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Table 1 Detailed information about the 11 detected associations using G and G × Y BLUPs for lgc and bs

From: Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

SNP IDa

Maj/Min Alleleb

Chrc

MAFd

Phenotype

GWAS model

P-vale

P-valregf

P-val FDRg

αh

PVEi

SNP location

Gene ID P. persica

v1.0 (v2.1)

TAIR10 BLASTp homologyj

Description

E-value

LG6_15273858

A/G

6

0.43

lgc G

multi-locus

1.22E-07

1.22E-07

–

0.20

41

Intron

ppa018341m.g

AT5G41980

Unknown Protein CONTAINS Harbinger transposase-derived nuclease domain

7E-51

GEMMA

2.88E-07

–

2.21E-03

0.21

–

bs G

0.28

–

0.42

lgc (G × Y)2013

multi-locus

3.85E-07

3.85E-07

–

0.14

40

0.43

lgc (G × Y)2015

multi-locus

1.04E-06

1.04E-06

0.26

46

LG5_5394803

G/A

5

0.19

lgc G

GEMMA

9.46E-06

–

4.88E-02

−0.15

–

Intron

ppa000004m.g

(Prupe.5G050700)

AT4G17140

Predicted: Pleckstrin (PH) domain containing protein

0.0

bs G

−0.38

multi-locus

8.10E-06

1.05E-08

–

−0.32

26

LG3_10897844

T/A

3

0.32

bs G

multi-locus

4.60E-03

2.73E-06

–

−0.31

19

CDS*

ppa017602m.g

(Prupe.3G152500)

AT5G17460

Glutamyl-tRNA (Gln) amidotransferase subunit C

2E-66

LG2_22535054

T/C

2

0.30

multi-locus

8.08E-05

2.27E-06

−0.29

17

Intron

ppa023961m.g

(Prupe.2G242100)

AT3G46850

Subtilisin-like protease SBT4.6

0.0

LG3_4322444

G/A

3

0.39

bs (G × Y)2015

multi-locus

7.22E-06

6.98E-06

0.46

43

CDS*

ppa008956m.g

(Prupe.3G072200)

AT1G52360

Coatomer subunit beta’-2

6.8e-117

LG5_4842835

T/A

5

0.19

multi-locus

7.00E-05

1.68E-05

−0.25

20

Intron

ppa020388m.g

(Prupe.5G044100)

AT4G18010

Type I inositol polyphosphate 5-phosphatase 2, IP5P2

0.0

LG7_18047191

C/T

7

0.45

lgc G

GEMMA

4.47E-07

–

2.72E-03

−0.05

3

Intron

ppa001722m.g

(Prupe.7G179600)

AT5G66030

GRIP Protein

0.0

bs G

0.19

12

  1. CDS* = Coding Sequence with SNP polymorphism impacting a non-synonymous substitution
  2. ppa018341m.g is not referenced in P.persica v2
  3. aSNP ID noted as LG[chromosome number]_[physical position in bp]
  4. bMajor/Minor Allele
  5. cChromosome
  6. dMinor Allele Frequency
  7. eSNP p-value (considered as the only fixed regressor in the model)
  8. fSNP p-value from the multi-locus optimal-model (multiple regressors)
  9. gSNP p-value in mvLMM corrected for FDR (False Discovery Rate)
  10. hAllelic effect (ln(x + 1) scale)
  11. iPercentage of phenotypic variance explained by the SNP
  12. jFunctional annotation obtained using BLASTp homology on A.thaliana (TAIR10 database)