Abstract

The vigorous shoots and roots help to improve drought resistance and post-transplanting recovery in rice seedlings (Oryza sativa L.). Hundreds of loci related to root system have been identified recently, but little research has been done on shoot traits, and the relationship between roots and shoots development is also still unclear. The objective of this study was to identify associated loci for roots and shoots in rice seedlings as well as to screen pleiotropic QTLs involved in coordinated development of roots and shoots. Using mini core collection of 273 cultivated rice accessions and 280 simple-sequence repeat markers, we investigated six traits [root length (RL), root thickness (RT), root weight (RW), shoot length (SL), shoot weight (SW) and ratio of root-to-shoot mass] in seedlings. Study was performed in hydroponic medium and genetic analysis was performed by association mapping using general linear model (GLM) with population structure (Q) and mixed linear model (MLM) involving Q and familial relatedness (K). Two subgroups indica and japonica showed significant differences in RT, RW and SW. Maximum correlation was observed between RW and SW. Using GLM 65 QTLs for root and 43 QTLs associated with shoot traits were detected. Among them, seven QTLs were present between RL and RW and five common QTLs were detected between SL and SW with high phenotypic variation effects (PVEs). Two key pleiotropic QTLs were also identified involved in collaborative development of roots and shoots in rice seedlings. Importantly, 17 and 10 QTLs were identified for root and shoot traits respectively in both studies of GLM and MLM. More common QTLs with high PVEs between root and shoot traits suggested that longitudinal growth (RL and SL) played an important role in accumulation of biomass (RW and SW). Considering the obvious phenotypic differences and fewer common QTLs between indica and japonica, we suggested that there could be different mechanisms of seedling development between both subpopulations. Key pleiotropic QTLs and QTLs identified for root and shoot traits in both studies of GLM and MLM could be preferentially used in marker-assisted breeding for strong rice seedling.

Highlights

  • The vigor of root system is essential for uptake of water and nutrients, structural support of the canopy and environmental sensing in rice (Oryza sativa L.) and other higher plants (Coudert et al 2010; Orman-Ligeza et al 2013)

  • The analyses of variance (ANOVA) showed extremely significant differences (P < 0.001) among varieties for each trait, which indicated the existence of a large amount of genetic variations in mini core collection (MCC)

  • Due to the highest correlation coefficients of root weight (RW) and shoot weight (SW) in both replications, we identified the common QTLs associated with root traits and shoot traits to explore the mechanism of collaborative development of roots and shoots in rice seedling (Fig. 3; Table S4)

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Summary

Introduction

The vigor of root system is essential for uptake of water and nutrients, structural support of the canopy and environmental sensing in rice (Oryza sativa L.) and other higher plants (Coudert et al 2010; Orman-Ligeza et al 2013). Root length (RL), root thickness (RT) and root weight (RW) are important traits required for best survival under severe conditions, such as water or nutrient deficiency. Many root traits QTLs have been identified in rice by bi-parental QTL mapping (Xu et al 2004; Yue et al 2006; Zhang et al 2001a, b). Many candidate genes were identified to be related to the development of roots and shoots, by using association mapping of 22,000 SNPs and 180 rice varieties from tropical country Vietnam under greenhouse conditions (Phung et al 2016). Traditional bi-parental mapping was conducive to explore useful QTL with low allele frequency in nature, and provided genetic information to further explore molecule basis of roots and shoots development in rice. Association mapping could greatly increase the range of natural variation and the number of significant loci (Huang et al 2010, 2012)

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