Quantitative Trait Locus Analysis for Rice Yield Traits under Two Nitrogen Levels

doi:10.1016/S1672-6308(14)60288-2

Abstract

Abstract:

A recombinant inbred line population derived from a super hybrid rice Xieyou 9308 (Xieqingzao B/Zhonghui 9308) and its genetic linkage map were used to detect quantitative trait loci (QTLs) for rice yield traits under the low and normal nitrogen (N) levels. A total of 52 QTLs for yield traits distributed in 27 regions on 9 chromosomes were detected, with each QTL explaining 4.93%-26.73% of the phenotypic variation. Eleven QTLs were simultaneously detected under the two levels, and 30 different QTLs were detected under the two N levels, thereby suggesting that the genetic bases controlling rice growth under the low and normal N levels were different. QTLs for number of panicles per plant, number of spikelets per panicle, number of filled grains per panicle, and grain density per panicle under the two N levels were detected in the RM135-RM168 interval on chromosome 3. QTLs for number of spikelets per panicle and number of filled grains per panicle under the two N levels, as well as number of panicles per plant and grain density per panicle, under the low N level, were detected in the RM5556-RM310 interval on chromosome 8. The above described QTLs shared similar regions with previously reported QTLs for rice N recycling.

Key words: nitrogen, quantitative trait locus, rice, yield trait

Yue Feng, Rong-rong Zhai, Ze-chuan Lin, Li-yong Cao, Xing-hua Wei, Shi-hua Cheng. Quantitative Trait Locus Analysis for Rice Yield Traits under Two Nitrogen Levels[J]. Rice Science, 2015, 22(3): 108-115.

Figures/Tables 4

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Level	Trait	Parent		RIL population
Level	Trait	Xieqingzao B	Zhonghui 9308	Mean	Range	Kurtosis	Skewness
Low N	Number of panicles per plant	10.8	7.7	10	5.7-19.0	0.48	0.55
	Panicle length (cm)	19.3	25.3	20.4	15.2-29.7	0.53	0.55
	Number of spikelets per panicle	74.6	193.2	111	51.8-242.8	0.72	0.89
	Number of filled grains per panicle	62.8	168.5	90.4	19.2-218.8	0.57	0.7
	Seed-setting rate (%)	84.2	87.2	80.7	41.2-94.5	1.69	-1.21
	Grain density per panicle (grains/cm)	3.9	7.6	5.4	3.0-9.3	0.08	0.61
	1000-grain weight (g)	26	21.6	23.3	19.4-29.6	0.09	0.59
	Grain yield per plant (g)	17.6	27.4	19.6	4.8-37.9	0.61	0.53
Normal N	Number of panicles per plant	13.5	9.8	11.8	7.2-18.2	-0.43	0.35
	Panicle length (cm)	20.7	26	20.6	15.5-29.2	0.86	0.6
	Number of spikelets per panicle	106.5	168.3	112.4	55.7-229.1	0.46	0.79
	Number of filled grains per panicle	90.9	135.6	91.4	29.7-198.0	0.43	0.65
	Seed-setting rate (%)	85.4	80.6	81.1	51.4-94.2	1.86	-1.28
	Grain density per panicle (grains/cm)	5.1	6.5	5.4	3.0-9.0	-0.1	0.55
	1000-grain weight (g)	26.4	21.5	23.2	14.5-29.4	0.69	0.15
	Grain yield per plant (g)	25.9	29.8	23.7	5.6-45.3	0.86	0.13

Level	Trait	Parent		RIL population
Level	Trait	Xieqingzao B	Zhonghui 9308	Mean	Range	Kurtosis	Skewness
Low N	Number of panicles per plant	10.8	7.7	10	5.7-19.0	0.48	0.55
	Panicle length (cm)	19.3	25.3	20.4	15.2-29.7	0.53	0.55
	Number of spikelets per panicle	74.6	193.2	111	51.8-242.8	0.72	0.89
	Number of filled grains per panicle	62.8	168.5	90.4	19.2-218.8	0.57	0.7
	Seed-setting rate (%)	84.2	87.2	80.7	41.2-94.5	1.69	-1.21
	Grain density per panicle (grains/cm)	3.9	7.6	5.4	3.0-9.3	0.08	0.61
	1000-grain weight (g)	26	21.6	23.3	19.4-29.6	0.09	0.59
	Grain yield per plant (g)	17.6	27.4	19.6	4.8-37.9	0.61	0.53
Normal N	Number of panicles per plant	13.5	9.8	11.8	7.2-18.2	-0.43	0.35
	Panicle length (cm)	20.7	26	20.6	15.5-29.2	0.86	0.6
	Number of spikelets per panicle	106.5	168.3	112.4	55.7-229.1	0.46	0.79
	Number of filled grains per panicle	90.9	135.6	91.4	29.7-198.0	0.43	0.65
	Seed-setting rate (%)	85.4	80.6	81.1	51.4-94.2	1.86	-1.28
	Grain density per panicle (grains/cm)	5.1	6.5	5.4	3.0-9.0	-0.1	0.55
	1000-grain weight (g)	26.4	21.5	23.2	14.5-29.4	0.69	0.15
	Grain yield per plant (g)	25.9	29.8	23.7	5.6-45.3	0.86	0.13

Trait	QTL	Chromosome	Marker interval	LOD value	Additive effect ^a	Variation (%)
PNP	qPNP-1	1	RM8147-RM10576	2.56	-0.54	5.2
	qPNP-3a	3	RM135-RM168	3.86	-0.88	13.62
	qPNP-7a	7	RM5436-RM3670	2.5	-0.61	6.09
	qPNP-8	8	RM5556-RM310	3.29	-0.68	8.11
PL (cm)	qPL-1a	1	RM8111-RM5359	2.62	0.65	5.03
	qPL-2	2	RM3865-RM6247	2.54	-0.64	5
	qPL-6a	6	RM5754-RM136	5.4	1.11	15.58
	qPL-7a	7	RM5436-RM3670	4.93	1.01	11.75
	qPL-8a	8	RM8266-RM5556	3.38	0.76	7.06
SP	qSP-1a	1	RM1-RM3746	4.82	13.7	12.78
	qSP-2	2	RM3865-RM6247	3.26	-9.79	6.58
	qSP-3a	3	RM282-RM6283	2.71	11.35	8.31
	qSP-3b	3	RM135-RM168	7.62	17.07	18.75
	qSP-6a	6	RM136-RM6302	3.55	10.45	6.4
	qSP-6b	6	RM3207-RM7193	3.22	9.87	6.1
	qSP-7a	7	RM5436-RM3670	2.99	8.99	5.42
	qSP-8a	8	RM5556-RM310	4.7	12.83	11.6
FGP	qFGP-1a	1	RM1-RM3746	3.47	12.2	11.21
	qFGP-2	2	RM3865-RM6247	2.53	-8.72	5.74
	qFGP-3a	3	RM135-RM168	4.98	14.23	14.43
	qFGP-8a	8	RM5556-RM310	4.63	12.38	11.16
SSR (%)	qSSR-3	3	RM6806-RM227	2.52	-2.96	8.81
GD (grains/cm)	qGD-1a	1	RM576-RM35	3.26	0.37	7.19
	qGD-3a	3	RM135-RM168	6.95	0.61	18.36
	qGD-8	8	RM5556-RM310	3.98	0.41	8.93
TWG (g)	qTWG-3a	3	RM6283-RM7370	10.97	-1.27	26.73
	qTWG-7	7	RM320-RM182	2.51	0.49	4.93
GYP (g)	qGYP-4	4	RM273-RM241	2.54	0.62	5.73

Trait	QTL	Chromosome	Marker interval	LOD value	Additive effect ^a	Variation (%)
PNP	qPNP-1	1	RM8147-RM10576	2.56	-0.54	5.2
	qPNP-3a	3	RM135-RM168	3.86	-0.88	13.62
	qPNP-7a	7	RM5436-RM3670	2.5	-0.61	6.09
	qPNP-8	8	RM5556-RM310	3.29	-0.68	8.11
PL (cm)	qPL-1a	1	RM8111-RM5359	2.62	0.65	5.03
	qPL-2	2	RM3865-RM6247	2.54	-0.64	5
	qPL-6a	6	RM5754-RM136	5.4	1.11	15.58
	qPL-7a	7	RM5436-RM3670	4.93	1.01	11.75
	qPL-8a	8	RM8266-RM5556	3.38	0.76	7.06
SP	qSP-1a	1	RM1-RM3746	4.82	13.7	12.78
	qSP-2	2	RM3865-RM6247	3.26	-9.79	6.58
	qSP-3a	3	RM282-RM6283	2.71	11.35	8.31
	qSP-3b	3	RM135-RM168	7.62	17.07	18.75
	qSP-6a	6	RM136-RM6302	3.55	10.45	6.4
	qSP-6b	6	RM3207-RM7193	3.22	9.87	6.1
	qSP-7a	7	RM5436-RM3670	2.99	8.99	5.42
	qSP-8a	8	RM5556-RM310	4.7	12.83	11.6
FGP	qFGP-1a	1	RM1-RM3746	3.47	12.2	11.21
	qFGP-2	2	RM3865-RM6247	2.53	-8.72	5.74
	qFGP-3a	3	RM135-RM168	4.98	14.23	14.43
	qFGP-8a	8	RM5556-RM310	4.63	12.38	11.16
SSR (%)	qSSR-3	3	RM6806-RM227	2.52	-2.96	8.81
GD (grains/cm)	qGD-1a	1	RM576-RM35	3.26	0.37	7.19
	qGD-3a	3	RM135-RM168	6.95	0.61	18.36
	qGD-8	8	RM5556-RM310	3.98	0.41	8.93
TWG (g)	qTWG-3a	3	RM6283-RM7370	10.97	-1.27	26.73
	qTWG-7	7	RM320-RM182	2.51	0.49	4.93
GYP (g)	qGYP-4	4	RM273-RM241	2.54	0.62	5.73

Trait	QTL	Chromosome	Marker interval	LOD value	Additive effect ^a	Variation (%)
PNP	qPNP-3b	3	RM135-RM168	5.12	-1.26	22.06
	qPNP-7b	7	RM5436-RM3670	3.5	-0.81	9.03
PL (cm)	qPL-1b	1	RM3520-RM5310	3.49	0.71	7.81
	qPL-3	3	RM148-RM85	4.4	0.73	9.48
	qPL-6b	6	RM5754-RM136	5.22	0.87	13.77
	qPL-7b	7	RM182-RM336	2.57	0.57	5.84
	qPL-8b	8	RM8266-RM5556	3.04	0.59	5.74
SP	qSP-1b	1	RM35-RM8147	2.93	8.43	6.12
	qSP-1c	1	RM212-RM265	2.56	8.31	5.78
	qSP-3c	3	RM135-RM168	6.25	14.08	15.82
	qSP-7b	7	RM182-RM336	3.93	10.58	8.91
	qSP-7c	7	RM234-RM118	3.38	-10.67	8.43
	qSP-8b	8	RM5556-RM310	3.88	9.96	8.22
FGP	qFGP-1b	1	RM212-RM265	2.95	9.25	8.48
	qFGP-3b	3	RM135-RM168	6.54	13.53	17.73
	qFGP-8b	8	RM5556-RM310	3.8	9.31	8.52
SSR (%)	qSSR-1	1	RM265-RM315	4.95	3.07	13.06
	qSSR-5	5	RM159-RM1248	2.73	-2.49	8.89
GD (grains/cm)	qGD-1b	1	RM576-RM35	2.73	0.34	6.04
	qGD-3b	3	RM135-RM168	6.11	0.66	21.93
	qGD-6	6	RM3430-RM494	2.56	-0.4	7.96
TWG (g)	qTWG-3b	3	RM6283-RM7370	4.61	-1.03	13.96
GYP (g)	qGYP-1	1	RM576-RM35	2.5	1.56	6.25
	qGYP-9	9	RM1553-RM2144	2.78	-1.62	6.8