QTL mapping and candidate gene mining of flag leaf size traits in Japonica rice based on linkage mapping and genome-wide association study.

Jiangxu Wang,Luomiao Yang,Xiaodong Tang,Qi Liu,Haiyan Zheng,Qi Wang,Yang Ren,Hongliang Zheng,Detang Zou,Hui Jiang,Tao Wang,Yidan Li,Kai Liu

doi:10.1007/s11033-021-06842-8

Jiangxu Wang, Luomiao Yang + Show 11 more

Open Access

https://doi.org/10.1007/s11033-021-06842-8

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Abstract

As one of the most important factors of the japonica rice plant, leaf shape affects the photosynthesis and carbohydrate accumulation directly. Mining and using new leaf shape related genes/QTLs can further enrich the theory of molecular breeding and accelerate the breeding process of japonica rice. In the present study, 2 RILs and a natural population with 295 japonica rice varieties were used to map QTLs for flag leaf length (FL), flag leaf width (FW) and flag leaf area (FLA) by linkage analysis and genome-wide association study (GWAS) throughout 2years. A total of 64 QTLs were detected by 2 ways, and pleiotropic QTLs qFL2 (Chr2_33,332,579) and qFL10 (Chr10_10,107,835; Chr10_10,230,100) consisted of overlapping QTLs mapped by linkage analysis and GWAS throughout the 2years were identified. The candidate genes LOC_Os02g54254, LOC_Os02g54550, LOC_Os10g20160, LOC_Os10g20240, LOC_Os10g20260 were obtained, filtered by linkage disequilibrium (LD), and haplotype analysis. LOC_Os10g20160 (SD-RLK-45) showed outstanding characteristics in quantitative real-time PCR (qRT-PCR) analysis in leaf development period, belongs to S-domain receptor-like protein kinases gene and probably to be a main gene regulating flag leaf width of japonica rice. The results of this study provide valuable resources for mining the main genes/QTLs of japonica rice leaf development and molecular breeding of japonica rice ideal leaf shape.

Highlights

Rice is one of the most important food crops on the planet, bearing the lifeline of human food security (Pane et al 2021; Barboza et al 2018; Timmer 2014)
Most of the absolute values of kurtosis and skewness were near 1, which basically conformed to the normal distribution and showed a typical genetic model of quantitative traits, was suitable for linkage analysis and genome-wide association analysis
Some genes or QTLs regulating flag leaf size were identified by classical mapping and reverse genetics, the number of studies on leaf genetic variation about japonica rice is still relatively small (Jiang et al 2010; Yang et al 2015; Hu et al 2012)

Summary

Introduction

Rice is one of the most important food crops on the planet, bearing the lifeline of human food security (Pane et al 2021; Barboza et al 2018; Timmer 2014). Leaf is an important part of rice plant histogenesis and morphogenesis, and the main organ for photosynthesis and respiration (Adachi et al 2014; Zhu et al 2014; Gu et al 2012). The photosynthetic energy storage and normal life function of rice are directly affected by leaf (He et al 2017). To be the top functional leaf of rice, flag leaf has significant effects on plant related physiological characters and field population structure (Zhu et al 2012; Giuliani et al 2013). It is an effective way to improve the quality and yield of rice by shaping and screening the leaf morphology in the process of breeding

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