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The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only <i>qPP2</i> was detected repeatedly two times. The candidate gene analysis showed that <i>LOC_Os02g57530 (ETR3)</i>, <i>LOC_Os01g57610 (GH3.1)</i> and <i>LOC_Os04g0425 (CTB2)</i> were the candidate genes for <i>qPP2</i>, <i>qPP1</i> and <i>qPP4</i>, respectively. The haplotype (Hap) analysis revealed that Hap1 of <i>ETR3</i>, Hap1 and 3 of <i>GH3.1</i> and Hap2 and 5 of <i>CTB2</i> are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of <i>ETR3</i> is a favorable allele for the germination percentage; Hap3 of <i>GH3.1</i> is an elite allele for seed germination; and Hap5 of <i>CTB2</i> is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.