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Table 2 GWAS sites stable over the two years

From: A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits

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

    
  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)