Skip to main content

Table 2 GWAS results: significant SNPs for association mapping using the carioca diversity panel (CDP) genotyped by 1,516 SNPs, evaluating seed coat lightness at harvest (HL) and seed coat post-harvest darkening (L30 and ΔL*)

From: Genome-wide association mapping reveals new loci associated with light-colored seed coat at harvest and slow darkening in carioca beans

Trait SNP Chr Position p value REF.a ALT.a MAF Effect nG
HL ss715650237 Pv04 8,305,412 2.2E-05 C A 0.09 -1.14 65
ss715650318 Pv04 38,357,623 2.7E-06 T C 0.12 -1.05 38
ss715640503 Pv10 2,562,874 4.4E-06 T C 0.27 0.66 88
L30 ss715646867 Pv01 42,399,057 5.3E-07 C T 0.12 -1.02 100
ss715648328 Pv04 5,499,065 5.1E-07 C T 0.13 -1.11 83
ss715650318 Pv04 38,357,623 1.6E-06 T C 0.12 -0.94 38
ss715647732 Pv07 32,272,598 1.8E-06 G A 0.14 1.41 110
ss715645851 Pv07 35,650,852 2.2E-05 A G 0.08 -1.19 113
ΔL ss715645575 Pv03 51,275,803 1.4E-05 C T 0.21 0.37 118
ss715646652 Pv08 58,966,240 7.8E-07 G A 0.29 0.45 109
ss715646104 Pv08 61,479,072 1.9E-06 A G 0.24 -0.43 235
ss715646121 Pv08 61,915,670 1.4E-05 C T 0.15 -0.40 235
ss715645744 Pv09 7,807,479 2.7E-06 C T 0.32 -0.38 92
ss715640510 Pv10 2,582,807 2.8E-05 C T 0.26 -0.31 88
  1. Chr Chromosomes, Ref. a Reference allele, Alt.a Alternative allele, MAF Minor allele frequency, Effect Allelic substitution effect, nG Number of genes in the 0.59 Mb confidence interval