Genetic architecture of end-use quality traits in soft white winter wheat

BMC Genomics

Table 4 Summary of SNP markers associated with cookie diameter in 672 soft white winter wheat genotypes

Trait	SNP^a	Chromosome	Position (bp)^b	Alleles^c	MAF^d	P value^e	FDR^f	Effect
Cookie diameter	S1A_586706397	1A	586,706,397	G/T	0.06	1.89E-09	3.83E-05	-0.08
Cookie diameter	S1B_573323546	1B	573,323,546	G/A	0.12	6.74E-06	2.62E-02	-0.06
Cookie diameter	S2D_28832058	2D	28,832,058	T/C	0.40	2.25E-06	1.01E-02	0.04
Cookie diameter	S4A_583968823	4A	583,968,823	G/A	0.10	8.52E-08	5.77E-04	0.06
Cookie diameter	S4A_688407511	4A	688,407,511	G/A	0.17	5.03E-08	5.09E-04	-0.05
Cookie diameter	S4B_667833352	4B	667,833,352	C/T	0.18	1.33E-06	6.73E-03	-0.06
Cookie diameter	S5A_555334864	5A	555,334,864	C/T	0.43	1.27E-09	3.83E-05	0.05
Cookie diameter	S5B_418463680	5B	418,463,680	A/T	0.18	9.94E-08	5.77E-04	-0.06
Cookie diameter	S5B_571725191	5B	571,725,191	T/A	0.36	7.11E-06	2.62E-02	0.03
Cookie diameter	S5B_580976632	5B	580,976,632	A/C	0.18	1.25E-05	3.89E-02	0.04
Cookie diameter	S7B_648784573	7B	648,784,573	G/A	0.10	4.48E-08	5.09E-04	0.07
Cookie diameter	S7D_56065854	7D	56,065,854	C/G	0.18	9.97E-08	5.77E-04	-0.05
Cookie diameter	SUN_82579190	UN	82,579,190	G/C	0.14	9.93E-06	3.35E-02	-0.05

^aSignificant single-nucleotide polymorphism (SNP). Markers in bold are markers with large effects
^bPhysical position of SNP sequence based on Wheat Chinese Spring IWGSC RefSeq v1.0
^cSNP major allele/minor allele, the allele in bold is the favorable allele in soft white wheat (associated with higher cookie diameter)
^dMinor allele frequency of the SNP
^eP value of the significant SNP
^fFalse discovery rate of the significant SNP

ISSN: 1471-2164