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

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Abstract

Background

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.

Methods

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 2 years.

Results

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 2 years were identified.

Conclusions

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.

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Funding

This research was supported by the Heilongjiang Provincial governmental Postdoctoral Foundation of China (LBH-Z16188), the Natural Science Foundation Joint Guide Project of Heilongjiang (LH2019C035) and the Province-Academy Science and Technology Cooperation Project of Heilongjiang (YS20B05). Application R & D Project of Heilongjiang Academy of Agricultural Science (2021YYYF037).

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Author notes

  1. Hongliang Zheng

    Present address: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China

  2. Jiangxu Wang and Tao Wang contributed equally to this work.

Authors and Affiliations

  1. Heilongjiang Academy of Agricultural Sciences, Institute of Crops Tillage and Cultivation, Harbin, 150030, China

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

  2. Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China

    Luomiao Yang & Detang Zou

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  1. Jiangxu Wang
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Contributions

JW and TW were the main writer of the whole paper. QW, XT, YR, HZ, KL responsible for field data collection. LY mainly engaged in data statistics and data processing. HJ responsible for sequencing data sorting and analysis. YL, QL proofread the full text. DZ, HZ guided the technical route of this study.

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Correspondence to Hongliang Zheng.

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Wang, J., Wang, T., Wang, Q. et al. QTL mapping and candidate gene mining of flag leaf size traits in Japonica rice based on linkage mapping and genome-wide association study. Mol Biol Rep 49, 63–71 (2022). https://doi.org/10.1007/s11033-021-06842-8

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