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作物学报 ›› 2023, Vol. 49 ›› Issue (3): 731-743.doi: 10.3724/SP.J.1006.2023.12081

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于水稻长大粒染色体片段代换系Z66的粒型QTL的鉴定及其聚合分析

向思茜(), 李儒香, 徐光益, 邓岢莉, 余金琎, 李苗苗, 杨正林, 凌英华, 桑贤春, 何光华, 赵芳明()   

  1. 西南大学水稻研究所 / 西南大学农业科学研究院 / 转基因植物与安全控制重庆市重点实验室, 重庆 400715
  • 收稿日期:2021-11-30 接受日期:2022-06-07 出版日期:2023-03-12 网络出版日期:2022-07-07
  • 通讯作者: 赵芳明
  • 作者简介:E-mail: 969937373@qq.com
  • 基金资助:
    国家自然科学基金项目(32072039);西南大学种质创制专项项目资助

Identification and pyramid analysis of QTLs for grain size based on rice long-large-grain chromosome segment substitution line Z66

XIANG Si-Qian(), LI Ru-Xiang, XU Guang-Yi, DENG Ke-Li, YU Jin-Jin, LI Miao-Miao, YANG Zheng-Lin, LING Ying-Hua, SANG Xian-Chun, HE Guang-Hua, ZHAO Fang-Ming()   

  1. Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University / Transgenic Plants and Safety Control, Chongqing Key Laboratory, Chongqing 400715, China
  • Received:2021-11-30 Accepted:2022-06-07 Published:2023-03-12 Published online:2022-07-07
  • Contact: ZHAO Fang-Ming
  • Supported by:
    National Natural Science Foundation of China(32072039);Germplasm Creation for Southwest University

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摘要：

水稻籽粒大小是一个复杂的农艺性状, 受多基因控制。染色体片段代换系是创造自然变异的有效手段, 也是复杂性状研究的理想材料。本研究构建了一个新的水稻长大粒染色体片段代换系Z66, Z66以日本晴的基因组为遗传背景, 含有来自R225的12个代换片段, 平均代换长度为3.32 Mb。然后, 以日本晴/Z66创建的次级F2群体定位出12个控制水稻籽粒大小的QTL, 并培育出具有目标QTL的5个新单片段代换系(S1~S5)和4个新双片段代换系(D1~D4)。其中有9个QTL (qGL3、qGL7、qGL10、qGW6、qGW10、qRLW3、qRLW10、qGWT3、qGWT10)可被单片段代换系所验证, 表明这些QTL遗传稳定。此外, 还利用单片段代换系鉴定到6个新的QTL (qGL9-2、qGW9-2、qRLW6、qRLW7、qRLW9-2、qGWT7)。在这18个QTL中, qGL9-2、qRLW9-1、qRLW9-2、qGW9-2、qGWT9-2可能是新鉴定的QTL。双基因聚合分析表明, 不同QTL间聚合产生不同的上位性效应。如qRLW3 (a=0.21)和qRLW9-2 (a=0.08)聚合产生了0.10的上位性效应, 使D2具有比受体日本晴、S1 (qRLW3)和S4 (qRLW9-2)更大的谷粒长宽比, 且差异显著。qGWT3 (a=3.99)和qGWT10 (a=3.98)聚合产生了-5.35的上位性效应, 其遗传效应(2.62)使D3的千粒重比日本晴显著增加, 而比S1 (qGWT3)和S5 (qGWT10)显著减少。了解QTL间的互作效应可对未来基因型的表型进行预测, 从而对实现智能型设计育种至关重要。

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

Abstract:

Rice grain size is a complex agronomic trait, controlled by multiple genes. Chromosome segment substitution lines are an effective method for creating natural occurring variations and are as the ideal materials for exploring the complex traits. In this study, a novel rice long-large grain chromosome segment substitution line Z66 was developed. Z66 contained 12 substitution segments from R225 (average substitution length was 3.32 Mb) based on the genetic backgrounds of Nipponbare. Then, 12 QTLs for rice grain size were identified by the secondary F2 population from Nipponbare/Z66, and 5 novel single-segment substitution lines (SSSLs, S1-S5), and 4 novel double-segment substitution lines (DSSLs, D1-D4) harboring target QTL were developed. Among them, 9 QTLs (qGL3, qGL7, qGL10, qGW6, qGW10, qRLW3, qRLW10, qGWT3, and qGWT10) could be verified by the SSSLs, indicating that these QTLs were genetically stable. In addition, 6 novel QTLs (qGL9-2, qGW9-2, qRLW6, qRLW7, qRLW9-2, and qGWT7) were detected by the SSSLs. Among 18 QTLs, 5 QTLs (qGL9-2, qRLW9-1, qRLW9-2, qGW9-2, and qGWT9-2) might be novel. Target QTLs pyramiding showed that the pyramid of different QTLs had various epistasis effects. For example, the pyramids of qRLW3 (a=0.21) and qRLW9-2 (a=0.08) produced an epistasis effect of 0.10, which made the ratio of grain length to width in D2 significantly larger than that in Nipponbare, S1 (qRLW3), and S4 (qRLW9-2). The pyramid of qGWT3 (a=3.99) and qGWT10 (a=3.98) yielded an epistasis effect of -5.35, and its genetic effects in D3 (2.62 g) significantly increased 1000-grain weight of D3 than in Nipponbare, but significantly decreased than that in S1 (qGWT3) and S5 (qGWT10). Understanding the interaction effects between target QTLs can predict the phenotype of futural QTL pyramid genotypes, which is important for intelligent design breeding in rice.

Key words: rice, grain shape, QTLs, chromosome segment substitution line, additive effect, epistasis effect

图1

包括Z66的CSSLs的选育过程 MAS: 分子标记辅助选择; CSSL: 染色体片段代换系。"

图2

双片段代换系DSSLij的Q1 (第i代换片段)和Q2 (第j代换片段)间的上位性互作示意图 Dij表示含有第i代换片段和第j代换片段的双片段代换系, 某一性状QTL (Q1和Q2)的加性效应由相应的的单片段代换系SSSLi (含“i”代换片段)和SSSLj (含“j”代换片段)鉴定。Q1和Q2间的加性×加性上位性效应, 由(日本晴+DSSLij)和(SSSLi+SSSLj)进行鉴定。Chr. 代表分别含Q1和Q2的2条水稻染色体, 黑色区表示来自受体日本晴的染色体遗传背景, 标记基因型用“(-1, -1)”表示, 红色区表示来自供体R225的代换区, 其标记基因型用“(1, 1)”表示, Q1和Q2分别表示某一性状的QTL, 位于红色的供体代换区内, Q1和Q2间的连线表示二者间存在上位性互作(P<0.05)。"

图3

Z66的染色体代换片段 每条染色体左侧为物理距离(Mb)和定位的QTL, 右侧为标记名称和代换长度(黑箭头指向)。GL: 粒长; GW: 粒宽; RLW: 谷粒长宽比; GWT: 千粒重。"

图4

日本晴和Z66的粒型及其统计分析 A: 株型; B: 粒长; C: 粒宽; D~G: 日本晴和Z66的粒长、粒宽、长宽比和千粒重统计分析;**表示日本晴和Z66性状间存在极显著(P < 0.01)差异。"

图5

粒型性状在日本晴/Z66构建的次级F2群体中的频率分布 A~D: 分别依次为粒长、粒宽、长宽比和千粒重的频率分布。"

表1

日本晴/Z66的次级F2群体检出的水稻粒型相关性状QTL"

性状
Trait		 QTL 染色体
Chr.		 连锁标记
Linked marker		 加性效应
Additive effect		 贡献率
R2 (%)		 P值
P-value
粒长
Grain length		 qGL3 3 RM5928 0.21 8.95 0.0028
qGL7 7 RM5481 0.10 2.61 0.0360
qGL10 10 RM6673 0.13 4.62 0.0210
粒宽
Grain width		 qGW6 6 RM3183 -0.11 30.78 0.0005
qGW9-1 9 RM5657 -0.10 14.87 0.0018
qGW10 10 RM6673 0.12 39.18 0.0003
长宽比
Ratio of length to width		 qRLW3 3 RM5928 0.09 14.78 0.0440
qRLW9-1 9 RM5657 0.25 44.93 0.0220
qRLW10 10 RM6673 0.049 6.40 0.0200
千粒重
1000-grain weight		 qGWT3 3 RM5928 1.14 9.48 0.0250
qGWT9-2 9 RM2144 -0.79 6.05 0.0360
qGWT10 10 RM6673 0.73 5.14 0.0430

图6

次级单片段代换系和双片段代换系培育及粒型QTL的加性和上位性效应分析 A: 培育的SSSLs (S1~S5), DSSLs (D1~D4)草图. N: 表示受体日本晴(Nipponbare); S: 单片段代换系(SSSL); D: 双片段代换系(DSSL); B: 粒长; C: 粒宽; D: 谷粒长宽比; E: 千粒重; 柱子上方最下面的小写字母表示Duncan’s多重比较结果(P < 0.05), 不同字母表示彼此差异显著。μ: 各系的平均值, ai : QTL的加性效应, I: QTL间加性×加性上位性效应, 单片段代换系的P表示SSSL与日本晴差异显著性, P < 0.05表示二者差异显著, 在代换片段上存在QTL。双片段代换系DSSL的P表示(日本晴+ DSSLij)和(SSSLi和SSSLj)的差异显著性, P < 0.05表示二者差异显著, 存在上位性效应。S1: Chr3, RM3766-RM2917; S2: Chr6, RM3330-RM3567; S3: Chr7, RM1186- RM3826; S4: Chr9, RM1553-长臂末端; S5: Chr10, RM4477-长臂末端; D1: Chr3, RM3766-RM2917; Chr6, RM3330-RM3567; D2: Chr3, RM3766-RM2917; Chr9, RM1553-RM205; D3: Chr3, RM3766-RM2917; Chr10, RM4477-RM6673; D4: Chr6, RM3330-RM3567; Chr9, RM1553-RM205; 用连字符连接的内部标记表示来自供体的替代段。"

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