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Table 1 Validation of the CoSSA SNPs

From: Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

SNP

R allele donor

Association with P2 resistance*

Association with P6 resistance*

Association with P18 resistance*

χ2

χ2 test significance

chr00_20792298

Kuba

2.1E−14

1.2E−14

8.3E−15

1.5

ns

chr00_20801212

Kuba

1.3E−14

7.3E−15

4.8E−15

1.2

ns

chr00_20858042

Kuba

2.1E−14

1.2E−14

8.3E−15

1.5

ns

chr00_20872536

Kuba

1.3E−14

7.3E−15

4.8E−15

1.2

ns

chr03_15683229

Ludmilla

6.8E−01

6.9E−01

3.0E−01

0.1

ns

chr04_64488861

Ludmilla

6.6E−01

9.7E−01

3.8E−01

0.1

ns

chr04_65204393

Ludmilla

4.5E−01

1.1E−01

2.0E−01

1.5

ns

chr05_2117034

Ludmilla

3.8E−01

9.4E−02

1.4E−01

0.0

ns

chr05_8795719

Ludmilla

2.0E−01

9.0E−02

1.6E−01

0.0

ns

chr05_9254557

Ludmilla

2.3E−01

8.4E−02

1.8E−01

0.0

ns

chr09_55113777

Ludmilla

2.4E−03

9.0E−04

4.2E−03

0.0

ns

chr09_55354021

Ludmilla

4.6E−03

1.3E−03

5.9E−03

0.1

ns

chr11_799292

Kuba

7.3E−13

6.7E−14

1.5E−13

0.4

ns

chr11_1259552

Kuba

2.0E−12

1.8E−13

4.5E−13

0.8

ns

chr11_1680269

Kuba

2.2E−14

1.2E−14

7.7E−15

1.5

ns

chr11_1772869

Kuba

2.9E−13

1.8E−13

1.4E−13

0.6

ns

chr11_1919971

Kuba

2.2E−13

1.4E−13

1.1E−13

0.8

ns

chr11_2040481

Kuba

2.2E−13

1.4E−13

1.1E−13

0.8

ns

chr11_2298154

Kuba

2.1E−12

9.7E−12

1.1E−12

1.8

ns

chr11_2687396

Kuba

3.6E−11

6.0E−11

1.9E−11

2.1

ns

chr11_2815640

Kuba

2.5E−11

5.5E−11

1.4E−11

1.5

ns

chr11_3325292

Kuba

1.2E−09

4.6E−09

7.7E−10

2.1

ns

chr11_4362386

Kuba

1.0E−09

3.0E−08

3.4E−09

1.0

ns

chr11_5505183

Kuba

4.8E−06

6.4E−04

4.3E−04

6.5

< 0.01

  1. χ2 tests: null hypothesis: the marker follows a 1:1 segregation pattern
  2. ns not significant
  3. *p-values of association between KASP marker results and Glynne-Lemmerzahl tests of 2016 (Kruskal–Wallis tests)