Abstract
The timing of transition from vegetative growth to flowering is important in nature as well as in agriculture. One of several pathways influencing this transition in plants is the gibberellin (GA) pathway. In maize (Zea mays L.), the Dwarf8 (D8) gene has been identified as an orthologue of the gibberellic acid-insensitive (GAI) gene, a negative regulator of GA response in Arabidopsis. Nine intragenic polymorphisms in D8 have been linked with variation in flowering time of maize. We tested the general applicability of these polymorphisms as functional markers in an independent set of inbred lines. Single nucleotide primer extension (SNuPe) and gel-based indel markers were developed, and a set of 71 elite European inbred lines were phenotyped for flowering time and plant height across four environments. To control for population structure, we genotyped the plant material with 55 simple sequence repeat markers evenly distributed across the genome. When population structure was ignored, six of the nine D8 polymorphisms were significantly associated with flowering time and none with plant height. However, when population structure was taken into consideration, an association with flowering time was only detected in a single environment, whereas an association across environments was identified between a 2-bp indel in the promoter region and plant height. As the number of lines with different haplotypes within subpopulations was a limiting factor in the analysis, D8 alleles would need to be compared in isogenic backgrounds for a reliable estimation of allelic effects.
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Acknowledgements
We thank the Danish Ministry of Food, Agriculture and Fisheries for Financial support. We also thank E.S. Buckler IV and colleagues for helpful discussions.
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Communicated by H.C. Becker
Appendices
Appendix 1
The 71 inbred lines included in the analysis with recorded phenotypic dataa at the four locationsb. DMF, DFF and PHT were recorded in EWE and HOH; DMF and DFF were recorded in SÜN, while DFF was recorded in POC
Line name | DMF, EWE | DFF, EWE | PHT, EWE | DMF, HOH | DFF, HOH | PHT, HOH | DMF, SÜN | DFF, SÜN | DFF, POC | |
|---|---|---|---|---|---|---|---|---|---|---|
Flint | F005 | 71.6 | 71.9 | 174.9 | 74.4 | 78 | 187.6 | 72.9 | 77.5 | 74 |
F012 | 65 | 63.9 | 127.9 | 73.1 | 73 | 178.4 | 71 | 71.5 | 74 | |
F013 | 63.9 | 63 | 132.8 | 72.4 | 73 | 182.4 | 70 | 71 | 73 | |
F023 | 74.4 | 75.4 | 134.3 | 77.6 | 81.5 | 199 | 73.1 | 78.5 | 76.5 | |
F030 | 71.7 | 72.1 | 129.6 | 75.9 | 80 | 181.2 | 74 | 76 | 74 | |
F034 | 71.7 | 71.5 | 130.1 | 74.1 | 77.5 | 178.3 | 73.1 | 77.5 | 76 | |
F037 | 69.3 | 68.9 | 148.7 | 73.1 | 74 | 200.2 | 72 | 73.5 | 74.5 | |
F039 | 74.5 | 76.9 | 127.8 | 74.5 | 81.5 | 197.3 | 74 | 80 | 76.5 | |
F040 | 64.1 | 63.8 | 119 | 72 | 71.5 | 165 | 71 | 71.5 | 73 | |
F043 | 71.9 | 71.9 | 125.8 | 74 | 74.5 | 169.7 | 73.7 | 75 | 74.5 | |
F045 | 66.7 | 66.5 | 131.3 | 73 | 75 | 179.2 | 74.5 | 76 | 75.5 | |
F047 | 70.4 | 72.9 | 153.8 | 74.5 | 75 | 177.4 | 73 | 75 | 73 | |
F048 | 71.6 | 71.9 | 142 | 75 | 76.5 | 189.6 | 72.6 | 75.5 | 73 | |
F052 | 67.6 | 68.6 | 141.3 | 74.3 | 77 | 184.1 | 74 | 76.5 | 76.5 | |
F054 | 69.9 | 69.3 | 146.7 | 74.8 | 75 | 190.6 | 72 | 73 | 73.5 | |
Flint/Lancaster | L005 | 78.3 | 78.9 | 127.5 | 77 | 84.5 | 160.2 | 81.5 | 82 | 82 |
L007 | 79.9 | 80.8 | 163.3 | 86.5 | 89.5 | 192.2 | 83 | 82.5 | 85.5 | |
L012 | 78.3 | 81.3 | 191.8 | 82.3 | 87 | 196 | 80 | 84 | 87 | |
L016 | 73.1 | 74.6 | 145.1 | 78 | 81 | 184.6 | 77.5 | 80 | 77.5 | |
L017 | 71.8 | 71.7 | 132 | 75 | 78.5 | 171 | 76.4 | 76.5 | 77 | |
L019 | 73.6 | 74.1 | 145.9 | 78.4 | 80.5 | 180.9 | 79 | 79 | 76 | |
L023 | 73.6 | 74.5 | 161.7 | 79 | 80.5 | 201.9 | 77.7 | 77.9 | 75 | |
L024 | 73.9 | 74.7 | 150.5 | 78.2 | 80 | 182.9 | 75.5 | 78 | 77 | |
L025 | 72.4 | 72.8 | 166.9 | 78.5 | 80 | 187.6 | 77 | 77 | 76.5 | |
L032 | 75.1 | 74.9 | 148.7 | 80 | 82.5 | 181.3 | 77.5 | 79.5 | 77 | |
L035 | 71 | 70.2 | 144.8 | 76 | 79 | 184.8 | 75 | 76 | 76.5 | |
L037 | 73.6 | 73.1 | 151.4 | 77 | 80 | 177.4 | 75.9 | 79 | 77 | |
L041 | 67 | 67.1 | 137.2 | 74.5 | 79 | 175.8 | 72.9 | 75 | 74.5 | |
L043 | 73.6 | 74 | 145 | 78 | 80.5 | 179.2 | 77.5 | 79 | 75 | |
L045 | 73.7 | 76.7 | 159.6 | 81 | 84.5 | 196.1 | 78 | 79.5 | 80.5 | |
L046 | 69.4 | 69.4 | 138 | 75 | 79 | 183.7 | 73.5 | 77 | 73.5 | |
L047 | 66.8 | 65.4 | 146.1 | 73.9 | 75 | 172.4 | 71.5 | 73 | 74.5 | |
L050 | 74.3 | 74 | 168.4 | 82.4 | 83 | 180.1 | 79.9 | 79.5 | 77 | |
Iodent and Iodent/Stiff stalk | P001 | 79.3 | 79.8 | 158 | 83.4 | 85.5 | 185.1 | 80.9 | 85 | 86.5 |
P006 | 73.9 | 75.3 | 157 | 79.4 | 79.5 | 193.6 | 75 | 78.5 | 78.5 | |
P024 | 78.8 | 79.9 | 167.3 | 82.1 | 85 | 187 | 79.5 | 82 | 80.5 | |
P027 | 77.9 | 78.7 | 154.5 | 82.2 | 82.5 | 188.3 | 79.6 | 80.5 | 78 | |
P033 | 77.1 | 76.8 | 149.3 | 80.5 | 82 | 163.9 | 79 | 79.5 | 78 | |
P034 | 76.7 | 76.7 | 163.3 | 78.5 | 80 | 215.5 | 77 | 80.5 | 77.5 | |
P036 | 74.7 | 72.9 | 158 | 79 | 78.5 | 192 | 78.5 | 76.5 | 76 | |
P038 | 73.9 | 75.5 | 121.6 | 80.1 | 83 | 164.6 | 75.1 | 79 | 77 | |
P040 | 77.8 | 78.4 | 148.7 | 82.1 | 86.5 | 182.7 | 78.9 | 80.5 | 80.5 | |
P042 | 77.3 | 76.7 | 160.6 | 80.9 | 81 | 193.7 | 80.5 | 80 | 76.5 | |
P045 | 70.7 | 70.2 | 138.4 | 77.4 | 79 | 179 | 73 | 76 | 75.5 | |
P046 | 69.4 | 68.6 | 139 | 75.5 | 78 | 173.7 | 73 | 77 | 75 | |
P047 | 73.5 | 72.7 | 140.5 | 78.6 | 78.5 | 177.3 | 74.9 | 75.5 | 76.5 | |
P048 | 75.1 | 75.3 | 143.1 | 80.5 | 81.5 | 168.2 | 76.5 | 78 | 81.5 | |
P053 | 75.3 | 77.5 | 144.4 | 80.2 | 83.5 | 166.4 | 76.5 | 80 | 80.5 | |
P060 | 77.4 | 77.3 | 132 | 82.5 | 86 | 187.3 | 79 | 81.5 | 84 | |
P063 | 78.2 | 80.9 | 149 | 83 | 86.5 | 183.7 | 81.4 | 83 | 82 | |
P064 | 79.7 | 80.7 | 160.4 | 83.5 | 86.5 | 190.8 | 79.3 | 83.9 | 86 | |
P065 | 81.1 | 81 | 167.9 | 84.7 | 85 | 204.5 | 80.9 | 82.5 | 86 | |
P066 | 74.7 | 75.7 | 144.2 | 80 | 81 | 189.3 | 79 | 79.5 | 77.5 | |
Stiff stalk | S002 | 74.6 | 74.8 | 142.9 | 81 | 83 | 163.7 | 77 | 78.5 | 76.5 |
S015 | 80 | 80.3 | 148.4 | 84 | 86 | 184.8 | 81.5 | 82.5 | 83.5 | |
S016 | 75.1 | 76.3 | 132.5 | 82.5 | 83.5 | 169.6 | 80 | 81 | 82 | |
S018 | 82.8 | 84 | 155.1 | 89.5 | 90 | 187.2 | 86 | 86.5 | 86.5 | |
S020 | 85 | 85.8 | 168.2 | 90.5 | 90.5 | 187.9 | 86 | 86.5 | 87.5 | |
S028 | 76.5 | 76.5 | 161.1 | 82.5 | 84 | 180.7 | 79.9 | 81 | 80 | |
S033 | 79.7 | 78.9 | 160.3 | 82.9 | 86.5 | 183.1 | 81.5 | 84.5 | 82.5 | |
S035 | 73.9 | 74.3 | 136.5 | 79 | 81 | 169.9 | 77 | 80 | 77 | |
S036 | 73.3 | 75.3 | 144.3 | 80.5 | 83.5 | 166.6 | 78.5 | 80 | 76.5 | |
S040 | 73.4 | 71.8 | 144.4 | 77.5 | 78.5 | 185.9 | 74.5 | 74 | 73 | |
S044 | 79.4 | 79.1 | 197.4 | 82.9 | 83.5 | 206 | 81.1 | 81.5 | 82 | |
S046 | 75 | 74.6 | 138 | 81 | 81.5 | 161.4 | 79.4 | 80 | 78.5 | |
S049 | 76 | 75.1 | 149.6 | 81.5 | 81.5 | 175 | 79.9 | 80 | 80.8 | |
S050 | 78.3 | 78.9 | 166.6 | 81.5 | 83.5 | 180.2 | 75.5 | 80.5 | 78 | |
S058 | 75.1 | 74.7 | 113.3 | 80 | 80.5 | 151.8 | 76.5 | 78 | 74.5 | |
S065 | 72.5 | 72.7 | 132.2 | 77 | 78.5 | 163.8 | 77.1 | 77.5 | 77 | |
S066 | 73 | 73.2 | 155.4 | 75.4 | 79 | 163.7 | 73 | 77 | 76 | |
S067 | 73.7 | 73.3 | 127.1 | 79 | 80 | 162.5 | 79 | 79.5 | 76.5 |
Appendix 2
The SSR analysis was performed with 55 publicly available SSR markers providing an even coverage of the maize genome
Chromosome | Bin | Marker name |
|---|---|---|
1 | 1 | phi427913 |
3 | phi109275 | |
4 | umc1169 | |
6 | umc1122 | |
9 | phi011 | |
11 | phi064 | |
2 | 1 | phi96100 |
3 | umc1555 | |
4 | phi083 | |
8 | phi127 | |
10 | phi101049 | |
3 | 1 | phi104127 |
2 | phi374118 | |
5 | phi053 | |
6 | phi102228 | |
7 | umc1489 | |
9 | umc1641 | |
4 | 1 | phi072 |
1 | phi213984 | |
4 | phi308090 | |
5 | phi079 | |
8 | phi093 | |
10 | umc1180 | |
5 | 2 | phi396160 |
4 | phi331888 | |
5 | phi333597 | |
7 | phi128 | |
9 | umc1153 | |
6 | 0 | umc1143 |
1 | phi423796 | |
3 | umc1887 | |
4 | phi031 | |
7 | phi123 | |
8 | phi089 | |
7 | 0 | umc1545 |
3 | phi114 | |
4 | phi328175 | |
5 | phi069 | |
6 | phi116 | |
8 | 0 | phi420701 |
2 | umc1304 | |
3 | phi121 | |
3 | phi100175 | |
8 | phi015 | |
9 | phi233376 | |
9 | 0 | umc1279 |
3 | phi065 | |
4 | phi032 | |
5 | phi108411 | |
7 | umc1675 | |
10 | 0 | phi041 |
1 | umc1152 | |
3 | phi050 | |
4 | phi084 | |
6 | umc1061 |
Appendix 3
Correspondence between D8 haplotypes (Fig. 2) and the 71 maize lines included in the analysis
Haplotype | Lines |
|---|---|
1 | F012, F013, F034, F045, F048, L016, L035 |
2 | P036, P060, S002, S015, S028, S033, S035, S036, S040, S050 |
3 | P034 |
4 | F040, L024 |
5 | L037 |
6 | L012, L045, L047, L050 |
7 | F005, F023, F030, F037, F039, F043, F047, F052, F054, L005, L007, L017, L019, L023, L025, L032, L041, L043, L046, P001, P006, P024, P027, P033, P038, P040, P042, P045, P046, P047, P048, P053, P064, P065, P066, S016, S018, S020, S044, S046, S058, S065 |
8 | P063, S049, S066, S067 |
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Andersen, J.R., Schrag, T., Melchinger, A.E. et al. Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111, 206–217 (2005). https://doi.org/10.1007/s00122-005-1996-6
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DOI: https://doi.org/10.1007/s00122-005-1996-6