Table 2 Overview of the significant scaffolds of the perennial ryegrass genome assembly (Byrne et al. 2015) detected for each studied trait (LOD ≥ 3.0). Significant differences (P ≤ 0.05) between phenotypic medians are indicated with letters. AP – albino plants; AC – anthers cultured; ELS – embryo-like structures; EC – ELS cultured; GP – green plants; LG – linkage groups; RA – responsive anthers | TRAIT | SCAFFOLD | LG | POSITION (cM) | LOD | ALLELE OR HAPLOTYPE | MEDIAN | ALLELE OR HAPLOTYPE | MEDIAN | ALLELE OR HAPLOTYPE | MEDIAN |
|---|
| 2015 | | | | | | | | | | |
| RA (%) | 815 | 1 | 33.0-33.3 | 3.0 | C/C | 21.0 a | C/T | 6.9 b | T/T | 6.1 b |
| 233 | 4 | 40.4-40.5 | 3.9 | AC/AC | 17.1 a | AC/GT | 10.8 a | GT/GT | 1.3 b |
| 16597 | 4 | 52.3-52.4 | 3.4 | GAG/GAG | 19.6 a | CGA/CGA | 5.2 b | CGA/GAG | 1.5 b |
| 1669 | 5 | 0 | 3.2 | G/G | 14.7 a | G/T | 1.3 b | | |
| 2554_2 | 5 | 28.5 | 3.8 | C/C | 11.7 a | C/T | 2.0 b | | |
| 2075 | 7 | 43.6-43.7 | 3.3 | GT/GT | 19.4 a | TC/TC | 13.8 a | GT/TC | 1.3 b |
| 4385 | 7 | 46.5 | 3.1 | TG/TG | 19.0 a | GA/TG | 14.2 a | GA/GA | 2.4 b |
| ELS/100AC | 815 | 1 | 33.0-33.3 | 3.4 | C/C | 73.6 a | C/T | 13.1 b | T/T | 21.6 b |
| 233 | 4 | 40.4-40.5 | 3.1 | AC/AC | 55.9 a | AC/GT | 36.9 ab | GT/GT | 1.7 b |
| 16597 | 4 | 52.3-52.4 | 3.9 | GAG/GAG | 62 a | CGA/CGA | 8.3 b | CGA/GAG | 2.4 b |
| 1669 | 5 | 0 | 3.4 | G/G | 41.9 a | G/T | 0.7 b | | |
| 2554_2 | 5 | 28.5 | 4.5 | C/C | 34.9 a | C/T | 3.4 b | | |
| 4385 | 7 | 46.5 | 3.9 | TG/TG | 54.6 a | GA/TG | 32.8 a | GA/GA | 0.8 b |
| 10161 | — | — | 3.5 | C/T | 49.7 a | T/T | 47 a | C/C | 5.0 b |
| Plants/100AC | 16597 | 4 | 52.3-52.4 | 3.0 | GAG/GAG | 27.0 a | CGA/CGA | 0.0 b | CGA/GAG | 0.0 b |
| 2554_2 | 5 | 28.5 | 4.8 | C/C | 4.9 a | C/T | 0.0 b | | |
| 10161 | — | — | 3.3 | C/T | 7.9 a | T/T | 3.8 a | C/C | 0.0 b |
| GP/100AC | 6436 | 2 | 79.6-79.8 | 3.1 | T/T | 1a | C/T | 0.0 b | C/C | 0.0 a |
| GP/100EC | 3723 | 5 | 4.5-25.4 | 3.1 | C/C | 64.2 a | C/T | 2.0 a | T/T | 0.0 b |
| AP/100AC | 16597 | 4 | 52.3-52.4 | 3.2 | GAG/GAG | 16.3 a | CGA/CGA | 0.0 b | CGA/GAG | 0.0 b |
| 2554_1 | 5 | 28.5 | 4.0 | G/G | 5.8 a | A/G | 0.0 b | | |
| 2554_2 | 5 | 28.5 | 5.3 | C/C | 4.0 a | C/T | 0.0 b | | |
| 6186 | 7 | 43.6-43.7 | 3.2 | CA/CA | 12.7 a | GT/GT | 9.7 a | CA/GT | 0.0 b |
| 1607 | 7 | 51.6-51.7 | 3.0 | A/A | 13.1 a | A/C | 6.1 a | C/C | 0.0 b |
| 123 | 7 | 62.4-62.8 | 3.3 | G/G | 13.8 a | A/G | 0.0 b | A/A | 0.0 b |
| 2016 | | | | | | | | | | |
| RA (%) | 8920 | 4 | 22.2-22.3 | 3.4 | CC/TT | 21.0 a | TT/TT | 13.0 a | CC/CC | 9.0 b |
| 15142 | 5 | 28.2 | 3.2 | A/G | 22.0 a | A/A | 11.0 ab | G/G | 8.0 b |
| 60 | 5 | 28.5 | 3.3 | T/T | 34.0 a | C/T | 11.0 b | C/C | 8.5 b |
| ELS/100AC | 8920 | 4 | 22.2-22.3 | 3.3 | CC/TT | 102.0 a | TT/TT | 89.0 a | CC/CC | 28.5 b |
| 813 | 5 | 28.5-28.5 | 3.2 | A/G | 173.0 a | G/G | 36.0 b | | |
| GP/100AC | 127 | 1 | 56.1-57.5 | 3.9 | G/G | 1.2 a | A/G | 0.0 b | A/A | 0.0 b |
| GP/100EC | 127 | 1 | 56.1-57.5 | 4.1 | G/G | 1.6 a | A/G | 0.0 b | A/A | 0.0 b |
| AP/100AC | 7045 | 7 | 37.5-38.6 | 3.3 | C/C | 21.1 a | C/T | 0.0 b | T/T | 0.0 b |
| AP/100EC | 3194 | 1 | 30.9-31.1 | 3.0 | TTTC/TTTC | 37.5 a | CCCG/TTTC | 0.0 b | CCCG/CCCG | 0.0 b |
| 7045 | 7 | 37.5-38.6 | 3.0 | C/C | 19.8 a | C/T | 0.0 b | T/T | 0.0 b |