LR is a Novel Gene Regulating Amylose Content in Rice Revealed by Genome-Wide Association Study

doi:10.1016/j.rsci.2024.12.010

Abstract

Li Huijuan, Yu Haipeng, Huang Guanrong, Huang Zengying, Tang Lu, Yang Pengfei, Zhong Zhengzheng, Hu Guocheng, Zhang Peng, Tong Hanhua. LR is a Novel Gene Regulating Amylose Content in Rice Revealed by Genome-Wide Association Study[J]. Rice Science, 2025, 32(3): 277-282.

Figures/Tables 1

Fig. 1. Genome-wide association analysis of amylose content (AC) in Ting’s core collection and functional analysis of LR. A, Manhattan plots for AC. Genes in red represent reported genes, while purple represent candidate genes. Red and blue horizontal dashed lines indicate significance thresholds at P ≤ 1.93 × 10-8 and P ≤ 1.93 × 10-9, respectively. Chr., Chromosome. B, Quantile-quantile plot for AC using MLM (Q + K) model. Blue line represents the expected -log10(P), and red line represents the observed -log10(P). C, Haplotypes of LR. Blue frame represents the exon of LR. Red nucleotides represent natural variations, causing amino acid changes. Numbers represent counts of indica (Ind.), japonica (Jap.), and all rice in the Ting’s core collection and MBKBASE website (in parentheses), respectively. D and E, Comparison of ACs among different haplotypes in the Ting’s core germplasm (D) and MBKBASE website (E). Horizontal lines represent medians, nearest points represent means, and whiskers mark the range from the 5th to the 95th percentile of the total data. F, AC of wild type (Nipponbare, NIP), knockout (Cr-lr-1 and Cr-lr-2), and complementation (CP-1 and CP-2) mutants. G, Transverse sections stained with iodine in wild type (NIP) and knockout mutant (Cr-lr-1 and Cr-lr-2). Scale bars, 500 µm. In D-F, ** represents P < 0.01 by the Student’s t-test. ns, Not significant.

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