Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability

Rice

Table 2 Genomic sequence variations in the 5′-regulatory and coding regions of OsGA2oxs analyzed with 4276 rice accessions

Classes	Genes	5′-Regulatory region^a	Coding region
Classes	Genes	SNP/INDEL^b	dN	dS	FS/INDEL^c
I	OsGA2ox1	9/3	3	4	0/0
I	OsGA2ox2	47/8	9	9	0/1
II	OsGA2ox3	23/7	4	4	0/0
	OsGA2ox4	48/22	10	5	1/1
	OsGA2ox7	37/1	7	5	0/2
	OsGA2ox8	45/9	3	0	0/0
	OsGA2ox10	29/5	20	12	3/7
III	OsGA2ox5	28/12	7	2	1/1
	OsGA2ox6	6/1	5	4	0/0
	OsGA2ox9	62/7	10	5	0/2

^aSequences 1 kb upstream from the start codon were analyzed
^bNumbers of SNPs and INDELs identified using/with the Rice/VarMap database (Zhao et al. 2015)
^cNumbers of FSs (frameshift mutations) in coding regions caused by INDELs are shown on top of the total numbers of INDELs