Table 3 Candidate genes for the major QTL identified in the MAGIC population. Genes are shown that harbor non-synonymous polymorphisms which had significant associations in GWAS. Most likely candidate genes for major QLT are shown, a complete list of candidate polymorphisms and genes in Additional file 15
Gene | Chr | QTL | Position (bp)a | Variant (# polymorphisms) | Gene annotation |
|---|---|---|---|---|---|
Phvul.001G077300 | Pv01 | DF1.2 - DPM1.2 | 11,441,607 | missense variant (1) | 26S proteasome regulatory subunit N6 |
Phvul.001G077700 | Pv01 | DF1.2 | 11,571,295 | splice region (2) | L-arabinokinase |
Phvul.001G085200 | Pv01 | DF1.2 | 13,124,249 | missense variant (1) | Light regulated protein Lir1 |
Phvul.001G087100 | Pv01 | DF1.2 - DPM1.2 | 13,513,228 | missense variant (1) | GRAM domain (GRAM) |
Phvul.001G087300 | Pv01 | DF1.2 | 13,548,191 | missense variant (1) | Zinc finger protein CONSTANTS-like 14-related |
Phvul.001G089400 | Pv01 | DF1.2 - DPM1.2 | 14,352,260 | missense variant (5) | PPR repeat (PPR) |
Phvul.001G089900 | Pv01 | DF1.2 | 14,661,652 | missense variant (1) | GRAS domain family (GRAS) |
Phvul.001G090100 | Pv01 | DF1.2 - DPM1.2 | 14,694,391 | missense variant (1) | Exocyst complex protein EXO70 |
Phvul.001G091400 | Pv01 | DF1.2 | 15,553,393 | missense variant (1) | Squamosa promoter-binding protein-like (SBP domain) |
Phvul.001G094300 | Pv01 | DF1.2 | 16,832,664 | missense variant (1) | SWIB/MDM2 domain |
Phvul.001G093700 | Pv01 | DF1.2 | 17,339,464 | missense variant (1) | Copine - DCD domain protein |
Phvul.002G309200 | Pv02 | PHI2.1 | 47,667,592 | missense variant (2) | AGAMOUS-like 29 |
Phvul.003G158500 | Pv03 | DPM3.1 | 37,464,971 | missense variant (1) | Chitinase-like protein-related |
Phvul.006G114800 | Pv06 | SdFe6.2 | 22,340,161 | missense variant (1) | MYB-like DNA-biding protein MYB4 |
Phvul.008G003500 | Pv08 | DPM8.1 | 325,238 | missense variant (3) | Protein NRT1/PTR family |
Phvul.008G005500 | Pv08 | DPM8.1 | 512,002 | missense variant (2) | LOB domain-containing protein 40 |
Phvul.008G006800 | Pv08 | DPM8.1 | 640,209 | premature start codon variant (1) | Transducin family protein / WD-40 |
Phvul.008G010800 | Pv08 | DPM8.1 | 946,243 | splice donor variant (1) | Dolichyl-phosphate beta-glucosyltransferase |
Phvul.008G012100 | Pv08 | DPM8.1 | 1,001,427 | missense variant (4) | transcription initiation factor TFIID subunit 6 |
Phvul.008G013300 | Pv08 | DPM8.1 | 1,091,953 | missense variant (1) | subtilase family protein |
Phvul.008G014000 | Pv08 | DPM8.1 | 1,154,068 | missense variant (1) | WUSCHEL-related homeobox 10-related |