不同环境基于高密度遗传图谱的稻米外观品质QTL定位

doi:10.3724/SP.J.1006.2018.01248

Abstract

Abstract:

To analyze the genetic basis of appearance quality of rice, explore QTL which controlled rice appearance quality related traits stably existing, a mapping population of 150 lines (recombination inbred lines, RIL), derived from a cross between rice varieties V20B and CPSLO17, was applied to analysis QTL location of appearance quality trait. The specific locus amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic map in rice (Oryza sativa L.). A genetic map included 8602 markers on the 12 linkage groups was successfully constructed, which with an average distance of 0.29 cM between adjacent markers. The ICIM-ADD method of IciMapping 4.0 software was used to analyze QTL location for four appearance quality traits, including grain length (GL), grain width (GW), chalky grain rate, and chalkiness degree in three environmental conditions (Guiyang, Guiding, and Sanya). A total of nine QTLs for grain length (GL), six QTLs for grain width (GW), four QTLs for chalkiness size, three QTLs for chalkiness degree traits were detested in three environments. Five QTLs were repeatedly detected in multiple environments, of which the QTL qGW5-1 and qCha5-1 with the same localization interval (Marker1642127-Marker1514505 on chromosome 5) were repeatedly located in all three environments. In addition, the positioning interval of chalkiness QTL qCha5-2 (Marker1554573-Marker1554589) is the same as the chalkiness size QTL qCGP5-2. The sequence alignment found that the location interval of QTL qCha5-1 was only 51.5 kb, which was a new main effect QTL for chalkiness trait. These results lay the foundation for further exploiting candidate gene of appearance quality, which also contribute to the development of new molecular markers for rice appearance quality traits genetic improvement.

Key words: rice, appearance quality, QTL, high-density genetic map, high throughput sequencing

Qiang PENG,Jia-Li LI,Da-Shuang ZHANG,Xue JIANG,Ru-Yue DENG,Jian-Qiang WU,Su-Song ZHU. QTL Mapping for Rice Appearance Quality Traits Based on a High-density Genetic Map in Different Environments[J].Acta Agronomica Sinica, 2018, 44(8): 1248-1255.

Figures/Tables 6

Fig. 1

Table 1

Table 2

Table 3

Fig. 2

Table 4

QTL analysis of appearance quality traits under different environments"

性状 Trait	环境Environments	基因座 QTL	染色体 Chr.	位置 Position (cM)	标记区间 Marker interval	LOD	表型贡献率PVE (%)	加性效应 Add.
粒长 Grain length	贵州贵阳Guiyang, Guizhou	qGL1-2	1	361	Marker693317-Marker532394	4.13	5.87	-0.1498
		qGL3-1	3	60	Marker910209-Marker823024	5.25	7.28	0.1693
		qGL3-3	3	127	Marker891931-Marker771788	4.03	5.42	0.1466
		qGL7-1	7	118	Marker275670-Marker347375	4.85	6.95	-0.1628
		qGL8-1	8	115	Marker201080-Marker118092	17.97	31.18	0.3496
		qGL8-2	8	119	Marker191958-Marker143502	7.88	11.87	-0.2175
		qGL10-1	10	19	Marker34448-Marker23092	9.60	15.71	0.2592
	贵州贵定Guiding,Guizhou	qGL1-1	1	266	Marker587391-Marker688101	3.91	10.15	-0.1972
	贵州贵定Guiding,Guizhou	qGL3-2	3	63	Marker922818-Marker757283	5.08	13.38	0.2283
	海南三亚 Sanya, Hainan	qGL1-2	1	361	Marker693317-Marker532394	3.05	8.10	-0.1673
	海南三亚 Sanya, Hainan	qGL3-1	3	60	Marker910209-Marker823024	3.79	10.22	0.1908
粒宽 Grain width	贵州贵阳Guiyang, Guizhou	qGW5-1	5	27	Marker1642127-Marker1514505	14.34	28.66	0.1051
		qGW7-2	7	114	Marker343862-Marker239518	6.18	10.49	0.0632
		qGW11-2	11	120	Marker1741595-Marker1645826	4.45	7.81	0.0545
	贵州贵定Guiding, Guizhou	qGW5-1	5	27	Marker1642127-Marker1514505	8.46	16.96	0.0721
	贵州贵定Guiding, Guizhou	qGW7-1	7	106	Marker322410-Marker237275	6.83	13.24	0.0638
	海南三亚 Sanya, Hainan	qGW5-1	5	27	Marker1642127-Marker1514505	5.84	12.59	0.0657
		qGW11-1	11	114	Marker1750082-Marker1683589	4.34	8.93	0.0550
		qGW12-1	12	71	Marker1486720-Marker1380718	4.09	8.88	-0.0567
垩白度Chalkiness	贵州贵阳Guiyang, Guizhou	qCha5-1	5	27	Marker1642127-Marker1514505	4.69	12.63	0.0322
	贵州贵定Guiding, Guizhou	qCha5-1	5	27	Marker1642127-Marker1514505	5.05	14.77	0.0284
	海南三亚 Sanya, Hainan	qCha4-1	4	147	Marker403659-Marker472670	3.98	7.71	0.0241
		qCha5-1	5	27	Marker1642127-Marker1514505	8.55	17.83	0.0366
		qCha5-2	5	102	Marker1554573-Marker1554589	3.75	7.46	0.0241
垩白粒率Chalky grain percentage	贵州贵阳Guiyang, Guizhou	qCGP2-1	2	1	Marker1152260-Marker1135261	3.91	9.95	2.9960
	贵州贵阳Guiyang, Guizhou	qCGP5-2	5	102	Marker1554573-Marker1554589	3.42	9.15	2.9475
	海南三亚 Sanya, Hainan	qCGP4-1	4	149	Marker472670-Marker400717	5.01	10.66	2.7694
		qCGP5-1	5	25	Marker1611496-Marker1557594	5.82	12.50	3.0122
		qCGP5-2	5	102	Marker1554573-Marker1554589	5.28	11.15	2.8968

Table 4

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性状 Trait	环境 Environment	亲本 Parents		均值 Mean	幅度 Variance	标准误 SE	偏度 Skewness	峰度 Kurtosis	W-test	P-value
性状 Trait	环境 Environment	V20B	CPSLO17	均值 Mean	幅度 Variance	标准误 SE	偏度 Skewness	峰度 Kurtosis	W-test	P-value
粒长 Grian length (mm)	贵州贵阳 Guiyang, Guizhou	6.9317	7.5079	7.1104	0.3837	0.6194	0.2445	-0.4229	0.9770	0
	贵州贵定 Guiding, Guizhou	6.8986	7.4041	7.0370	0.3853	0.6207	-0.0375	0.2419	0.9885	0
	海南三亚 Sanya, Hainan	6.8264	7.6673	7.0589	0.3469	0.589	0.1212	-0.6511	0.9725	0
粒宽 Grain width (mm)	贵州贵阳 Guiyang, Guizhou	2.7864	1.9939	2.4299	0.0383	0.1956	-0.005	0.1085	0.9844	0
	贵州贵定 Guiding, Guizhou	2.8194	2.1133	2.4330	0.0305	0.1746	-0.4667	-0.2171	0.9588	0
	海南三亚 Sanya, Hainan	2.9044	2.1920	2.5347	0.0341	0.1846	-0.3713	-0.3784	0.9602	0
垩白度 Chalkiness (%)	贵州贵阳 Guiyang, Guizhou	23.0488	0	9.0864	81.8183	9.0453	1.0115	0.5006	0.8656	0.2495
	贵州贵定 Guiding, Guizhou	23.4848	0	6.0706	54.2400	7.3648	1.5925	2.0456	0.7781	0.8978
	海南三亚 Sanya, Hainan	23.4286	0	8.9570	74.5756	8.6357	1.0951	0.8017	0.8732	0.0977
垩白粒率 Chalky grain percentage (%)	贵州贵阳 Guiyang, Guizhou	26.2500	0	14.5078	90.7359	9.5255	0.6304	1.1792	0.9337	0.6898
	贵州贵定 Guiding, Guizhou	25.0000	0	10.6941	78.7201	8.8724	0.7583	-0.0918	0.8983	0.0019
	海南三亚 Sanya, Hainan	25.6250	0	11.9539	71.8795	8.4782	0.7945	0.7856	0.9134	0.0030

样品 Sample	SLAF数量 SLAF number	读取数 Reads number	平均深度 Average depth (×)
V20B	58473	2889072	49.41
CPSLO17	51837	2760145	53.25
合计 Total	110310	193277	51.21

染色体 Chr.	长度 Length (cM)	标记数量 Marker number	标记间距 Marker interval (cM)		Spearman相关系数^? Spearman correlation coefficient^?
染色体 Chr.	长度 Length (cM)	标记数量 Marker number	平均值 Mean	最大值 Max	Spearman相关系数^? Spearman correlation coefficient^?
1	365.11	1334	0.27	2.45	0.9996
2	184.38	818	0.23	6.00	0.9999
3	262.99	438	0.60	10.50	0.9995
4	241.09	908	0.27	3.67	0.9956
5	105.26	504	0.21	3.36	0.9996
6	363.05	1028	0.35	2.91	0.9900
7	149.03	817	0.18	3.09	0.9831
8	157.91	386	0.41	3.58	0.9996
9	130.07	525	0.25	7.04	0.9632
10	103.98	415	0.25	4.92	0.9791
11	245.23	782	0.31	2.82	0.9913
12	200.54	647	0.31	4.83	0.9978
合计 Total	2508.65	8602	0.29	10.50

QTL Mapping for Rice Appearance Quality Traits Based on a High-density Genetic Map in Different Environments

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