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Table 2 List of candidate genes within the QTL interval and their exonic polymorphisms between fast (TARS-HT1) and slow imbibing (PR9920–171) genotypes

From: The genetics and physiology of seed dormancy, a crucial trait in common bean domestication

Gene ID Start End Arabidopsis homolog Annotation Abbreviation Location Indels a Point mutations b
Phvul.003G277400 51,431,904 51,434,651 AT4G19440.1 Tetratricopeptide repeat -like TPR-like Chloroplast 1(T➔ M)
Phvul.003G277500 51,439,244 51,444,213 AT4G19420.1 Pectin acetylesterase 8 PAE-8-1 Extracellular region
Phvul.003G277600 51,454,061 51,458,474 AT4G19420.1 Pectin acetylesterase 8 PAE-8-2 Extracellular region 1(5 bp)
Phvul.003G277700 51,459,936 51,468,848 AT5G45290.1 RING/U-box superfamily   Nucleus
Phvul.003G277800 51,469,994 51,475,970 AT1G31650.1 RHO guanyl-nucleotide exchange factor 14   Mitochondrion
Phvul.003G277900 51,479,760 51,480,383 AT5G45320.1 Late embryogenesis abundant protein LEA Chloroplast
Phvul.003G278000 51,490,499 51,496,568 AT1G77360.1 Arabidopsis pentatricopeptide repeat 6 APPR-6 Mitochondrion
Phvul.003G278100 51,504,483 51,504,979 AT2G35612.1 Precursor of CEP4 – regulate nitrogen uptake   Extracellular region
Phvul.003G278200 51,514,163 51,522,692 AT4G19380.1 Long-chain fatty alcohol oxidase − 4 FAO-4 Chloroplast 4(G➔D, M➔L,I➔V, I➔F)
Phvul.003G278300 51,525,377 51,527,087 AT4G19370.1 MODIFYING WALL LIGNIN-2 MWL-2 Extracellular region
Phvul.003G278400 51,539,102 51,541,642 AT4G19230.1 Cytochrome P450–707 – A - polypeptide 1 CYP707A1 Chloroplast 1(P➔A)
  1. a Size of indels in bp is in parenthesis
  2. b The number of non-synonymous point mutations. The amino acid change is in parenthesis. There was no synonymous point mutation detected within these genes