Table 1.
Candidate genes for SHR: sources of selection and features for genotyping the association mapping population
| Source of selection | Target locus | Sunflower gene ID a | Sequence length b | SNPs in CS c | Indels in CS d | Haplotypes in CS e | Genotyping method f | Primers for AMP genotyping |
|---|---|---|---|---|---|---|---|---|
|
B. napus expression |
At1g34580 |
HaMT |
580 (191) |
8 (8) |
3 (11) |
3 (2) |
FCE |
F:5′GAAAGGACATGCTACTTTATGG3′ |
| |
|
|
|
|
|
|
|
R:5′CTTTACTTGAATTAAAGTTACT3′ |
| profile |
At5g51550 |
HaPRP1 |
431 |
0 |
- |
1 |
|
|
| |
|
HaPRP2 |
437 (166) |
11 (11) |
- |
3 (2) |
dHPLC |
F: 5′GGACGGGAACGTAAAATAATG3′ |
| |
|
|
|
|
|
|
|
R: 5′CCGTCTGTCCGTACAATCG3′ |
| |
At3g48310 |
HaCYP450A |
786 |
1 (0) |
- |
2 |
|
|
| |
|
HaCYP450B |
310 |
2 (0) |
- |
2 |
|
|
| |
|
HaCYP450C |
400 (260) |
2 (2) |
1 (1) |
2 (6) |
dHPLC |
F: 5′AAGTGACTTTAGCAACGTCC3′ |
| |
|
|
|
|
|
|
|
R: 5′GAGTTGGTATGGGTGGATGAA3′ |
| |
At5g05940 |
HaROPGEF1 |
447 |
12 (11) |
3 (50) |
4 |
|
|
| |
|
HaROPGEF2 |
403 (197) |
2 (2) |
2 (11) |
2 (2) |
FCE |
F: 5′TGCGTAGTGGTTCTAAAATTGG3′ |
| |
|
|
|
|
|
|
|
R: 5′CGTCAATCATTACCCCAACC3′ |
| |
|
HaROPGEF3 |
801 |
0 |
- |
1 |
|
|
| |
At1g48040 |
HaPP2C |
514 (398) |
4 (4) |
- |
2 (4) |
Direct sequencing |
F: 5′ACTGGGACTACGGCATTGAC3′ |
| |
|
|
|
|
|
|
|
R: 5′TGCTGAATTTCTGGCTCTGA3′ |
| |
At1g04450 |
HaRIC_A |
940 (261) |
8 (8) |
4 (6) |
3 (2) |
FCE |
F: 5′GCACGAATAGTGACATTGAAAC3′ |
| |
|
|
|
|
|
|
|
R:5′ACATAAAACAGTTTTCGGTCC3′ |
| |
|
HaRIC_B |
1424 (537) |
12 (0) |
2 (15) |
3 (3) |
FCE |
F: 5′GGCTTGCGTTACATCTCTGA3′ |
| |
|
|
|
|
|
|
|
R: 5′CCCAACTAGGAGCATTGGAA 3′ |
| |
At1g03687 |
HaHP1 |
198 |
0 |
1(1) |
1 |
|
|
| |
At4g09180 |
HaHP2 |
309 (256) |
1 (1) |
- |
2 (5) |
Direct sequencing |
F: 5′CTGCTATCCAGGCTCATTCA3′ |
| |
|
|
|
|
|
|
|
R: 5′AGAATGGCAGGGCGACCAAG3′ |
| |
At1g13200 |
HaFbox1 |
265 |
11 (11) |
- |
3 |
|
|
| |
|
HaFbox2 |
262 |
8 (5) |
1 (1) |
5 |
|
|
| |
At1g14687 |
HaZFHD |
166 (166) |
9 (7) |
- |
4 (9) |
Direct sequencing |
F:5′TCATGCCCTCACTAACATGC 3′ |
| |
|
|
|
|
|
|
|
R: 5′TTTGTCCGGAATCTTTTTCG 3′ |
| Sunflower EST library |
TC49193 |
HaDRP |
587 |
14 (12) |
1 (1) |
2 |
|
|
| |
BQ973243 |
HaCP |
542 |
14 (10) |
- |
3 |
|
|
| |
- |
HaGDPDI |
620 (707) |
18 (14) |
2 (2) |
3 (10) |
Direct sequencing |
F: 5′CAGAAACTGATCAACCCGAAA 3′ |
| |
|
|
|
|
|
|
|
R: 5′TGCATGCATCTTGGAAAATAG 3′ |
| |
- |
HaCWP |
351 (177) |
4 (4) |
3 (10) |
2 (2) |
FCE |
F: 5′CAGGAATCACGGTCCCTAGT3′ |
| |
|
|
|
|
|
|
|
R: 5′TGAAACATGAGGGATGAGCA3′ |
| |
TC42391 |
HaPI |
658 (235) |
14 (9) |
3 (4) |
5 (2) |
FCE |
F: 5′TCCAACAGTGTGTGACCTTTG3′ |
| |
|
|
|
|
|
|
|
R: 5′CATTAGTTACGTTACAAAGCTAT3′ |
| |
TC57179 |
HaPAL |
343 (343) |
2 (2) |
- |
2 (2) |
dHPLC |
F:5′TGTGGTCTTCAAATTCATTAATAAC3′ |
| |
|
|
|
|
|
|
|
R: 5′GGCCATTCCTAACAGGATCA3′ |
| Defense responses |
CF088675 |
HaWRKY5 |
1395 (227) |
39 (33) |
14 (56) |
8 (6) |
FCE |
F: 5′CCGATCAAAGGCTCAATCTA3′ |
| |
|
|
|
|
|
|
|
R: 5′CACATCCGCTAGTTCACACC3′ |
| |
BU016906 |
HaWRKY7 |
1163 (174) |
1 (1) |
2 (22) |
3 (2) |
FCE |
F: 5′CATTGTTGGTCAACCCTGTG3′ |
| |
|
|
|
|
|
|
|
R: 5′AGGGAAGCATAACCATGACG3′ |
| |
EU112647 |
HaGLP1 |
876 |
0 |
3 (3) |
3 |
|
|
| |
AJ540203 |
HaGLP2 |
794 |
6 (6) |
- |
2 |
|
|
| |
TC17527 |
HaGLP3 |
621 |
13 (9) |
- |
6 |
|
|
| |
TC18217 |
HaGLP4 |
761 (209) |
9 (2) |
3 (11) |
4 (4) |
FCE |
F: 5′TGGCTGCAACAACTTTCCTT3′ |
| |
|
|
|
|
|
|
|
R: 5′TTCAATCCAGAAACAAACTTCTAA3′ |
| TC17648 | HaGLP5 | 1710 | 2 (1) | 2 (3) | 3 |
a Acronyms used throughout this article, candidate genes genotyped in the AMP are underlined.
b Length of PCR products sequenced in the CS. Length of PCR products genotyped in the AMP are given in parentheses.
c Parsimony informative sites are given in parentheses.
d Base pairs of indels are given in parentheses.
e Number of haplotypes detected in the AMP are given in parentheses.
f FCE: fluorescent capillary electrophoresis, dHPLC: denaturing high liquid performance chromatography.
g Primers 5’-end 6-FAM labeled.