Table 3.

SNP associated (-log₁₀ P-value ≥ 4) with bean rust disease severity scored 12 days after infection, their position within bean chromosomes, allelic reference and variant for each SNP, the frequency and effect of the variant allele, and the amount of phenotypic variance explained by each SNP associated with DS transf (BLUEs) in the common bean collection. Results are shown for two association mappings after removal of the 16 accessions showing mixed reactions: one with all the remaining accessions except the six considered incomplete hypersensitive resistant (to identify genes controlling partial resistance), and the other with all the remaining accessions except the 20 partially resistant (to detect genes controlling for incomplete hypersensitive resistance). All 11 associations were significant according to the Benjamini-Yekutieli (BY) FDR test

GWAS	Marker name	Phaseolus vulgaris chromosome	Position (Mbp)	-log10 (P-value)	Adjusted P-value (BY test)	Allelic reference	Allelic variant	Minor allele frequency	Effect of the allelic varianta	VQTL / Vphenob
Partial Resistance	SNP03379	Pv08	5.580	4.680	0.0001126	G	A	0.210	1.266	0.0580
	SNP03383	Pv08	5.858	4.680	0.0001407	C	T	0.210	1.266	0.0598
	DART07386	Pv08	5.990	5.075	0.0000281	G	C	0.218	1.321	0.0669
	SNP03385	Pv08	6.002	4.680	0.0001689	T	C	0.210	1.266	0.0598
	DART07388	Pv08	6.061	5.040	0.0000563	G	C	0.218	1.315	0.0667
	DART07389	Pv08	6.121	4.961	0.0000844	T	A	0.210	1.295	0.0632
Incomplete hypersensitive resistance	DART05945	Pv06	25.75	4.311	0.0000563	A	T	0.224	2.658	0.1980
	DART06294	Pv07	2.452	4.585	0.0000281	A	T	0.271	-2.184	0.1907
	DART06303	Pv07	2.571	4.078	0.0001407	T	A	0.262	-2.171	0.1869
	SNP03819	Pv08	60.18	4.279	0.0000844	T	C	0.215	2.969	0.2631
	SNP03850	Pv08	61.49	4.279	0.0001126	G	A	0.215	2.969	0.2631

^aIf the effect is positive, an increase in susceptibility is expected, whereas if the effect is negative it is expected an increase in resistance to bean rust

^bAmount of the variance explained by each association, V_QTL = 2freq(1-freq)effect² and V_pheno = phenotypic variance of the DS transf (BLUEs)