Table 3 Significant marker–trait associations for evaluated traits
GenomeTraitSNP PositionChromosomep-valueFDR Adjusted p-valuesGeneSNP position relative to the candidate geneaCandidate gene annotation
CriolloDeformed branches WBD9,316,99122 E-080.138Tc02v2_g0141300G-type lectin S-receptor-like serine/threonine protein
29,572,89835 E-090.182Tc03v2_g0159700Protein IWS1
Flower cushion broom WBD1,064,43224 E-072 E-3Tc02v2_g0016500Ion channel DMI1
770,43624 E-072 E-3Tc02v2_g0010900Xyloglucan galactosyltransferase
4,523,32422 E-072 E-3Tc02v2_g0073300MLO-like protein
Pods FPRD18,354,97612 E-040.280Tc00cons_t021470.1−11.4 kbS-locus lectin protein kinase family
Harvested healthy pods10,111,35684 E-070.330Tc08v2_g012850+5.2 kbRNA-directed DNA polymerase
21,845,07127 E-090.330Tc00cons_t021570.1−22,0 kbTy3-gypsy retrotransposon
MatinaDeformed branches WBD9,415,42226 E-090.300Unkown
27,458,38531 E-040.300Thecc1EG0153420Protein IWS1
Flower cushion broom WBD1,107,77925 E-072 E-3Thecc1EG0061800Ion channel DMI1
794,29625 E-072 E-3Thecc1EG0060990Xyloglucan galactosyl transferase
4,567,39922 E-084 E-3Thecc1EG0069390MLO-like protein
Pods FPRD18,890,74013 E-040.655Thecc1EG0030680Unknown
27,025,49914 E-040.655Thecc1EG0038300Retrotransposon-like protein
Harvested healthy pods9,466,34881 E-040.309Unkown
8,295,77483 E-040.309
9,491,29143 E-040.309Thecc1EG0179820Ty3-gypsy retrotransposon
  • a SNP position relative to the closest candidate gene: upstream and downstream SNPs of candidate genes are specified with “–” and “+,” respectively. 0 indicates that SNPs are located within the candidate gene.