Table 2 Loci significantly associated with phenotypes related to fruit shape with genome-wide significance.

From: Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

Chr:Position

Genomic region

Nearest gene (kb)

Min/Maj alleles

MAF

Phenotype

β

SE

p-value

3:183386147

CA03g16080

0

C/T

0.13

Circular

0.10

0.016

1.36E-08

Ellipsoid

0.03

0.005

1.58E-10

Fruit Shape Index External I

0.91

0.145

4.93E-09

Lobedness Degree

16.97

2.449

1.38E-10

10:28759675

Intergenic

CA10g04730 (−911)

T/C

0.36

Distal Angle Macro

18.47

2.962

4.97E-09

10:28759685

Intergenic

CA10g0473 (-910)

T/G

0.36

Distal Angle Macro

18.47

2.962

4.97E-09

10:33533810

Intergenic

CA10g05040 (166) CA10g05050 (-156)

C/T

0.22

Ovoid

−0.08

0.012

8.87E-10

Proximal Fruit Blockiness

−0.12

0.018

1.91E-10

10:33533831

Intergenic

CA10g05040 (167) CA10g05050 (156)

T/A

0.22

Ovoid

−0.08

0.012

8.87E-10

Proximal Fruit Blockiness

−0.12

0.018

1.91E-10

10:33534094

Intergenic

CA10g05040 (169) CA10g05050 (-156)

A/G

0.22

Ovoid

−0.08

0.012

8.87E-10

Proximal Fruit Blockiness

−0.12

0.018

1.91E-10

10:33557960

Intergenic

CA10g05040 (408) CA10g05050 (-132)

C/G

0.1

Ovoid

−0.15

0.024

5.43E-09

Proximal Fruit Blockiness

−0.24

0.036

4.04E-10

11:18204293

Intergenic

CA11g04570 (849) CA11g04580 (-892)

T/A

0.06

Ellipsoid

0.04

0.006

4.39E-09

  1. Min/Maj = minor and major alleles; MAF = Minor Allele Frequency; β = Coefficient describing the effect size of the marker in the univariate linear model of association; SE = Standard Error of β; p-value = genome-wide Bonferroni corrected p-value for association.
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