水稻苗期根部性状的遗传分析和最长根长QTL qLRL4的精细定位

doi:10.3724/SP.J.1006.2021.02088

Abstract

Abstract:

In order to analyze the genetic basis of root traits at seedling stage, we performed QTL analysis of root morphology with 148 recombinant inbred lines derived from indica variety 9311 and japonica variety Nipponbare (NPB). In two repetitions, a total of 26 QTLs were detected for the longest root length, total root length, root surface area, root volume, and root diameter, distributed on chromosomes 1, 2, 4, 7, 9, 10, and 11 in rice. Four QTL clusters on chromosomes 2, 4, 7, and 10 were found, including a major QTL qLRL4 controlling the longest root length. To fine mapping of the major QTL, we constructed a near isogenic line NIL-qLRL4 with a segment from NPB between markers IND4-1 and IND4-4 with 9311 background. With a F₂ population derived from the NIL-qLRL4 and 9311, we fine mapped the qLRL4 within ~68.23 kb region between markers IND4-1 and IND4-3, where eight candidate genes located. Fine mapping of this QTL for root length will help explore genetic mechanism of root elongation and morphogenesis in rice.

Key words: rice, root trait, the longest root length, qLRL4, fine mapping

TIAN Biao, DING Shi-Lin, LIU Chao-Lei, RUAN Ban-Pu, JIANG Hong-Zhen, GUO Rui, DONG Guo-Jun, HU Guang-Lian, GUO Long-Biao, QIAN Qian, GAO Zhen-Yu. Genetic analysis of seedling root traits and fine mapping of the QTL qLRL4 for the longest root length in rice[J].Acta Agronomica Sinica, 2021, 47(10): 1863-1873.

Figures/Tables 15

Table 1

Table 2

Table 3

Fig. 1

Table 4

Fig. 2

Table 5

Table 6

Fig. 3

Table 7

QTLs for root traits in the RIL population"

重复 Repeat	性状 Trait		染色体 Chromosome		QTL		LOD	P值 P-value	分子标记 Marker		遗传位置 Genetic position (cM)		贡献率 PEV (%)			加性效应 Additive effect
I	最长根长 LRL		1		qLRL1		2.30	0.01	M1-16-M1-19		173.3-188.0		10.3			-1.48
			4		qLRL4		2.38	0.01	M4-10-M4-13		161.1-190.6		4.8			1.47
			10		qLRL10		2.33	0.01	M10-4-M10-7		15.2-43.4		6.3			1.16
	总根系长 TRL		1		qTRL1		4.62	0.01	M1-20-M1-22		224.4-256.0		42.5			-102.52
			2		qTRL2		12.92	0.01	M2-10-M2-13		153.9-178.1		17.0			64.91
			7		qTRL7		5.84	0.01	M7-1-M7-3		0.0-18.6		9.1			47.36
			11		qTRL11		8.47	0.01	M11-11-M11-13		126.5-136.0		7.8			43.95
	根表面积 RSA		2		qRSA2		4.59	0.01	M2-10-M2-13		153.9-178.1		15.7			5.67
			7		qRSA7		3.60	0.01	M7-2-M7-4		18.6-62.2		17.7			6.03
			11		qRSA11		3.19	0.01	M11-9-M11-13		92.0-136.0		7.1			3.81
	根体积 RV		2		qRV2		3.49	0.01	M2-10-M2-13		153.9-178.1		11.3			0.05
			7		qRV7		3.27	0.01	M7-2-M7-4		18.6-62.2		15.9			0.06
			10		qRV10		2.37	0.01	M10-4-M10-7		15.2-43.4		4.6			0.03
			11		qRV11		3.77	0.01	M11-2-M11-6		24.1-41.2		9.4			0.05
	根直径 RD		1		qRD1		4.38	0.01	M1-2-M1-4		15.1-49.3		8.7			0.02
			4		qRD4		4.04	0.01	M4-10-M4-13		161.1-190.6		26.3			-0.04
II	最长根长 LRL		4		qLRL4		2.03	0.04	M4-10-M4-13		161.1-190.6		8.3		1.99
	总根系长 TRL		1		qTRL1		13.53	0.01	M1-18-M1-21		185.0-254.8		22.1		-53.10
重复 Repeat	性状 Trait	染色体 Chromosome		QTL		LOD		P 值 P-value	分子标记 Marker	遗传位置 Genetic position (cM)		贡献率 PEV (%)		加性效应 Additive effect
		7		qTRL7		16.84		0.01	M7-2-M7-4	18.6-62.2		18.6		48.80
		9		qTRL9		10.29		0.01	M9-7-M9-10	86.2-97.6		11.7		-38.67
		11		qTRL11		6.95		0.01	M11-9-M11-13	92.0-136.0		24.7		56.19
	根表面积RSA	2		qRSA2		4.61		0.01	M2-10-M2-14	153.9-192.0		15.6		16.63
		7		qRSA7		3.64		0.01	M7-2-M7-4	18.6-62.2		17.9		17.84
		11		qRSA11		3.36		0.01	M11-9-M11-13	92.0-136.0		7.4		11.48
	根体积RV	10		qRV10		2.00		0.04	M10-4-M10-7	15.2-43.4		6.5		0.03
	根直径 RD	4		qRD4		3.10		0.01	M4-10-M4-13	161.1-190.6		9.4		-0.04
		11		qRD11		2.83		0.01	M11-4-M11-7	29.0-60.2		8.1		0.04

Table 7

Fig. 4

Table 8

Fig. 5

Table 9

Fig. 6

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分子标记 Marker	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)
IND4-1	TTGGCAGGTAGAGTCCAAAGG	TGGCTTAAGAGACGTCCCTAAC
IND4-2	TGCCCTGGAAGTATAAGGATG	ATGTCTGCATACCAGAACAAAAG
IND4-3	GCGACCACATAAATACTGTTG	AGGTGGGACTATATATTAATGG
IND4-4	AGTTGTTATTCATCGCCATCGG	TGATATACCCGAGACCAAAAGTAGC

基因 Gene	正向序列 Forward primer (5′-3′)	反向序列 Reverse primer (5′-3′)
LOC_Os04g58870	AATCACTTGAGCAAGCTCTTGG	ATGCAAACATGCACAATGCAG
LOC_Os04g58880	AAGAGCTGCGGTCAAAGAGAG	ACTCACGCAACTCCGTATCTGG
LOC_Os04g58890	TCGTCGCCGACAGGGTG	AGGTCGGTCCCCTCCTCG
LOC_Os04g58900	ACGTATGATTTCCCTGTTGATGTG	ACCTCATCTTCCTTCCCAGTAAATC
LOC_Os04g58910	AGAAATGGAAGCCTGTGAACGAC	TCATGCTGGCCTCTGCGTC
LOC_Os04g58920	AGCTGTGCGTGGTGGCGC	CTGCAAGCAGGGCGAGTTCC
LOC_Os04g58940	AGGCTCTTCGGCTACCTGC	ATCAGCTCATCCCCATCACC
LOC_Os04g58960	AGCAGATGACCAATGGTGGG	TGGTTGCTGGGTGAGCTAGAAC
Histone H3	GGTCAACTTGTTGATTCCCCTCT	AACCGCAAAATCCAAAGAACG

重复 Repeat	品种 Variety	最长根长 LRL (cm)	总根系长 TRL (cm)	根表面积 RSA (cm²)	根体积 RV (cm³)	根直径 RD (mm)
I	9311	17.3 ± 0.4^**	331.38 ± 30.07^**	34.23 ± 3.93^**	0.36 ± 0.05^**	0.32 ± 0.01^**
	NPB	15.9 ± 0.8	253.08 ± 36.76	27.33 ± 1.65	0.20 ± 0.06	0.25 ± 0.03
II	9311	17.9 ± 0.5^**	360.36 ± 31.64^**	34.46 ± 0.99^**	0.37 ± 0.01^**	0.33 ± 0.01^**
	NPB	15.6 ± 0.6	277.22 ± 28.44	24.44 ± 2.27	0.21 ± 0.02	0.26 ± 0.01

重复 Repeat	统计参数 Parameter	最长根长 LRL (cm)	总根系长 TRL (cm)	根表面积 RSA (cm²)	根体积 RV (cm³)	根直径 RD (mm)
I	均值 Mean	14.8	296.35	25.26	0.22	0.25
	标准差 SD	2.3	86.90	7.40	0.08	0.04
	变幅 Range	8.9-24.0	132.88-562.92	9.26-45.12	0.06-0.45	0.15-0.34
	偏度 Skewness	0.50	0.85	0.40	0.31	-0.44
	峰度 Kurtosis	0.90	0.72	-0.09	-0.27	-0.08
II	均值 Mean	14.3	331.61	25.62	0.26	0.23
	标准差 SD	2.9	57.19	7.27	0.08	0.07
	变幅 Range	8.9-24.0	186.30-481.50	9.82-45.33	0.09-0.62	0.08-0.59
	偏度 Skewness	0.39	0.01	0.39	0.62	0.85
	峰度 Kurtosis	0.24	0.03	-0.08	1.45	3.53

重复 Repeat	性状 Trait	最长根长 LRL (cm)	总根系长 TRL (cm)	根表面积 RSA (cm²)	根体积 RV (cm³)
I	总根系长 TRL	0.359^**
	根表面积 RSA	0.399^**	0.946^**
	根体积 RV	0.365^**	0.859^**	0.975^**
	根直径 RD	0.011	0.408^**	0.571^**	0.671^**
II	总根系长 TRL	0.041
	根表面积 RSA	0.030	0.684^**
	根体积 RV	0.043	0.749^**	0.831^**
	根直径 RD	0.084	0.799^**	0.737^**	0.914^**

Genetic analysis of seedling root traits and fine mapping of the QTL qLRL4 for the longest root length in rice

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