水稻CSSL-Z481代换片段携带的穗部性状QTL分析及次级代换系培育

doi:10.3864/j.issn.0578-1752.2023.07.003

摘要/Abstract

摘要：

【背景】粮食安全是保障国家安全的重要基础，水稻是人民赖以生存的主要粮食作物，提高其产量是重要的育种目标。水稻产量由每株有效穗数、每穗实粒数和粒重等性状构成，其中，粒重与籽粒形状、充实程度等密切相关。但这些性状都是由多基因控制，遗传基础复杂。染色体片段代换系(CSSL)可将这些复杂性状的QTL较准确地分解为单个孟得尔因子研究，且与育种工作紧密衔接，因而是理想的遗传研究和育种材料。【目的】前期以4代换片段的水稻染色体片段代换系Z481精细定位了一个易落粒基因SH6，但Z481与受体日本晴间还存在多个显著差异的穗部性状。明晰控制这些差异性状的QTL在代换片段上如何分布，并分解为单片段代换系，对目标QTL的图位克隆及应用于水稻分子设计育种有重要应用价值。【方法】利用受体亲本日本晴与Z481杂交构建的次级F₂分离群体以SAS9.3统计软件的混合线性模型（mixed linear model，MLM）法进行穗部性状QTL定位（P<0.05），然后，根据基因型和表型，从F₂选择42个单株在F₃株系利用MAS法培育单片段及双片段代换系，并利用IBM SPSS Statistics 25.0的ONE-WAY ANOVA和TWO-WAY ANOVA分析及LSD和Duncans多重比较（P<0.05）分析这些单片段代换系（SSSL）和双片段代换系（DSSL）的QTL加性和上位性效应。【结果】以日本晴/Z481构建的次级F₂群体共定位出12个控制水稻穗部性状的QTL，并培育出相应QTL的11个单片段代换系（S1—S11）和3个双片段代换系（D1—D3）。其中，有8个QTL（qGL1、qGL3、qGL6、qGW1、qGW3、qRLW1、qRLW3和qRLW6）可被单片段代换系所验证，表明这些QTL遗传稳定。此外，利用单片段代换系鉴定到qGL1-2、qGL1-3、qGL3-2等33个QTL。其中，qNSB1-1等15个可能为新鉴定的QTL。且利用3个DSSL分析了非等位QTL间的上位性效应，结果表明，不同QTL聚合会产生不同的上位性效应，如qGL3（a=1.26）和qGL6-2（a=0.86）聚合产生了-0.77的上位性效应，据DSSL遗传模型，D2的粒长遗传效应（1.35）产生了更长的粒长表型；qGWT3-2（a=3.18）和qGWT6-2（a=3.39）聚合产生了-5.46的上位性效应，则D2的千粒重遗传效应（1.11）产生了更小的籽粒。【结论】 Z481的4个代换片段上共携带45个水稻穗部性状的QTL，并进一步分解到11个次级单片段代换系上，单片段代换系具有比F₂群体更高的QTL检测效率。利用SSSL和DSSL解析的水稻穗部性状QTL的加性效应和上位性效应，有助于根据这些遗传信息预测设计基因型的表型，从而选择合适的SSSL进行育种设计。

关键词: 水稻, 穗部性状, QTL, 染色体代换片段, 加性效应, 上位性效应

Abstract:

【Background】 Food safety is key for ensuring national security. Rice is the staple food crop upon which people life depend. It is an important breeding target to improve its yield. Rice yield is composed of panicle number per plant, grain number per panicle and grain weight, among which grain weight relates closely to grain size and filling degree. However, these traits are controlled by multiple genes, and their genetic basis are complex. Chromosome segment substitution lines (CSSLs) can accurately dissect QTL for complex trait into a single Mendel’s factor, which is closely linked with the breeding work, so they are ideal materials for genetic research and breeding. 【Objective】 In the early stage, we fine-mapped a seed shattering gene SH6 using a rice chromosome segment substitution line Z481 carrying four substitution segments, However, there are still some significant differences in the panicle traits between Z481 and its recipient parent Nipponbare. It is important to understand how to distribute for these QTLs controlling panicle traits on 4 substitution segments of Z481 and then to dissect them into single segment substitution lines (SSSLs) for map-cloning of target QTL in theory meaning and for rice breeding by design in application value.【Method】 Here, the secondary F₂population constructed by crossing Nipponbare with Z481 was used to map QTL for these traits by mixed linear model (MLM) method in SAS9.3 statictic shoftware (P<0.05), and then by MAS method to develop SSSLs and dual-segment substitution lines (DSSLs) in F₃ derived from 42 F₂ indiviuals according to their genotypes and phynotypes. Finally, the additive effect and epistasis effect of QTL were analyzed using these SSSLs and DSSLs by ONE-WAY ANOVA,TWO-WAY ANOVA, LSD and Duncan’s multiple comparasion (P<0.05) in IBM SPSS Statistics 25.0.【Result】 12 QTLs controlling rice panicle traits are mapped from the secondary F₂ population constructed by Nipponbare/Z481, and 11 single segment substitution lines (S1-S11) and 3 dual-segment substitution lines (D1-D3) with each corresponding single substitution segment are developed. Among them, 8 QTLs (qGL1, qGL3, qGL6, qG-W1, qGW3, qRLW1, qRLW3, qRLW6) can be verified by 11 SSSLs, indicating that these QTLs are genetically stable. In addition, 33 QTLs such as qGL1-2, qGL1-3, qGL3-2 etc. are only detected by 11 single segment substitution lines. Among them, 15 QTLs such as qNSB1-1 etc. might be novel QTLs identified in the study. Furthermore, the epistasis effect between non-allelic QTLs was analyzed by three DSSLs and corresponding SSSLs, the results showed that pyramid of different QTL produce various epistasis effect. For example, the pyramid of qGL3 (a=1.26) and qGL6-2(a=0.86) yield epistasis effect of -0.77, according to the genetic model of DSSL, D2 with the genetic effect of 1.35 produce longer grain length than any of two SSSLs with qGL3 or qGL6-2; the pyramid of qGWT3-2 (a=3.18) and qGWT6-2 (a=3.39) produce epistasis effect of -5.46, making the 1000-grain weight of D2 significantly smaller than that of the corresponding SSSLs due to its genetic effect of 1.11.【Conclusion】 In total 45 QTLs for rice panicle traits are deteted on the 4 substitution segments of Z481 and then further dissected into 11 secondary SSSLs. SSSL have higher efficiency for QTL detection than the F₂ population. The additive effect and epistasis effect of these QTLs detected by SSSL and DSSL are necessary for breeders to predict the phenotype of the designed genotype according to these genetic informations and then to screen favorable SSSLs to breed by design.

Key words: rice, panicle traits, QTL, chromosome segment substitution line, additive effect, epistasis effect

李儒香, 周恺, 王大川, 李巧龙, 向奥妮, 李璐, 李苗苗, 向思茜, 凌英华, 何光华, 赵芳明. 水稻CSSL-Z481代换片段携带的穗部性状QTL分析及次级代换系培育[J]. 中国农业科学, 2023, 56(7): 1228-1247.

LI RuXiang, ZHOU Kai, WANG DaChuan, LI QiaoLong, XIANG AoNi, LI Lu, LI MiaoMiao, XIANG SiQian, LING YingHua, HE GuangHua, ZHAO FangMing. Analysis of QTLs and Breeding of Secondary Substitution Lines for Panicle Traits Based on Rice Chromosome Segment Substitution Line CSSL-Z481[J]. Scientia Agricultura Sinica, 2023, 56(7): 1228-1247.

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性状 Trait	QTL	染色体 Chr.	临近连锁标记 Near liked- marker	加性效应 Additive effect	贡献率 Var. (%)	P值 P-value
二次枝梗数NSB	qNSB6	6	RM3183	2.32	10.53	0.0106
每穗实粒数GPP	qGPP6	6	RM3183	9.10	5.76	0.0482
粒长GL (mm)	qGL1	1	RM5501	0.12	10.15	0.0317
	qGL3	3	RM6266	0.20	26.67	<.0001
	qGL6	6	RM276	0.10	7.00	0.0199
粒宽GW (mm)	qGW1	1	RM5501	-0.05	9.30	0.0464
粒宽GW (mm)	qGW3	3	RM6266	-0.04	5.90	0.0375
长宽比RLW	qRLW1	1	RM5501	0.16	89.81	<.0001
	qRLW3	3	RM6266	0.11	46.66	<.0001
	qRLW6	6	RM276	0.06	11.25	0.0436
千粒重GWT (g)	qGWT3	3	RM6266	0.43	4.66	0.0403
千粒重GWT (g)	qGWT6	6	RM276	0.41	4.15	0.0430

性状 Trait	粒长GL	粒宽GW	长宽比RLW	二次枝梗数NSB	千粒重GWT	每穗实粒数GPP
粒长GL	1
粒宽GW	-0.062	1
长宽比RLW	0.751**	-0.699**	1
二次枝梗数NSB	0.114	-0.394**	0.345**	1
千粒重GWT	0.220*	0.213*	0.025	-0.128	1
实粒数GPP	0.133	-0.423**	0.380**	0.876**	-0.054	1

性状 Trait	模型Model			代换系 Substitution line
性状 Trait	座位1 Q1	座位2 Q2	座位1×座位2 Q1×Q2	代换系 Substitution line
粒长GL	-(P=0.237)	qGL6-2(P=0.000)	-×qGL6-2(P=0.000)	D1
	qGL3(P=0.000)	qGL6-2(P=0.000)	qGL3×qGL6-2(P=0.000)	D2
	qGL3-2(P=0.000)	qGL6 (P=0.000)	qGL3-2×qGL6 (P=0.000)	D3
粒宽GW	qGW1-3(P=0.000)	-(P=0.134)	qGW1-3×-(P=0.002)	D1
	qGW3(P=0.000)	-(P=0.134)	qGW3×-(P=0.082)	D2
	qGW3-2(P=0.000)	-(P=0.156)	qGW3-2×-(P=0.000)	D3
长宽比RLW	qRLW1-3(P=0.003)	qRLW6-2(P=0.000)	qRLW1-3×qRLW6-2(P=0.000)	D1
	qRLW3(P=0.000)	qRLW6-2(P=0.000)	qRLW3×qRLW6-2(P=0.000)	D2
	qRLW3-2(P=0.000)	qRLW6(P=0.001)	qRLW3-2×qRLW6 (P=0.000)	D3
千粒重GWT	-(P=0.209)	qGWT6-2(P=0.000)	-×qGWT6-2(P=0.000)	D1
	qGWT3-2(P=0.000)	qGWT6-2(P=0.000)	qGWT3-2×qGWT6-2(P=0.000)	D2
	qGWT3-2(P=0.000)	-(P=0.291)	qGWT3-2×-(P=0.002)	D3
穗长PL	-(P=0.574)	-(P=0.235)	-×- (P=0.000)	D1
	qPL3(P=0.000)	-(P=0.235)	qPL3×-(P=0.020)	D2
	qPL3-2(P=0.023)	qPL6-2(P=0.007)	qPL3-2×qPL6-2(P=0.418)	D3
一次枝梗数NPB	qNPB1(P=0.019)	-(P=0.098)	qNPB1×-(P=0.432)	D1
	qNPB3(P=0.000)	-(P=0.098)	qNPB3×-(P=0.001)	D2
	-(P=0.946)	qNPB6-2(P=0.000)	-×qNPB6-2(P=0.706)	D3
二次枝梗数NSB	-(P=0.109)	-(P=0.042)	-×-(P=0.000)	D1
	qNSB3(P=0.000)	-(P=0.042)	qNSB3×-(P=0.000)	D2
	qNSB3-2(P=0.001)	qNSB6-2(P=0.000)	qNSB3-2×qNSB6-2(P=0.000)	D3
每穗实粒数GPP	-(P=0.446)	-(P=0.455)	-×-(P=0.424)	D1
	qGPP3(P=0.026)	-(P=0.455)	qGPP3×-(P=0.239)	D2
	-(P=0.094)	-(P=0.398)	-×-(P=0.863)	D3