Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

Yuan, Yang; Zhang, Qijun; Zeng, Shuiyun; Gu, Longjiang; Si, Weina; Zhang, Xiaohui; Tian, Dacheng; Yang, Sihai; Wang, Long

doi:10.1186/s12864-017-3702-x

Table 2 Genome-wide identification of selective sweep regions with low diversity (π ≤ 0.0002) within each of the two subspecies, respectively, but with high divergence (D _xy ≥0.002) between these two subspecies, which were defined as DR-I. Six regions showed slightly higher π values (≥0.0002 but ≤0.0003, flagged by * in this table) because these were merged regions (See methods)

From: Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

	Chr	Range of the blocks	Length (bp)	π_Jap *10⁵	π_Tro *10⁵	π_Tem *10⁵	π_Ind *10⁵	D _Jap-Ind *10⁵	D _Tro-Ind *10⁵	D _Tmp-Ind *10⁵	π_Wild *10⁵	D _Jap-Wild *10⁵	D _Ind-Wild *10⁵
1	chr01	35499730–35510003	10274	4	2	6	14	242	246	241	89	178	121
2*	chr01	35839043–35890683	51641	19	10	13	21	468	478	467	232	320	263
3	chr02	13139975–13160003	20029	18	5	6	18	295	305	301	133	209	142
4	chr02	13349983–13360044	10062	13	2	4	11	241	249	246	101	149	131
5	chr02	14944936–14962544	17609	15	3	4	14	250	260	252	121	157	145
6	chr02	27708263–27721727	13465	11	4	11	14	263	271	263	87	143	145
7	chr03	1579192–1602557	23366	16	4	15	14	302	307	311	153	183	193
8*	chr03	2483329–2542460	59132	16	20	9	25	434	444	435	198	275	239
9	chr03	2706518–2724355	17838	13	18	7	18	440	453	440	188	310	210
10	chr03	2832279–2854311	22033	3	3	4	16	304	310	306	214	210	243
11	chr03	2896026–2923841	27816	5	3	5	15	321	327	323	151	178	220
12*	chr03	2997394–3195565	198172	18	11	22	21	578	590	580	260	356	316
13	chr03	3479756–3498823	19068	3	2	3	14	241	245	243	132	180	138
14*	chr03	24189350–24230136	40787	20	14	28	22	504	511	508	289	341	306
15	chr03	28469725–28489493	19769	14	21	7	12	429	437	427	245	327	308
16	chr04	34409908–34420007	10100	13	6	15	19	314	316	319	159	216	176
17	chr04	34469603–34500654	31052	14	6	16	16	262	264	265	123	169	136
18*	chr05	21659599–21670204	10606	16	7	25	21	289	295	291	156	177	202
19	chr05	22789981–22800012	10032	17	6	16	15	319	328	331	472	379	421
20	chr05	22869880–22880236	10357	6	2	3	17	295	305	302	137	155	208
21	chr05	24026607–24070766	44160	20	9	35	18	604	614	616	318	438	349
22	chr05	24300403–24330214	29812	16	8	13	11	343	356	350	348	346	329
23	chr05	26824033–26840483	16451	11	2	4	17	233	243	239	131	172	137
24	chr07	4149981–4163826	13846	9	8	2	18	214	220	217	420	365	365
25	chr07	25598750–25620217	21468	8	10	5	16	323	327	323	155	219	190
26	chr09	22759164–22771433	12270	6	1	3	18	251	258	254	171	164	204
27	chr09	22910542–22930021	19480	14	8	11	18	345	356	349	242	251	256
28*	chr10	21289972–21400480	110509	18	10	12	23	517	534	521	250	336	263
Average			31829	13	7	11	17	344	352	347	203	247	227

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ISSN: 1471-2164

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