Table 2 Environmental associations successfully confirmed by either PMTs and/or LFMMs in the independent population data set of Arabidopsis halleri

SNP	r (PMTs)^a	\|Z\| (LFMMs)^a	Associated with	Chromosome	Position	TAIR ID	Primary gene name
2	−0.080	2.738	Precipitation	Chr1	1 710 422	AT1G05700	Leucine-rich repeat transmembrane protein kinase protein
4	0.266	3.141	Temperature	Chr1	2 139 123	AT1G06970	CHX14—cation/hydrogen exchanger 14
10	0.254	2.587	Solar radiation	Chr1	19 775 226	AT1G53050	Protein kinase superfamily protein
17	0.500	0.632	Site water balance	Chr1	30 325 655	AT1G80680	SAR3—suppressor of auxin resistance 3
20	−0.116	3.588	Solar radiation	Chr2	13 940 829	AT2G32860	BGLU33—β-glucosidase 33
44	−0.033	2.871	Temperature	Chr3	6 573 965	AT3G19040	HAF2—histone acetyltransferase of the TAFII250 family 2
51	0.163	2.451	Solar radiation	Chr3	9 547 624	AT3G26120	TEL1—terminal ear1-like 1
56^b	0.346	1.936	Site water balance	Chr3	19 101 737	AT3G51480	GLR3.6—glutamate receptor 3.6
64	0.153	4.086	Site water balance	Chr4	11 250 166	AT4G21070	BRCA1—breast cancer susceptibility 1
69	0.166	2.995	Precipitation	Chr5	22 937 358	AT5G56680	SYNC1
70	0.065	3.040	Precipitation	Chr5	22 937 500	AT5G56680	SYNC1
73	0.144	2.413	Temperature	Chr5	25 328 983	AT5G63140	PAP29—purple acid phosphatase 29
74	0.162	3.754	Temperature	Chr5	25 329 190	AT5G63140	PAP29—purple acid phosphatase 29

Abbreviations: LFMMs, latent factor mixed models; PMTs, partial Mantel tests; SNP, single-nucleotide polymorphism.
^aSignificant values are shown in bold. Significance threshold for PMTs: r>0.189. Significance threshold for LFMMs: |Z|>2.385.
^bTop candidate gene from Fischer et al. (2013).

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