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Table 3 Association statistics of markers significantly associated with seven traits by Mixed Linear Model (MLM) with two different MAF thresholds (5% and 10%)

From: An association mapping approach to identify favourable alleles for tomato fruit quality breeding

ASSOCIATION STATISTICS

      

MAF >5%

MAF >10%

Traita

Marker Index

SolCap ID

Geneb

Ch

Site bp

p value

R2

p value

R2

AsA

2383

solcap_snp_sl_20936

Solyc03g112630.2.1

3

57066578

2.74E-04

0.140

1.30E-04

0.145

 

7588

solcap_snp_sl_9377

Solyc03g112670.2.1

3

57099944

2.74E-04

0.140

1.30E-04

0.145

 

1241

solcap_snp_sl_105

Solyc05g052410.1.1

5

61782821

3.92E-04

0.179

4.35E-04

0.176

log (β-C)

2022

solcap_snp_sl_17063

Solyc01g087600.2.1

1

74314683

3.61E-04

0.198

4.58E-04

0.173

 

2025

solcap_snp_sl_17072

Solyc01g087670.2.1

1

74360789

2.44E-04

0.206

  
 

2028

solcap_snp_sl_17076

Solyc01g087880.2.1

1

74515488

4.94E-04

0.192

2.48E-04

0.185

log (t-LYC)

3525

solcap_snp_sl_27094

Solyc03g031480.2.1

3

8291198

1.82E-04

0.175

  
 

3526

solcap_snp_sl_27099

Solyc03g031820.2.1

3

8571009

1.82E-04

0.175

  
 

3104

solcap_snp_sl_24679

ND

10

60360427

2.38E-04

0.203

9.66E-05

0.208

log (PHE)

354

solcap_snp_sl_100367

Solyc08g082350.2.1

8

62345755

6.2E-04

0.147

7.62E-05

0.213

 

4365

solcap_snp_sl_34253

Solyc11g010170.1.1

11

3259108

5.13E-05

0.198

2.03E-04

0.150

log (FW)

2992

solcap_snp_sl_23884

Solyc02g078790.2.1

2

38009446

4.49E-04

0.175

  
 

2272

solcap_snp_sl_19779

Solyc08g006170.1.1

8

886583

2.04E-04

0.165

  
 

2273

solcap_snp_sl_19780

Solyc08g006170.1.1

8

886634

2.04E-04

0.165

  
 

2274

solcap_snp_sl_19782

Solyc08g006170.1.1

8

887192

2.04E-04

0.165

  
 

2275

solcap_snp_sl_19783

ND

8

887435

3.49E-06

0.239

  
 

1081

solcap_snp_sl_44897

Solyc11g071840.1.1

11

52280165

5.66E-04

0.132

1.57E-04

0.170

log (pH)

2246

solcap_snp_sl_19556

Solyc11g017070.1.1

11

7863387

2.65E-04

0.168

5.27E-04

0.131

log (TA)

955

solcap_snp_sl_54697

Solyc01g107550.2.1

1

86813075

4.59E-06

0.254

  
 

2032

solcap_snp_sl_17161

Solyc02g084520.2.1

2

42190707

5.25E-04

0.156

4.83E-04

0.137

 

443

solcap_snp_sl_100446

Solyc03g083440.2.1

3

46891412

6.52E-04

0.149

  
 

3999

solcap_snp_sl_30911

Solyc03g093310.2.1

3

47931799

4.15E-04

0.159

  
 

1210

solcap_snp_sl_101075

ND

4

222976

1.98E-04

0.175

  
 

1010

solcap_snp_sl_45282

Solyc04g005510.2.1

4

344863

1.98E-04

0.175

  
  1. Marker index, SolCAP ID, corresponding gene, locus position (Ch and site), p-value and marker R2 are reported for each marker.
  2. aAsA: Ascorbic Acid, β-C: β-carotene, t-LYC:trans-lycopene, PHE:phenolics, FW: Fresh weight, TA: Titratable acidity. bND = Not detected gene for the marker.