Plant Breeding and Biotechnology

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Table. 2.

Table. 2.

Information on SNPs that may serve as specific markers of species and cultivars (log2FC ≥ 1 and P ≤ 0.01).

Specific marker in SNP ID Variant type Minor allele Major allele NO vs. REST* NW vs. REST NP vs. REST NS vs. REST NY vs. REST PS vs. REST RS vs. REST
Papaver somniferum chr1:14440360 synonymous_variant T C NA NA NA NA NA 5.09E-09 0.05652
Papaver somniferum chr1:63408681 missense_variant C A NA NA NA NA NA 5.09E-09 0.05652
Papaver rhoeas chr1:50543171 synonymous_variant A G NA NA NA NA NA 0.000533 4.49E-27
Papaver rhoeas chr1:50543171 synonymous_variant A G NA NA NA NA NA 0.000533 4.49E-27
Papaver rhoeas chr1:50543180 synonymous_variant T C NA NA NA NA NA 0.000533 4.49E-27
Papaver rhoeas chr1:50543180 synonymous_variant T C NA NA NA NA NA 0.000533 4.49E-27
Papaver nudicaule chr11:106698721 missense_variant T A 0.1355 0.1084 0.1084 4.27E-10 0.1084 0.005217 0.2716
Papaver nudicaule chr5:141967375 upstream_gene_variant G A 0.1004 0.1835 0.1004 4.18E-12 0.0241 0.00062 0.02911
Papaver nudicaule chr5:141967375 upstream_gene_variant G A 0.1004 0.1835 0.1004 4.18E-12 0.0241 0.00062 0.02911
Papaver nudicaule chr1:100614208 missense_variant T C 0.09464* 0.07218 0.07218 0.3179 5.90E-10 0.001417 0.2279
Papaver nudicaule chr10:40112008 missense_variant T G 5.62E-08 0.008627 0.0456 0.4568 0.8548 1.20E-05 0.08619
Papaver nudicaule chr5:215123172 missense_variant A G 4.92E-09 0.07218 0.07218 0.8417 0.07218 0.001417 0.2279
Papaver nudicaule chr6:2099249 synonymous_variant G C 0.04679 0.7934 1.35E-10 0.03231 0.03231 0.000195 0.1631
Papaver nudicaule chr6:58448114 5_prime_UTR_premature_start_codon_gain_variant A C 0.07889 1.97E-13 0.05873 0.05873 0.05873 0.001527 0.1929
Papaver nudicaule chr7:161966122 synonymous_variant G A 0.6802 0.1781 0.03854 0.03854 4.13E-09 0.000277 0.1695
Papaver nudicaule chr7:242821166 synonymous_variant A G 0.1355 0.1084 4.27E-10 0.1084 0.1084 0.2878 0.08486
Papaver nudicaule chr7:242821166 synonymous_variant A G 0.1355 0.1084 4.27E-10 0.1084 0.1084 0.2878 0.08486
Papaver nudicaule unplaced-scaffold_158:2741063 synonymous_variant T C 0.09464 2.71E-12 0.07218 0.07218 0.07218 0.8978 0.09378

*REST, reference genome. REST means the reference genome with the exception of the given group. For example, NO vs. REST indicates a comparison of genetic variation (SNP) between NO and all others except NO.

Plant Breed. Biotech. 2021;9:55-64 https://doi.org/10.9787/PBB.2021.9.1.55
© 2021 Plant Breed. Biotech.