Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies

Rice

Table 3 Comparisons of model genomes (upper panel) with alleles of OsAPS1 (lower panel) identified in a survey of rice cultivars

Plant	APS1	2698	2778	2865	2951	3020	3072	3131	3293	3298	3321	Frequency
O. nivara	OnAPS1	T	G	A	T	G	G	A	A	G	G
O. sativa 9311	OsAPS1	T	G	A	T	G	G	A	A	G	G
O. rufipogon	OrAPS1	A	A	G	G	C	G	G	G	A	G
O. sativa Nipponbare	OsAPS1	T	A	G	G	C	G	G	G	A	G
Other 206 cultivars of O. sativa	*OsAPS1_a*	T	G	A	T	G	G	A	A	G	G	0.32
	OsAPS1_b	T	A	A	G	G	G	A	A	A	G	0.03
	OsAPS1_c	T	A	A	G	G	G	A	A	A	A	0.09
	*OsAPS1_d*	T	A	G	G	C	G	G	G	A	G	0.44
	OsAPS1_b′	T	A	A	G	G	A	A	A	A	G	0.12

The nucleotide numbering starts at the first nucleotide (1) of the first exon of OnAPSL. The comparison covers nucleotides numbered 2670–3565 between the 2nd exon and the 3rd exon
The most frequent alleles are in bold