Plant Breeding and Biotechnology

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Table. 2.

Table. 2.

Details of SNP loci associated with flowering time in cowpea identified by genome-wide association study using enrichment of the compressed mixed linear model (ECMLM).

Year SNP marker Chr. Position (bp) P-value MAFz) R2y) Effectx)
2018 2_06981 2 21,120,081 1.45E-06 0.021 0.047 10.316
2_48274 2 15,616,162 2.47E-05 0.059 0.035 ‒7.46
2_27201 2 15,590,209 2.47E-05 0.059 0.035 7.46
2_18947 11 29,228,351 2.12E-05 0.045 0.036 8.635
2019 2_07930 3 3,749,050 3.00E-07 0.03 0.043 ‒7.524
2_39739 7 9,599,445 3.00E-06 0.01 0.036 ‒9.86
2_49778 7 9,508,214 3.00E-06 0.01 0.036 ‒9.86
2_18350 7 38,100,144 8.00E-06 0.458 0.033 3.955
2_18351 7 38,099,882 8.00E-06 0.458 0.033 3.955
2_23266 7 38,118,029 8.00E-06 0.458 0.033 3.955
2_17728 7 38,106,355 1.00E-05 0.455 0.032 3.896
2_23267 7 38,118,317 1.00E-05 0.455 0.032 3.896
2_54832 7 38,121,357 1.00E-05 0.455 0.032 3.896
2_17729 7 38,109,623 1.00E-05 0.461 0.032 3.875
2_06047 7 38,123,502 2.00E-05 0.455 0.031 3.784
2_00153 7 24,076,659 2.00E-05 0.058 0.03 ‒6.445
2_50584 7 24,092,777 2.00E-05 0.058 0.03 ‒6.445
2_32517 7 24,094,841 2.00E-05 0.058 0.03 6.445
2_02058 7 24,097,697 2.00E-05 0.063 0.029 6.478
2_02059 7 24,097,968 2.00E-05 0.063 0.029 ‒6.478
2_41121 7 24,080,674 3.00E-05 0.059 0.029 ‒6.388
2_11217 9 643,886 3.00E-06 0.01 0.036 ‒9.86
Average 2_06981 2 21,120,081 2.26E-07 0.021 0.044 8.459

z)Minor allele frequency.

y)Difference between R2 of model with SNPs and R2 of model without SNPs.

x)The average effect of gene substitution or the difference between allelic effects.
Plant Breed. Biotech. 2020;8:413-25 https://doi.org/10.9787/PBB.2020.8.4.413
© 2020 Plant Breed. Biotech.