Table 3.

Distribution of genes among rice populations or between species.

Rice lines		R Gene present in 9311 only											In Nipponbare only						In both lines-single gene								In both-multigene					Non-R
Country	lines	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33
Japan	Nipponbare	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	9311	+	+	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
USA	Calrose	-	-	-	-	-	+	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
USA	S4542	-	-	+	+	-	+	-	-	-	-	-	-	-	-	+	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Haiti	Grassy	+	-	-	-	-	+	-	-	-	-	-	-	-	-	+	+	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+
Guyana	Vintula	+	-	-	+	-	+	-	-	-	-	-	+	+	-	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Zaire	CI	+	+	-	+	-	+	+	+	-	-	+	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Tanzania	WC	-	-	-	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Japan	Beiguang	+	-	-	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
South Korea	Milyang46	+	+	+	+	+	+	+	+	+	-	+	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
India	Dular	+	-	-	-	-	-	+	+	+	-	-	-	+	-	+	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Philippines	IR24	+	+	+	+	+	+	-	-	+	+	+	+	-	-	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	NJ16	+	-	+	+	-	+	+	+	+	+	+	+	+	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	Dadaotou	-	-	-	+	-	-	-	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	Zhenshan97	+	+	+	-	+	+	+	-	+	-	-	-	+	-	-	-	-	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+
China	Yunjing	-	-	+	-	-	+	-	-	-	-	-	-	+	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	C416	-	+	-	-	+	+	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
China	PA64	-	-	+	+	-	+	+	+	+	-	-	-	-	-	+	-	-	+	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+
Wild Rice	S03005	+	-	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Wild Rice	S01169	-	+	-	+	+	+	-	-	-	-	+	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Present frequency%		55	35	45	65	30	75	40	35	45	20	40	35	65	20	80	60	40	85	90	85	100	100	100	100	100	100	100	100	100	100	100	100	100
π value (‰)		2.4	2.0	12	1.3	0.7	48	2.8	0.6	0.0	0.0	12	0.0	0.5	0.0	2.9	0.0	0.0	38	13	0.8	2.0	1.8	2.1	4.0	0.0	135	2.9	79	74	41	0.0	5.0	2.8a
Related sp.	0. offcinalis	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	+	+	-	+	-	-	+	+	+	+	+	-	-	-	+	+	+	+
Related sp.	0. meyeriana	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	+	+

Note. + stands for the presence of gene, and – for absence of gene suggested by PCR and sequencing; Gene 1-30 are R genes, and 31-33 are house keeping genes. The accession number or name of gene 1-33 is OsIFCC009208, OsIFCC035754, OsIFSC047991, OsIFCC019895, OsIFCC035751, OsIFCC035229, OsIFCC043050, OsIFCC045542, OsIFCC023444, OsIFCC026523, OsIFSC046156, Os12g31620, Os11g45330, Os06g16790, Os12g09730, Os10g04670, Os11g11550, Os12g28250, Os11g15670, Os01g20720, Os12g18360 (Pi-ta), Os04g41370, Os07g29820, Os02g25900, OsIFCC040819, Os12g37270 and Os12g37280 (Pib homologue), Os12g03750 (OsIFCC032042 and OsIFCC032029 in 93-11), Os01g57270 (and Os01g57280, Os01g57310, Os01g57340), Os05g16180 (and Os05g16200, Os11g47780), Os08g10430 (and Os08g10440), Os01g05490 (triosephosphate isomerase), Os03g61120 (anthranilate synthase), and Os05g49760 (isocitrate dehydrogenase), respectively.

^aπ, valued as 1/1000, denotes the average nucleotide diversity and the values for the five multigene families and three house keeping genes were calculated from allelic pairs between Nipponbare and 93-11.