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Table 2 Candidate transcripts identified for bulb-yield traits

From: Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum)

Traits

Candidate transcript

CEM a

P value b

 

RD c

Annotation

Genotype

Expression

  

BW

ASTG1209

M16

8.9 × 10−7

4.2 × 10−2

alpha-1,4 glucan phosphorylase L-1 isozyme

 

ASTG34835

M3

1.9 × 10−6

2.0 × 10−2

+

lncRNA

CN

ASTG1099

M41

2.2 × 10−6

1.4 × 10−2

+

uncharacterized protein

 

ASTG13201

M15

2.0 × 10−6

3.1 × 10−5

+

homeobox-leucine zipper protein

 

ASTG208

M43

1.0 × 10−6

1.3 × 10−9

+

lncRNA

 

ASTG2382

M43

1.6 × 10−6

4.5 × 10−5

+

Cystathionine beta-lyase

 

ASTG28883

M43

1.0 × 10−7

1.4 × 10−2

+

phospholipase

 

ASTG29757

M43

1.1 × 10−6

8.1 × 10−7

+

cytokinin riboside 5′-monophosphate phosphoribohydrolase

 

ASTG29985

M8

1.9 × 10−6

4.0 × 10−3

uncharacterized protein

 

ASTG3011

M43

4.9 × 10−8

1.1 × 10−9

+

lncRNA

 

ASTG34481

M43

2.9 × 10−9

3.5 × 10− 9

+

lncRNA

 

ASTG34606

M43

1.8 × 10−6

7.0 × 10−10

+

uncharacterized protein

 

ASTG35290

M43

3.6 × 10−7

2.1 × 10−7

+

lncRNA

 

ASTG36040

M43

3.2 × 10−8

1.8 × 10−4

+

lncRNA

 

ASTG36172

M9

2.3 × 10−6

3.2 × 10−4

+

U11/U12 small nuclear ribonucleoprotein

 

ASTG639

M41

4.7 × 10−9

9.5 × 10−3

+

UBX domain-containing protein

 

ASTG9975

M15

4.5 × 10−9

1.3 × 10−3

+

ankyrin repeat and SAM domain-containing protein

  1. aCEM, co-expression modules; b The genotype P value indicates the associated significance between SNPs of candidate transcript and traits, and the expression P value represents the significance of correlation between the expression of candidate transcript and traits; c RD is an abbreviation of regulation direction, and “+” and “-” indicates that the candidate transcript positively and negatively regulates the trait, respectively