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

Zhou, Huaqian; Yang, Weifeng; Ma, Shuaipeng; L, Xin; Zhu, Haitao; Wang, Aimin; Huang, Congling; Rong, Biao; ShangZhi, Dong; Meng, Liang; Wang, Shaokui; Zhang, Guiquan; Liu, Guifu

doi:10.1038/s41598-020-73047-7

Cited by 13 publications

(22 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One of major goals in developmental genetics is to explore gene expression (Zhu 1995;Atchley and Zhu 1997). Conditional QTL mapping makes this possible, which can estimate the net expression of QTL in a certain of time interval (Wang et al 1999;Zhu 1999 (Zhou et al 2020) and was well validated by the results estimated in this paper. The correlation coefficient between QTL effects at the final stage 9 t and the sum of all conditional QTL effects before 9 t reached 0.9379 ** in the previous paper (Zhou et al 2020) and 0.7208 ** in this paper, respectively(data not shown).…”

Section: Dynamic Patterns Of Qtl Expressionssupporting

confidence: 56%

“…The similar experimental materials as the previous study (Zhou et al 2020), Huajingxian 74 (HJX74) and its five single segment substitution lines (SSSLs) (Table 1), were applied in this trial.…”

Section: Materials and Mapping Populationmentioning

confidence: 99%

“…Where only did a series of conditional QTLs truly reflected the expression periods and quantities of a QTL throughout the whole developmental stage. Conditional QTL mapping had widely been applied to reveal gene dynamic patterns for developmental traits (Yan et al 1998a, b;Wang et al 1999;Gao et al 2001;Jiang et al 2008;Liu et al 2010b;Zhou et al 2020). There were four representative patterns for the genetic control of growth trajectories, permanent QTLs, early QTLs, late QTLs and inverse QTLs (Wu et al 2006).…”

Section: Dynamic Patterns Of Qtl Expressionsmentioning

confidence: 99%

See 2 more Smart Citations

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

Zhao

Huang

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Dynamic Patterns Of Qtl Expressionssupporting

confidence: 56%

Section: Materials and Mapping Populationmentioning

confidence: 99%

Section: Dynamic Patterns Of Qtl Expressionsmentioning

confidence: 99%

See 1 more Smart Citation

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

Zhao

Huang

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…When multiple substitution segments in NILs with target trait overlapped, the QTL was located in the overlapping region (Tan et al 2020 ). Additive effect of a QTL was defined as the phenotypic difference between SSSL and HJX74 (Zhou et al 2020 ). QTLs were named followed the method of McCouch et al ( 1997 ).…”

Section: Methodsmentioning

confidence: 99%

Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice

Yang

Liang

Hao

et al. 2021

Rice

Self Cite

View full text Add to dashboard Cite

Background Grain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11–09 with substitution segment from O. sativa and HP67–11 with substitution segment from O. glaberrima. Results The grain chalkiness of SSSLs 11–09 and HP67–11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS). Conclusions qPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.

show abstract

“…When multiple substitution segments overlapped in NILs, the QTL was located in the overlapping region (Eshed and Zamir, 1995;Tan et al 2020). Additive effect of a QTL was defined as the phenotypic difference between SSSL and HJX74 (Zhou et al 2020). QTLs were named followed the method of McCouch et al (1997).…”

Section: Genotyping Of Molecular Markers and Substitution Mappingmentioning

confidence: 99%

Substitution Mapping of Two Closely Linked QTLs Controlling Grain Chalkiness and Grain Shape on Rice Chromosome 8

Yang

Xiong

Liang

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Results: Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness and for grain length and grain width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by heat stress. Conclusions: Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to high temperature.

show abstract

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

Cited by 13 publications

References 40 publications

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

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

Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice

Substitution Mapping of Two Closely Linked QTLs Controlling Grain Chalkiness and Grain Shape on Rice Chromosome 8

Contact Info

Product

Resources

About