1. Rvi2, Rvi4, Rvi11: SNP markers and surprises
Melanie Jänsch, Juliane Weger, Giovanni Broggini, Vincent Bus, Sue Gardiner,
Heather Bassett and Andrea Patocchi

2. Objectives
1. Identification of 5 single nucleotide polymorphisms
(SNPs) within an interval of 1 cM
2. Check for level of polymorphism of SNPs in 8 founders
3. Focus of this talk: apple scab resistance genes Rvi 11
(Vbj), Rvi 2 (Vh2) and Rvi 4 (Vh4)
(Bus et al., 2011)

3. repeat
Method – SNP development
or reject region
BLAST
available flanking markers on GD sequence
Primer Design + PCR
SEQ and SNP analysis
SNP found
SNP confirmation of map position
with subset of resistant , susceptible and
recombinant individuals closest to the gene
SNP polymorphism
test with 8 founders
SNP identified and validated
ok
ok
ok
ok
reject region
reject region

4. SNP polymorphism example - Rvi4 (Vh4)
250 260 270 280 290 300 310 320
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
2249_TNL1 CGTGTTTCTGAAATGCTTCAGCTAAATCTCCGTCCTGCTTCCTGACATGCGAAGGATCAACGTGATAGAATATTGGCAMA
Gala_TNL1 CGTGTTTATGAAATGCTTCGGCAAAATCTCCGTCCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Braeburn_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Cox_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Delicious_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
F2_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Golden_TNL1 CGTGTTTATGAAATGCTTCGGCAAAATCTCCGTCCTGCTTCTTGACATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Granny_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
Jonathan_TNL1 CGTGTTCCCGAAATGCTTCAGCTAAATCTCCGTTCTGATTCCTGACATGCGAAGGATCAACGTGATAGAATATTGGCAAA
McIntosh_TNL1 CGTGTTTCTGAAATGCTTCGGCTAAATCTCCGTTCTGCTTCCTGATATGCGAAGGATCAACGTGATAGAATATTGGCAAA
330 340 350 360 370 380 390 400
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
2249_TNL1 ACATG---CCCCAGTTTGCCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACCTCCT
Gala_TNL1 ACATGTCGCTCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Braeburn_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Cox_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Delicious_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
F2_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Golden_TNL1 ACATGTCGCTCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Granny_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Jonathan_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
McIntosh_TNL1 ACATGTCGCCCCAGTTTGTCTCTGCACTCCATGATCTTCACCAGCTCGTCAAGACACCAACTCGAATCCGCATACATCTT
Parents and 8 founders included
2nd choice SNPs
1st choice SNPs

5. FVbj3
Z13_SCAR
CH02c06
SNP_region_20(8)
B8
CH05e03
Rvi11
SNP_region_34(9)
CH03d01
0.1
0.1
2.0
0.7
0.7
0.8
3.8
Rvi11
Rvi11 (Vbj)
• Plant material: GD x A722-7, 145 plants
• 55 regions tested
• In 2 regions SNPs identified
• Vbj SNPs mapped between 0.7 and 3 cM
• 17 SNPs found in total
(Gygax et al., 2004)

6. Rvi2 (Vh2)
• Plant material: GD x X2250, 146 plants
• 44 regions tested
• In 8 regions SNPs identified
• Vh2 SNPs mapped between 0.7 and 2.8 cM
• 61 SNPS found in total
(Bus et al., 2005)
CH02b10
CH2-Z13SCAR
SNP_region_53(8)
SNP_region_41(1)
CH05e03
SNP_region_20.4(1)
CH-Vbj2
SNP_region_21(15)
SNP_region_23(5)
Rvi2
SNP_region_27(21)
L19SCAR
SNP_region_34.3(6)
SNP_region_36(4)
CH03d01
0.7
0.7
0.7
0.7
1.4
Rvi2

7. Rvi4 (Vh4)
Hi22d06
SNP_region_TNL1(20)
SNP_region_3(2)
SNP_region_10(1)
SNP_region_Vr2_3(3)
Rvi4
SNP_region_ARGH37(1)
CH02c02a
Hi02a07
SCAR-S22
2.1
0.4
1.3
Rvi4
• Plant material: Gala x X2249, 242 plants
• 30 regions tested
• In 5 regions SNPs identified
• Vh4 SNPs mapped at 0 cM
• 27 SNPs found in total
(Bus et al., 2005)

8. Rvi2 vs. Rvi11
CH02b10
Z13_SCAR
SNP_region_53(8)
SNP_region_41(1)
CH05e03
SNP_region_20(1)
CH-Vbj2
SNP_region_21(15)
SNP_region_23(5)
Rvi2
SNP_region_27(21)
L19SCAR
SNP_region_34(6)
SNP_region_36(4)
CH03d01
0.7
0.7
0.7
0.7
1.4
Rvi2
Z13_SCAR
CH02c06
SNP_region_20(8)
B8
CH05e03
Rvi11
SNP_region_34(9)
FVbj3
CH03d01
0.1
0.1
2.0
0.7
0.7
0.8
3.8
Rvi11
• Indication that Rvi2 and Rvi11 may
derive from the same region
• Allelic?
• Phenotype of the two genes is
similar (SC vs. SN)
• Difference due to difference level
of enhancement of the resistance
cascade?
(Bus et al., 2011)

9. Rvi4 vs. Rvi15
• Indication that Rvi4 and Rvi15 may
derive from the same region
• Allelic?
• Phenotype of the two genes is the
same (PPP)
• Rvi4 symptoms visible after 3-4
days, Rvi15 after 7 days
• Difference due to difference level of
enhancement of the resistance
cascade?
005
Hi22d06
SNP_region_TNL1(20)
SNP_region_3(2)
SNP_region_10(1)
SNP_region_Vr2_3(3)
Rvi4
SNP_region_ARGH37(1)
CH02c02a
Hi02a07
S22_SCAR
2.1
0.4
1.3
Rvi4
CH02f06
ARGH37
Rvi15
ARGH17
CH02c02a
2.9
1.2
0.3
1.7
Rvi15
(Bus et al., 2011)

10. Conclusion
• SNP markers for resistance genes most used in breeding
will be soon available.
• This will simplify marker assisted selection (MAS) and will
allow a reduction of its costs .
• The precise mapping of the genes increases the precision of
MAS and indicates the possible allelism of:
– Rvi2 and Rvi11
– Rvi4 and Rvi15