09190 | OsPILS2 | MI0001133 | osa-MIR171b |
| QTL_20 | PBintL | 8 | FP | 8,439,811–8,673,644 | 1 | ||||
| QTL_21 | PBintL | 8 | FP | 18,989,868–19,215,198 | 8 | ||||
| QTL_22 | RL | 9 | FP | 799,160–1,092,267 | 6 | ||||
| QTL_23 | PBintL | 10 | FP | 15,641,392–15,741,392 | 1 | ||||
| QTL_24 | PBN | 10 | FP | 17,498,080–18,064,123 | 5 | LOC_Os10g33780* | TAW1 | ||
| LOC_Os10g33940 | OsARF22 | ||||||||
| LOC_Os10g33310* | OsiICK6 | ||||||||
| QTL_25 | RL | 11 | FP & jap | 20,176,565–20,269,954 | 1 | LOC_Os11g34460* | OsFKF1 | ||
| QTL_26 | PBN | 11 | FP | 21,409,189–21,444,141 | 1 | ||||
| QTL_27 | PBintL | 11 | ind | 22,513,863–22,549,787 | 2 | ||||
| QTL_28 | SBintL | 12 | FP | 5,748,587–5,859,468 | 3 | ||||
| QTL_29 | SBN | 12 | FP | 15,423,955–15,784,175 | 1 | ||||
FP: full panel; ind: indica subpanel; jap: japonica subpanel; Chrom.: chromosome; Sig. SNPs_nb: number of significant SNPs; SBN: secondary branch number; PBN: primary branch number; SpN: spikelet number; SBintL: secondary branch internode length; PBintL: primary branch internode length; PBL: primary branch length; SBL: secondary branch length; RL: Rachis length; Locus-id: locus identification number in MSU7.0 (for coding genes) and mirBase v21 (for miRNAs); (*) Functionally characterized candidate genes in rice from OGRO and funRiceGenes databases (qtaro.abr.affrc.go.jp/ogro; funricegenes.ncpgr.cn)