Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Table 1 Summary of genotyping and re-sequencing of 11 genes determining growth habit and one gene determining inflorescence type

Locus	VRN-H1	VRN-H2	VRN-H2	VRN-H2	VRN-H2	VRN-H3	VRS1	PPD-H2	PPD-H1	FR-H2	FR-H2	FR-H2
Gene	BM5A	ZCCT-Ha †	ZCCT-Hb †	ZCCT-Hc †	HvSNF2	HvFT1	HvHOX1	HvFT3	HvPRR7	HvCBF3	HvCBF6	HvCBF9
Accessions Genotyped⁽¹⁾	102	102	102	102	102	102	102	102	102	0	102	0
Number of alleles/amplicon sizes	5	2	2	2	2	2	6	2	2	0	2	0
Accessions re-sequenced⁽²⁾	102	-	-	-	30	102	102	26	30	30	30	30
Number of haplotypes	6	-	-	-	4	7	7	3	6	5	6	6
Sequence length (bp)	668	-	-	-	632	5670	1192	1467	1355	874	913	988

(1) Gel-based characterization of SNP, InDels
(2) Cloning and sequencing of a gene or putative functional domain within a gene
† ZCCT-H gene family members are present or absent

ISSN: 1471-2164