A New Approach for Fine-mapping and Map-based Cloning of Minor-Effect QTL in Rice

doi:10.16819/j.1001-7216.2021.201206

Abstract

Abstract:

Important agronomic traits in rice are generally controlled by a few major-effect QTLs and a large number of minor-effect QTLs. Great progresses have been made in the cloning of major QTLs, while minor QTLs remain difficult to be cloned due to their small genetic effects and the influence of measurement error. A new approach for fine-mapping and map-based cloning of rice minor-effect QTL was introduced in this article. The approach includes two steps: 1) Use the residual heterozygote to construct near isogenic lines for fine-mapping of the target QTL; 2) Use the genome editing to create mutants of candidate genes for gene function identification. Using the strategy, we fine-mapped six minor QTLs for grain weight and grain size on the long arm of chromosome 1, and successfully cloned the first minor QTL for grain weight. We expect that this approach could provide more options for QTL cloning and new germplasm creation.

Key words: rice (Oryza sativa L.), grain size, minor QTL, map-based cloning

摘要：

水稻重要农艺性状一般由少数主效QTL和大量微效QTL共同控制。水稻主效QTL克隆已取得显著进展,而微效QTL由于遗传作用弱,表型鉴定易受测量误差影响,克隆进展缓慢,但微效QTL在水稻重要农艺性状调控中的作用不容忽视。本文介绍了一种水稻微效QTL精细定位和克隆的新途径。该途径包含2个阶段：1）应用剩余杂合体构建近等基因系群体进行目标QTL的精细定位;2）应用基因编辑技术创制候选基因突变体验证基因功能。应用该策略笔者所在团队在水稻第1染色体长臂精细定位了6个微效粒重和粒型QTL,并成功克隆首个微效粒重QTL。该技术可在方法上为水稻QTL克隆及新种质创制提供更多选择。

关键词: 水稻, 粒型, 微效QTL, 图位克隆

Yujun ZHU, Ziwei ZUO, Zhenhua ZHANG, Yeyang FAN. A New Approach for Fine-mapping and Map-based Cloning of Minor-Effect QTL in Rice[J]. Chinese Journal OF Rice Science, 2021, 35(4): 407-414.

朱玉君, 左紫薇, 张振华, 樊叶杨. 一种水稻微效QTL精细定位和克隆新途径[J]. 中国水稻科学, 2021, 35(4): 407-414.

Figures/Tables 3

References 58

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名称 Name	染色体 Chr.	群体 Population				区间 Region/kb	遗传效应 Genetic effect	颖壳细胞变化 Alteration of integument cell	文献 Reference
名称 Name	染色体 Chr.	母本 Female	父本 Male	世代 Generation	大小 Size	区间 Region/kb	遗传效应 Genetic effect	颖壳细胞变化 Alteration of integument cell	文献 Reference
GW2	2	丰矮占1号	WY3	BC₃F₂	6013	8.2	粒宽、千粒重主效;粒长微效	增殖	[33]
GS2/GL2	2	中花11	宝大粒	BC₄F₂	2114	7.4	粒长、千粒重主效;粒宽微效	增殖和扩展	[34]
		秀水09	巨大粒	BC₂F₂	未知	31.0		扩展	[35]
		日本晴	RW11	BC₃F₂	3891	21.0		扩展	[36]
TGW2	2	培矮64S	9311	BC₃F₂	9638	11.6	粒宽、千粒重主效;粒长微效	增殖和扩展	[11]
OsLG3	3	自然群体					粒长、千粒重主效;粒宽微效	扩展	[37]
OsLG3b/qLGY3	3	日本晴	SLG-1	BC₅F₂	4100	23.0	粒长、千粒重主效;粒宽无效应	扩展	[38]
		RD23	RIL186	BC₃F₂	4272	8.9		扩展	[39]
GS3	3	明恢63	川7	BC₃F₂	5740	7.9	粒长、千粒重主效;粒宽微效	伸长	[40]
SG3	3	南洋占	川7	BC₄F₃	3400	42.0	粒长主效;千粒重微效;粒宽无效应	未知	[13]
GL3.1/qGL3	3	丰矮占1号	WY3	BC₃F_2:3	5542	20.0	粒长、千粒重主效;粒宽微效	增殖和伸长	[41]
		9311	N411	BC₂F₃	2968	46.6		增殖和伸长	[42]
GSA1	3	武运粳	CG14	BC₄F₂	5260	29.5	粒长、粒宽、千粒重主效	增殖和扩展	[14]
qTGW3/GL3.3/ TGW3	3	培矮64S	CW23	BC₃F₃	3986	15.6	粒长、千粒重主效;粒宽微效	伸长	[43]
		南洋占	珍汕97	BC₄F₃	5200	15.0		伸长	[44]
		黄华占	吉资1560	F₂	2148	18.7		伸长	[26]
GS5	5	珍汕97	H94	BC₃F₂	9638	11.6	粒宽、千粒重主效;粒长微效	增殖和伸长	[45]
GSE5	5	日本晴	Kasalath	BC₃F₃	4501	2.3	粒宽、千粒重主效;粒长微效	增殖	[46]
		Asominori	IR24	BC₄F₂	2180	22.0		增殖	[47]
GW6	6	华粳籼74	南洋占	BC₅F₆	7400	15.5	粒宽、千粒重主效;粒长无效应	扩展	[12]
TGW6	6	日本晴	Kasalath	BC₁F₂	6240	4.9	粒长、千粒重主效;粒宽无效应	增殖	[48]
GW6a	6	日本晴	Kasalath	F₂	3012	40.0	粒长、千粒重主效;粒宽微效	增殖	[49]
GL6	6	GLA4	W1943	BC₁F₅	2181	6.1	粒长、千粒重主效;粒宽无效应	增殖	[10]
GLW7	7	自然群体					粒长、千粒重主效;粒宽无效应	增殖	[50]
GL7/GW7	7	日本晴	P13	BC₆F₂	20160	20.4	粒长、粒宽主效;千粒重无效应	伸长	[51]
		华粳籼74	天丰A	BC₃F₂	4500	20		增殖	[52]
GW8	8	华粳籼74	Basmati 385	BC₂F₂	2000	7.5	粒宽、千粒重主效;粒长微效	增殖	[53]
GS9	9	N138	日本晴	F₃	2400	5.9	粒长、粒宽主效;千粒重无效应	增殖	[25]

名称 Name	染色体 Chr.	群体 Population				区间 Region/kb	遗传效应 Genetic effect	颖壳细胞变化 Alteration of integument cell	文献 Reference
名称 Name	染色体 Chr.	母本 Female	父本 Male	世代 Generation	大小 Size	区间 Region/kb	遗传效应 Genetic effect	颖壳细胞变化 Alteration of integument cell	文献 Reference
GW2	2	丰矮占1号	WY3	BC₃F₂	6013	8.2	粒宽、千粒重主效;粒长微效	增殖	[33]
GS2/GL2	2	中花11	宝大粒	BC₄F₂	2114	7.4	粒长、千粒重主效;粒宽微效	增殖和扩展	[34]
		秀水09	巨大粒	BC₂F₂	未知	31.0		扩展	[35]
		日本晴	RW11	BC₃F₂	3891	21.0		扩展	[36]
TGW2	2	培矮64S	9311	BC₃F₂	9638	11.6	粒宽、千粒重主效;粒长微效	增殖和扩展	[11]
OsLG3	3	自然群体					粒长、千粒重主效;粒宽微效	扩展	[37]
OsLG3b/qLGY3	3	日本晴	SLG-1	BC₅F₂	4100	23.0	粒长、千粒重主效;粒宽无效应	扩展	[38]
		RD23	RIL186	BC₃F₂	4272	8.9		扩展	[39]
GS3	3	明恢63	川7	BC₃F₂	5740	7.9	粒长、千粒重主效;粒宽微效	伸长	[40]
SG3	3	南洋占	川7	BC₄F₃	3400	42.0	粒长主效;千粒重微效;粒宽无效应	未知	[13]
GL3.1/qGL3	3	丰矮占1号	WY3	BC₃F_2:3	5542	20.0	粒长、千粒重主效;粒宽微效	增殖和伸长	[41]
		9311	N411	BC₂F₃	2968	46.6		增殖和伸长	[42]
GSA1	3	武运粳	CG14	BC₄F₂	5260	29.5	粒长、粒宽、千粒重主效	增殖和扩展	[14]
qTGW3/GL3.3/ TGW3	3	培矮64S	CW23	BC₃F₃	3986	15.6	粒长、千粒重主效;粒宽微效	伸长	[43]
		南洋占	珍汕97	BC₄F₃	5200	15.0		伸长	[44]
		黄华占	吉资1560	F₂	2148	18.7		伸长	[26]
GS5	5	珍汕97	H94	BC₃F₂	9638	11.6	粒宽、千粒重主效;粒长微效	增殖和伸长	[45]
GSE5	5	日本晴	Kasalath	BC₃F₃	4501	2.3	粒宽、千粒重主效;粒长微效	增殖	[46]
		Asominori	IR24	BC₄F₂	2180	22.0		增殖	[47]
GW6	6	华粳籼74	南洋占	BC₅F₆	7400	15.5	粒宽、千粒重主效;粒长无效应	扩展	[12]
TGW6	6	日本晴	Kasalath	BC₁F₂	6240	4.9	粒长、千粒重主效;粒宽无效应	增殖	[48]
GW6a	6	日本晴	Kasalath	F₂	3012	40.0	粒长、千粒重主效;粒宽微效	增殖	[49]
GL6	6	GLA4	W1943	BC₁F₅	2181	6.1	粒长、千粒重主效;粒宽无效应	增殖	[10]
GLW7	7	自然群体					粒长、千粒重主效;粒宽无效应	增殖	[50]
GL7/GW7	7	日本晴	P13	BC₆F₂	20160	20.4	粒长、粒宽主效;千粒重无效应	伸长	[51]
		华粳籼74	天丰A	BC₃F₂	4500	20		增殖	[52]
GW8	8	华粳籼74	Basmati 385	BC₂F₂	2000	7.5	粒宽、千粒重主效;粒长微效	增殖	[53]
GS9	9	N138	日本晴	F₃	2400	5.9	粒长、粒宽主效;千粒重无效应	增殖	[25]