Dynamic Analysis of QTLs on Plant Height with Single Segment Substitution Lines in Rice

Abstract Dynamic regulation of QTLs remains mysterious. Single segment substitution lines (SSSLs) and conditional QTL mapping and functional QTL mappings are ideal materials and methods to explore dynamics of QTLs for complex traits. This paper analyzed the dynamics of QTLs on plant height with SSSLs in rice. Five SSSLs were verified with plant height QTLs first. All five QTLs had significant positive effects at one or more developmental stages except QTL1. They interacted each other, with negative effects before 72 d after transplanting and positive effects since then. The five QTLs selectively expressed in specific periods, mainly in the periods from 35 to 42 d and from 49 to 56 d after transplanting. Expressions of epistasis were dispersedly in various periods, negative effects appearing mainly before 35 d. The five QTLs brought the inflexion point ahead of schedule, accelerated growth and degradation, and changed the peak plant height, while their interactions had the opposite effects. The information will be helpful to understand the genetic mechanism for developmental traits.

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Dynamic Mapping Based on Single Segment Substitution Lines for Plant Height in Rice

10.21203/rs.3.rs-757574/v1 ◽

2021 ◽

Author(s):

Yu Fu ◽

Hongyuan Zhao ◽

Jiongkai Huang ◽

Haitao Zhu ◽

Xin Luan ◽

...

Keyword(s):

Qtl Mapping ◽

Plant Height ◽

Expression Patterns ◽

Negative Effects ◽

Substitution Lines ◽

Epistatic Interactions ◽

Single Segment ◽

Conditional Qtl Mapping ◽

Single Segment Substitution Lines ◽

Segment Substitution

Abstract Background: Dynamic regulations of QTLs still remain mysterious. Single segment substitution lines and conditional QTL mapping, functional QTL mappings are ideal materials and methods to explore epistatic interactions, expression patterns and functions of QTLs for complex traits.Results: Based on single segment substitution lines five QTLs on plant height in rice were identified first in this paper, and then their epistatic interactions, expression patterns and functions were systemmatically studied by tailing after each QTL. Unconditional QTL mapping showed the five QTLs were with significant effects at one or more stages, all of which increased plant height except QTL1. They interacted each other as homeostatic mechanisms to regulate plant height with negative effects before 72d after transplanting and positive since then. Conditional QTL mapping revealed the expression quantities and periods for the five QTLs and their epistases. Temporal expression pattern was verified again by selective expressions of QTLs in specific periods. QTL1 expressed negatively while QTL2 and QTL4 positively, mainly occurring in the periods from 35 to 42d and from 49 to 56d after transplanting. Epistatic expressions were dispersedly in various periods, mainly with negative effects before 35d while positive since then. Functional QTL mapping discovered the five QTLs brought the inflexion point ahead of schedule, accelerated the growth and the degradation, and changed the peak of plant height, while their interactions had the opposite effects approximately. This paper uncovered the dynamic rules of five QTLs and their interactions on plant height systematically, which will be helpful to understand the genetic mechanism for developmental traits.Conclusions: Five single segment substitution lines were tested with significant additive, dominant and epistatic effects of QTLs on plant height. Additive and dominant expressions were mainly in two periods, while epistasis dispersedly. The five QTLs and their interactions significantly regulated the developmental trajectory of plant height.

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Additive and Epistasis Effects of Quantitative Trait Loci for Plant Height and Its Components in Single Segment Substitution Lines of Rice

Acta Agronomica Sinica ◽

10.1016/s1875-2780(08)60054-1 ◽

2009 ◽

Vol 35 (1) ◽

pp. 48-56

Author(s):

Fang-Ming ZHAO ◽

Gui-Quan ZHANG ◽

Rui-Zhen ZENG ◽

Zeng-Lin YANG ◽

Hai-Tao ZHU ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Plant Height ◽

Quantitative Trait ◽

Substitution Lines ◽

Single Segment ◽

Single Segment Substitution Lines ◽

Trait Loci ◽

Segment Substitution

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Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.)

Genome ◽

10.1139/g06-005 ◽

2006 ◽

Vol 49 (5) ◽

pp. 476-484 ◽

Cited By ~ 82

Author(s):

Zhang-Ying Xi ◽

Feng-Hua He ◽

Rui-Zhen Zeng ◽

Ze-Min Zhang ◽

Xiao-Hua Ding ◽

...

Keyword(s):

Oryza Sativa ◽

Quantitative Trait ◽

Complex Traits ◽

Genetic Background ◽

Oryza Sativa L ◽

Substitution Lines ◽

Single Segment ◽

Single Segment Substitution Lines ◽

Segment Substitution ◽

Wide Population

Naturally occurring allelic variations underlying complex traits are useful resources for the functional analysis of plant genes. To facilitate the genetic analysis of complex traits and the use of marker-assisted breeding in rice, we developed a wide population consisting of 217 chromosome single-segment substitution lines (SSSLs) using Oryza sativa L. 'Hua-Jing-Xian74' (HJX74), an elite Indica cultivar, as recipient, and 6 other accessions, including 2 Indica and 4 Japonica, as donors. Each SSSL contains a single substituted chromosome segment derived from 1 of the 6 donors in the genetic background of HJX74. The total size of the substituted segments in the SSSL population was 4695.0 cM, which was 3.1 times that of rice genome. To evaluate the potential application of these SSSLs for quantitative trait loci detection, phenotypic variations of the quantitative traits of days to heading and grain length in the population consisting of 210 SSSLs were observed under natural environmental conditions. The results demonstrated that there was a wide range of phenotypic variation in the traits in the SSSL population. These genetic materials will be powerful tools to dissect complex traits into a set of monogenic loci and to assign phenotypic values to different alleles at the locus of interest.Key words: rice, mapping population, single segment substitution lines, marker-assisted selection, quantitative trait loci.

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Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines

Breeding Science ◽

10.1270/jsbbs.65.192 ◽

2015 ◽

Vol 65 (3) ◽

pp. 192-200 ◽

Cited By ~ 10

Author(s):

Haitao Zhu ◽

Ziqiang Liu ◽

Xuelin Fu ◽

Ziju Dai ◽

Shaokui Wang ◽

...

Keyword(s):

Plant Height ◽

Substitution Lines ◽

Single Segment ◽

Single Segment Substitution Lines ◽

Segment Substitution

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Additive Effects and Epistasis Effects of QTL for Plant Height and Its Components Using Single Segment Substitution Lines (SSSLs) in Rice

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2009.00048 ◽

2009 ◽

Vol 35 (1) ◽

pp. 48-56

Author(s):

Fang-Ming ZHAO ◽

Gui-Quan ZHANG ◽

Rui-Zhen ZENG ◽

Zheng-Lin YANG ◽

Hai-Tao ZHU ◽

...

Keyword(s):

Plant Height ◽

Additive Effects ◽

Substitution Lines ◽

Single Segment ◽

Single Segment Substitution Lines ◽

Segment Substitution

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Unconditional and conditional analysis of epistasis between tillering QTLs based on single segment substitution lines in rice

Scientific Reports ◽

10.1038/s41598-020-73047-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Huaqian Zhou ◽

Weifeng Yang ◽

Shuaipeng Ma ◽

Xin Luan ◽

Haitao Zhu ◽

...

Keyword(s):

Cumulative Effect ◽

Time Interval ◽

Negative Effects ◽

Substitution Lines ◽

Epistatic Effects ◽

Unconditional Qtl ◽

Single Segment ◽

Single Segment Substitution Lines ◽

Segment Substitution ◽

Half Diallel

Abstract Epistasis plays an important role in manipulating rice tiller number, but epistatic mechanism still remains a challenge. Here we showed the process of epistatic analysis between tillering QTLs. A half diallel mating scheme was conducted based on 6 single segment substitution lines and 9 dual segment pyramiding lines to allow the analysis of 4 epistatic components. Additive-additive, additive-dominance, dominance-additive, and dominance-dominance epistatic effects were estimated at 9 stages of development via unconditional QTL analysis simultaneously. Unconditional QTL effect (QTL cumulative effect before a certain stage) was then divided into several conditional QTL components (QTL net effect in a certain time interval). The results indicated that epistatic interaction was prevalent, all QTL pairs harboring epistasis and one QTL always interacting with other QTLs in various component ways. Epistatic effects were dynamic, occurring mostly within 14d and 21–35d after transplant and exhibited mainly negative effects. The genetic and developmental mechanism on several tillering QTLs was further realized and perhaps was useful for molecular pyramiding breeding and heterosis utilization for improving plant architecture.

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