Identification of QTL for Milling and Appearance Quality Traits in Rice (Oryza sativa L.)

doi:10.16819/j.1001-7216.2023.220908

Abstract

Abstract:

【Objective】 Milling and appearance quality(MAQ) are the key factors affecting the production efficiency and commodity value of rice. Exploring the major QTLs for MAQ related traits help further clarify the molecular genetic mechanism of quality traits, which also provides genetic materials for high-quality breeding in rice.【Method】 A recombinant inbred line(RIL) population derived from the cross between Longdao 5 (high-quality japonica) and Zhongyouzao 8 (high-yield indica) was used to identify QTLs for milling and appearance quality traits in multiple environments.【Result】 Thirty-seven QTLs related to processing and appearance quality were detected on 12 chromosomes. 15, 15, and 21 QTLs were found in the three environments, respectively. Only 10 QTLs were stably expressed in two environments, and two QTLs were repeatedly detected in all the three environments. Processing and appearance quality related QTLs showed significant genetic overlap effects. In addition, QTLs of the milling and appearance quality had obvious genetic overlap effect. There were five major QTL clusters on the chromosomes 2, 6, 7, 10 and 11, which had obvious regulatory effects on milling and appearance quality.【Conclusion】 qMAQ7 (qChlak7) is a novel pleiotropic QTL cluster on chromosome 7 between RM1306 and RM420, which exerts obvious regulatory effects on percentage of chalky grains and chalkiness degree. In addition, the epistatic effect plays an important role in the regulation of milling and appearance quality traits, and then the major effect QTL was involved in epistatic interaction effect.

Key words: rice, milling quality, appearance quality, QTL mapping, qChalk7

摘要：

【目的】 稻米加工与外观品质是影响水稻生产效益和商品价值的关键因素，发掘相关性状主效QTL有助于进一步阐明水稻品质性状的分子遗传机制，也可为水稻优质育种提供材料。【方法】 以优质粳稻龙稻5号为母本和高产籼稻中优早8号为父本杂交衍生的重组自交系群体为试验材料，在3个环境条件下对稻米加工和外观品质进行性状比较和QTL分析。【结果】 检测到37个与加工和外观品质相关的QTL，分布在12条染色体上，三个环境分别发现15、15和21个QTL，其中仅10个QTL在2个环境中稳定表达，2个QTL在3个环境中重复检测到。加工和外观品质相关QTL具有明显的遗传重叠效应，第2、6、7、10和11染色体上存在主效QTL簇，对加工和外观品质存在明显的调控作用。【结论】 第7染色体RM1306−RM420区间存在一个新的QTL qMAQ7（qChlak7），该区间对垩白粒率和垩白度具有较强的调控效应；此外，上位性互作也是调控加工和外观品质的重要组成部分，主效QTL参与上位性互作效应。

关键词: 水稻, 加工品质, 外观品质, QTL分析, qChalk7

YAO Xiaoyun, CHEN Chunlian, XIONG Yunhua, HUANG Yongping, PENG Zhiqing, LIU Jin, YIN Jianhua. Identification of QTL for Milling and Appearance Quality Traits in Rice (Oryza sativa L.)[J]. Chinese Journal OF Rice Science, 2023, 37(5): 507-517.

姚晓云, 陈春莲, 熊运华, 黄永萍, 彭志勤, 刘进, 尹建华. 水稻加工和外观品质性状QTL鉴定[J]. 中国水稻科学, 2023, 37(5): 507-517.

Figures/Tables 7

References 44

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性状 Trait	环境 Environment	亲本 Parent			重组自交系群体 RIL population
性状 Trait	环境 Environment	龙稻5 LD5	中优早8 ZYZ8	差值 Difference	均值±标准误 Mean±SD	变幅 Range	峰度 Skewness	偏度 Kurtosis
糙米率	E1	74.28	77.67	3.39	77.50±3.30	61.60−89.00	−1.59	1.84
BR	E2	80.65	77.15	−3.50	78.42±2.51	61.70−83.60	−2.17	1.62
	E3	79.65	78.65	−1.00	76.93±2.18	68.98−80.90	−0.80	0.63
精米率	E1	72.36	58.06	−14.30**	58.29±5.82	41.90−78.90	−0.26	0.69
MR	E2	74.45	67.70	−6.75*	64.30±4.00	51.40−72.10	−0.82	0.95
	E3	70.34	63.66	−6.68**	63.98±3.47	52.23−71.54	−0.78	1.09
整精米率	E1	52.72	39.74	−12.98**	39.97±13.02	11.70−78.30	−0.17	−0.62
HR	E2	70.03	42.28	−4.33*	53.82±9.68	22.90−70.10	−1.10	1.14
	E3	44.62	30.42	−14.20**	54.92±7.36	26.73−66.60	−1.16	1.65
长宽比	E1	2.01	2.76	0.75**	2.00±0.11	1.60−2.61	0.45	0.09
MLW	E2	2.15	2.80	0.65**	2.12±0.09	1.82−2.75	0.30	0.10
	E3	2.23	2.65	0.42**	2.17±0.21	1.64−2.69	0.50	−0.03
垩白粒率	E1	45.17	88.88	43.71**	66.79±22.74	9.40−99.80	−0.52	−0.42
PGWC	E2	17.59	44.21	26.62**	52.71±20.04	8.20−98.40	0.11	−0.42
	E3	10.60	27.50	16.90**	31.39±21.04	5.57−96.79	1.10	0.78
垩白度	E1	13.76	44.03	30.27**	29.03±15.44	2.50−65.60	0.41	−0.58
DGWC	E2	3.75	11.20	7.45*	17.96±9.97	2.60−51.70	1.05	0.99
	E3	1.20	15.17	13.97*	8.92±7.59	1.57−46.00	2.06	1.27

性状 Trait	环境 Environment	亲本 Parent			重组自交系群体 RIL population
性状 Trait	环境 Environment	龙稻5 LD5	中优早8 ZYZ8	差值 Difference	均值±标准误 Mean±SD	变幅 Range	峰度 Skewness	偏度 Kurtosis
糙米率	E1	74.28	77.67	3.39	77.50±3.30	61.60−89.00	−1.59	1.84
BR	E2	80.65	77.15	−3.50	78.42±2.51	61.70−83.60	−2.17	1.62
	E3	79.65	78.65	−1.00	76.93±2.18	68.98−80.90	−0.80	0.63
精米率	E1	72.36	58.06	−14.30**	58.29±5.82	41.90−78.90	−0.26	0.69
MR	E2	74.45	67.70	−6.75*	64.30±4.00	51.40−72.10	−0.82	0.95
	E3	70.34	63.66	−6.68**	63.98±3.47	52.23−71.54	−0.78	1.09
整精米率	E1	52.72	39.74	−12.98**	39.97±13.02	11.70−78.30	−0.17	−0.62
HR	E2	70.03	42.28	−4.33*	53.82±9.68	22.90−70.10	−1.10	1.14
	E3	44.62	30.42	−14.20**	54.92±7.36	26.73−66.60	−1.16	1.65
长宽比	E1	2.01	2.76	0.75**	2.00±0.11	1.60−2.61	0.45	0.09
MLW	E2	2.15	2.80	0.65**	2.12±0.09	1.82−2.75	0.30	0.10
	E3	2.23	2.65	0.42**	2.17±0.21	1.64−2.69	0.50	−0.03
垩白粒率	E1	45.17	88.88	43.71**	66.79±22.74	9.40−99.80	−0.52	−0.42
PGWC	E2	17.59	44.21	26.62**	52.71±20.04	8.20−98.40	0.11	−0.42
	E3	10.60	27.50	16.90**	31.39±21.04	5.57−96.79	1.10	0.78
垩白度	E1	13.76	44.03	30.27**	29.03±15.44	2.50−65.60	0.41	−0.58
DGWC	E2	3.75	11.20	7.45*	17.96±9.97	2.60−51.70	1.05	0.99
	E3	1.20	15.17	13.97*	8.92±7.59	1.57−46.00	2.06	1.27

环境Environment	性状Trait	糙米率BR	精米率MR	整精米率HR	长宽比MLW	垩白粒率PGC
早稻	精米率MR *	0.482**
E1	整精米率HR	0.159*	0.482**
	长宽比MLW	−0.191*	−0.021	0.019
	垩白粒率PGWC	0.125*	−0.63*	−0.025	−0.303**
	垩白度DGWC	0.118	−0.216**	−0.042	−0.315**	0.929**
晚稻	精米率MR	0.672**
E2	整精米率HR	0.313**	0.560**
	长宽比MLW	−0.136*	0.007	0.019
	垩白粒率PGWC	0.075	−0.222**	−0.233*	−0.335**
	垩白度DGWC	0.333**	−0.261**	−0.285**	−0.310**	0.927**
海南	精米率MR	0.572**
E3	整精米率HR	0.061	0.557**
	长宽比MLW	−0.120*	−0.029	0.077
	垩白粒率PGWC	−0.281**	−0.282**	−0.252**	−0.300**
	垩白度DGWC	−0.299**	−0.252**	0.166*	−0.278**	0.938**

环境Environment	性状Trait	糙米率BR	精米率MR	整精米率HR	长宽比MLW	垩白粒率PGC
早稻	精米率MR *	0.482**
E1	整精米率HR	0.159*	0.482**
	长宽比MLW	−0.191*	−0.021	0.019
	垩白粒率PGWC	0.125*	−0.63*	−0.025	−0.303**
	垩白度DGWC	0.118	−0.216**	−0.042	−0.315**	0.929**
晚稻	精米率MR	0.672**
E2	整精米率HR	0.313**	0.560**
	长宽比MLW	−0.136*	0.007	0.019
	垩白粒率PGWC	0.075	−0.222**	−0.233*	−0.335**
	垩白度DGWC	0.333**	−0.261**	−0.285**	−0.310**	0.927**
海南	精米率MR	0.572**
E3	整精米率HR	0.061	0.557**
	长宽比MLW	−0.120*	−0.029	0.077
	垩白粒率PGWC	−0.281**	−0.282**	−0.252**	−0.300**
	垩白度DGWC	−0.299**	−0.252**	0.166*	−0.278**	0.938**

性状 Trait	位点 Locus	标记 Marker	LOD值LOD value			贡献率PVE / %			加性效应Additive effect
性状 Trait	位点 Locus	标记 Marker	E1	E2	E3	E1	E2	E3	E1	E2	E3
糙米率BR	qBR1	RM6547−RM1198		2.91			6.67			−0.93
精米率MR	qMR2	RM1358−RM324	2.79			5.00			−1.91
	qMR7	STS7.1−RM5481			3.90			11.78			−1.27
整精米率	qHR2	RM5897−RM5699	3.25		2.62	5.58		6.07	3.92		2.50
HR	qHR4	RM5688−RM471		2.52	3.10		8.41	11.80		−5.25	−4.01
	qHR7	RM1135−RM11			4.01			11.68			−2.51
	qHR10	RM5620−R10M40			2.93			9.48			2.25
	qHR11	STS11.5−RM144			2.73			7.93			2.06
长宽比	qMLW1	RI02519−RM259			2.98			8.98			−0.07
MLW	qMLW2	RM1361−MM1065			4.12			4.77			0.07
	qMLW3.1	STS3.8−R3M30	6.90	9.65	12.89	22.63	23.07	17.3	0.13	0.13	0.12
	qMLW3.2	RM3199−RM1352	6.76	5.81		13.61	11.55		0.09	0.09
	qMLW5	R5M13−RM3476	5.45	8.71		10.33	15.27		0.08	0.10
	qMLW6	RM6395−RM5814	2.92		4.99	6.51		8.54	−0.09		−0.08
	qMLW8	RM1376−RM4085			4.08			3.33			0.09
	qMLW10	R10M40−STS10.3	7.02			14.47			0.11
	qMLW11	STS11.2−RM21	3.42	3.60	3.12	5.87	5.44	7.78	0.06	0.06	0.07
	qMLW12	RM7120−STS12.2			6.58			7.67			−0.08
垩白粒率	qPGWC1	RM1361.1−RM6321		2.82			7.32			−9.28
PGWC	qPGWC2	STS2.4−RM13603	4.28			12.02			−9.24
	qPGWC3	RM468−RM7000		3.24	2.93		9.75	5.94		−5.81	−4.96
	qPGWC4	STS4.2−R4M13			2.58			7.59			5.66
	qPGWC6.1	RM190−RM587	3.70			11.53			−8.86
	qPGWC6.2	RM3827−RM1340			3.38			10.53			6.72
	qPGWC7	RM3555−RM1306		3.14	3.70		5.30	11.87		−7.32	−7.02
	qPGWC10	RM6737−RM5620		2.62			6.07			−6.13
	qPGWC11	STS11.2−RM1124		3.89			4.61			−6.93
垩白度	qDGWC1	RM428−RM323			2.85			6.94			2.08
DGWC	qDGWC2	STS2.4−RM13603	4.62			11.53			−6.28
	qDGWC3.1	STS3.3−STS3.4			2.55			21.25			8.23
	qDGWC3.2	MM3778−RM3513		2.59			6.13			−3.25
	qDGWC6.1	RM190−RM587	5.51			9.61			−6.14
	qDGWC6.2	RM1340−R6M44	2.87		4.20	4.50		10.31	4.90		2.56
	qDGWC7	RM3555−RM1306		2.67	3.23		6.94	7.84		−3.44	−2.20
	qDGWC10	RM467−RM6737		2.53			5.71			−3.16
	qDGWC11	STS11.2−RM1124	2.49	3.53		6.02	11.71		3.86	−3.29