Table 1.
Loci significantly associated with coleoptile length using two MAF (q < 0.01)
| GLM model MAF > 0.05 | ||||||
|---|---|---|---|---|---|---|
| SNP ID* | Alleles | MAF† | R2 (%)§ | q value¶ | Candidate gene IDδ | Annotation |
| 1H500582726 | C:T | 0.24 | 6.52 | 8.75E-03 | HORVU1Hr1G073010 | unknown function |
| 1H514098702 | A:C | 0.23 | 6.68 | 8.75E-03 | HORVU1Hr1G076430 | Protein FLOWERING LOCUS T |
| 1H516785422 | A:G | 0.2 | 6.28 | 8.75E-03 | HORVU1Hr1G077230 | Cellulose-synthase-like C6 |
| 2H026308852 | A:G | 0.25 | 6.32 | 8.75E-03 | .ζ | . |
| 2H640651652 | G:C | 0.14 | 6.45 | 8.75E-03 | . | . |
| 4H015498974 | C:G | 0.09 | 6.33 | 8.75E-03 | . | . |
| 5H456061421 | A:C | 0.06 | 6.45 | 8.75E-03 | HORVU5Hr1G058300 | trehalose-6-phosphate phosphatase |
| 6H071685909 | C:T | 0.35 | 6.65 | 8.75E-03 | . | . |
| 6H114729800 | T:C | 0.32 | 6.81 | 8.75E-03 | . | . |
| 2H025712787 | C:T | 0.44 | 6.14 | 8.87E-03 | . | . |
| 3H159754241 | A:G | 0.11 | 6.16 | 8.87E-03 | . | . |
| 5H014097066 | A:G | 0.08 | 6.10 | 8.87E-03 | HORVU5Hr1G007340 | Leucine-rich repeat receptor-like protein kinase family protein |
| 6H095840955 | T:C | 0.12 | 6.12 | 8.87E-03 | . | . |
| 1H510799369 | A:C | 0.26 | 6.01 | 9.48E-03 | . | . |
| 3H325190801 | T:G | 0.05 | 6.00 | 9.48E-03 | . | . |
| 4H009849212 | C:T | 0.23 | 5.91 | 9.48E-03 | . | . |
| 6H060392776 | T:C | 0.36 | 5.92 | 9.48E-03 | . | . |
| 6H72969182 | G:A | 0.37 | 5.91 | 9.48E-03 | HORVU6Hr1G022770 | Protein VERNALIZATION INSENSITIVE 3 |
| 6H071745828 | A:G | 0.36 | 5.87 | 9.77E-03 | HORVU6Hr1G022500 | BTB/POZ domain-containing protein |
| GLM model MAF > 0.01 | ||||||
| SNP ID | Alleles | MAF | R2(%) | q value | Candidate gene ID | Annotation |
| 1H514098702 | A:C | 0.23 | 6.71 | 5.45E-03 | HORVU1Hr1G076430 | Protein FLOWERING LOCUS T |
| 4H015498974 | C:G | 0.09 | 6.42 | 5.45E-03 | . | . |
| 6H53910826 | C:T | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53910924 | T:A | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53911180 | T:A | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53911713 | A:C | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53912147 | C:T | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53912695 | T:C | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53913050 | A:C | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53913075 | C:T | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53913335 | G:A | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53913549 | C:T | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H53915124 | T:A | 0.02 | 5.54 | 5.45E-03 | HORVU6Hr1G019700 | Squamosa promoter-binding-like protein 3 |
| 6H071685909 | C:T | 0.35 | 6.53 | 5.45E-03 | . | . |
| 6H114729800 | T:C | 0.32 | 6.69 | 5.45E-03 | . | . |
| 1H500582726 | C:T | 0.24 | 6.37 | 5.50E-03 | HORVU1Hr1G073010 | unknown function |
| 2H640651652 | G:C | 0.14 | 6.35 | 5.50E-03 | . | . |
| 1H516785422 | A:G | 0.2 | 6.29 | 5.63E-03 | HORVU1Hr1G077230 | Cellulose-synthase-like C6 |
| 2H026308852 | A:G | 0.25 | 6.29 | 5.63E-03 | . | . |
| 5H456061421 | A:C | 0.06 | 6.25 | 5.81E-03 | HORVU5Hr1G058300 | trehalose-6-phosphate phosphatase |
| 6H095840955 | T:C | 0.12 | 6.22 | 5.82E-03 | . | . |
| 2H025712787 | C:T | 0.44 | 6.20 | 5.83E-03 | . | . |
| 1H510799369 | A:C | 0.26 | 6.08 | 7.09E-03 | . | . |
| 3H159754241 | A:G | 0.11 | 6.03 | 7.67E-03 | . | . |
| 5H014097066 | A:G | 0.08 | 5.99 | 7.98E-03 | HORVU5Hr1G007340 | Leucine-rich repeat receptor-like protein kinase family protein |
| 3H325190801 | T:G | 0.05 | 5.90 | 9.17E-03 | . | . |
*the ID consists of the chromosome number followed by the marker’s physical position
†minor allele frequency
§contribution to phenotypic variation
¶adjusted P value, significant at q < 0.01; the association list of q < 0.05 see supplementary data
δannotated in barley genome assembly IBSC v
ζintergenic region