Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar

Rice

Table 1 Gene diversity, linkage disequilibrium and genetic differentiation between populations estimated by F_ST statistic

					Asian panel										Malagasy panel
Population	N	Gene diversity	Distance^a (kb) for r² ≤ 0.2	Genetic differentiation between subpopulations estimated by F_ST statistic
Population	N	Gene diversity	Distance^a (kb) for r² ≤ 0.2	indica	XI-1A	XI-1B	XI-2	XI-3	cAus	japonica	GJ- trop	GJ-sbtrop	GJ-temp	cBas	G1	Gm	G6
Indica (XI)	1139	0.19 ± 0.09	75–100
- XI-1A	178	0.13 ± 0.06	250–300		0.00
- XI-1B	49	0.15 ± 0.07	250–300		0.25	0.00
- XI-2	179	0.18 ± 0.08	125–150		0.23	0.17	0.00
- XI-3	392	0.16 ± 0.06	125–150		0.25	0.18	0.15	0.00
cAus	169	0.16 ± 0.08	200–250	0.42	0.53	0.49	0.42	0.49	0.00	0.73
japonica (GJ)	495	0.11 ± 0.04	350–400	0.66
- GJ-trop	210	0.09 ± 0.04	500–600		0.74	0.74	0.68	0.68	0.70		0.00
- GJ-sbtrop	105	0.05 ± 0.02	700–800		0.76	0.78	0.69	0.69	0.71		0.25	0.00
- GJ-temp	150	0.03 ± 0.01	700–800		0.79	0.83	0.72	0.71	0.75		0.30	0.43	0.00
cBas	62	0.12 ± 0.06	500–600	0.54	0.65	0.62	0.56	0.59	0.56	0.51	0.48	0.56	0.64	0.00
G1	156	0.14 ± 0.09	125–150	0.07	0.14	0.14	0.11	0.16	0.44	0.73	0.69	0.70	0.74	0.56	0.00
Gm	220	0.09 ± 0.05	600–700	0.42	0.57	0.58	0.41	0.52	0.55	0.78	0.77	0.80	0.82	0.70	0.46	0.00
G6	45	0.10 ± 0.05	1250–1500	0.66	0.70	0.69	0.63	0.65	0.64	0.17	0.13	0.34	0.43	0.46	0.62	0.75	0.00

N number of accessions; in the cases of indica (XI) and japonica (GJ), N includes 342 XI-adm and 30 GJ-adm accessions, respectively. r²: Linkage disequilibrium (LD); ^a: threshold of pairwise distance between markers above which the mean r² reaches values below 0.2. The 64 Admix accessions of the A-panel, the 196 Admix, 1 cAus and 2 cBas accessions of the M-Panel were excluded from LD, gene diversity and genetic differentiation analyses