Table 1 Differences between Desi and Kabuli seed types in allele frequencies of GWAS SNPs.

From: Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

Chromosome

Position

Allele

Desi allele frequencies

Kabuli allele frequencies

P-value

1

1732351

C/G

0.09/0.91

0.46/0.54

2.368e-08

2

32154998

T/A

0.98/0.02

0.52/0.48

6.521e-15

4

2145082

T/G

0.98/0.02

0.38/0.62

6.286e-21

4

3235996

A/T

0.85/0.15

0.23/0.77

3.992e-15

4

3242507

G/A

0.90/0.10

0.24/0.76

1.414e-15

4

3302269

A/G

0.81/0.19

0.19/0.81

5.547e-10

4

9410036

T/C

0.81/0.19

0.27/0.73

3.088e-11

4

29186930

C/A

0.63/0.37

0.16/0.84

4.740e-06

4

30315118

G/C

0.81/0.19

0.31/0.69

7.545e-10

4

37188483

T/C

0.29/0.71

0.00/1.00

5.539e-05

4

37659499

G/A

0.42/0.58

0.05/0.95

5.447e-05

4

37659516

A/G

0.42/0.58

0.05/0.95

5.447e-05

4

37659524

G/A

0.44/0.56

0.05/0.95

1.762e-05

4

37805026

T/C

0.42/0.58

0.10/0.90

6.665e-05

4

37824651

C/G

0.43/0.57

0.10/0.90

8.924e-05

4

37824675

C/G

0.43/0.57

0.10/0.90

8.923e-05

4

37878401

A/G

0.43/0.57

0.09/0.91

0.0001

4

48998832

T/C

0.91/0.09

0.67/0.33

0.0001

5

33132457

T/A

0.71/0.29

0.96/0.04

0.001

7

5407505

G/T

0.42/0.58

0.95/0.05

1.257e-08

7

5782593

C/G

0.41/0.59

0.94/0.06

5.922e-10

  1. Chi-square test showed that 21 of 28 significant SNPs have significant associations (p-value < 0.05) with either Desi or Kabuli market class. Fisher’s exact test was used for alleles with less than 10 representatives.
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