Population genomics of Zea species identifies selection signatures during maize domestication and adaptation

BMC Plant Biology

Table 3 Summary of maize adaptation loci that were significantly associated with flowering-time traits

Candidate Gene^a	Lead trait^b	Lead SNP^c	Position^d	Allele^e	MAF^f	P-value	Other trait^g	Annotation
GRMZM2G382569	DTS_BJ	S1_62146730	Chr1_62146730	G/T	0.05	6.0 × 10⁻⁶		Flavonol synthase/flavanone 3-hydroxylase
GRMZM2G180847	DTA_GX	S2_194077681	Chr2_194077681	T/C	0.13	1.5 × 10⁻⁶	DTS_GX	Probable transcription factor PosF21
GRMZM2G151044	DTA_YN	S4_180919965	Chr4_180919965	C/T	0.10	3.7 × 10⁻⁶		Trehalose-6-phosphate phosphatase4
GRMZM2G111537	DTA_HB	S5_31012027	Chr5_31012027	A/C	0.48	5.1 × 10⁻⁷	APR_BLUP/DTS_HB	Adenine nucleotide alpha hydrolases-like superfamily protein
GRMZM5G812923	DTA_DHN	S5_81991055	Chr5_81991055	G/A	0.09	1.3 × 10⁻⁶	DTS_DHN	Protein SCO1 homolog 1 mitochondrial
GRMZM2G147867	DTA_YN	S6_147732326	Chr6_147732326	G/A	0.07	1.1 × 10⁻⁶		NAC domain-containing protein 35
GRMZM2G435034	DTA_BJ	S8_156956875	Chr8_156956875	C/T	0.10	1.1 × 10⁻⁶		MACPF domain-containing protein
GRMZM2G169293	DTA_BJ	S8_167550959	Chr8_167550959	C/G	0.10	6.0 × 10⁻⁷		Ceramide inositol phosphotransferase 1
GRMZM2G166780	DTA_GX	S9_139587213	Chr9_139587213	C/T	0.15	4.5 × 10⁻⁶		THO complex subunit 4B
GRMZM2G425427	DTA_BJ	S10_85333950	Chr10_85333950	C/G	0.08	6.6 × 10⁻⁹		Putative MYB DNA-binding domain superfamily protein

^aA plausible biological candidate gene at the locus or the nearest annotated gene to the lead associated SNP
^bThe trait with the most significant association signals among the tested traits. The trait is named by the abbreviation of flowering-time traits and locations for field trails. APR, anthesis photoperiod response; SPR, silking photoperiod response; DTA, days to anthesis; DTS, days to silking. DHN, Hainan; YN, Yunnan; GX, Guangxi; CQ, Chongqing; HB, Hubei; HN, Henan; BJ, Beijing; BLUP, best linear unbiased prediction
^cThe SNP with the most significant association signals for the lead trait at a given locus, where the major allele is underlined
^dChromosome and physical position for SNPs according to B73 RefGenV3 reference genome
^eThe major allele for each SNP is underlined
^fMAF, minor allele frequency
^gThe remaining associated traits at a given locus

ISSN: 1471-2229