Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

Ding, Xiaowen; Shi, Jubin; Gui, Jinxin; Zhou, Huang; Yan, Yuntao; Zhu, Xiaoya; Xie, Binying; Liu, Xionglun; He, Jiwai

doi:10.3390/plants13010134

Open AccessArticle

Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

by

Xiaowen Ding

,

Jubin Shi

,

Jinxin Gui

,

Huang Zhou

,

Yuntao Yan

,

Xiaoya Zhu

,

Binying Xie

,

Xionglun Liu

^* and

Jiwai He

^*

College of Agronomy, Hunan Agricultural University, Changsha 410128, China

^*

Authors to whom correspondence should be addressed.

Plants 2024, 13(1), 134; https://doi.org/10.3390/plants13010134

Submission received: 16 November 2023 / Revised: 19 December 2023 / Accepted: 23 December 2023 / Published: 3 January 2024

(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)

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Abstract

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 qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 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.

Keywords: rice; protrusion percentage; QTL; GWAS; germplasm; haplotype

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MDPI and ACS Style

Ding, X.; Shi, J.; Gui, J.; Zhou, H.; Yan, Y.; Zhu, X.; Xie, B.; Liu, X.; He, J. Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. Plants 2024, 13, 134. https://doi.org/10.3390/plants13010134

AMA Style

Ding X, Shi J, Gui J, Zhou H, Yan Y, Zhu X, Xie B, Liu X, He J. Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. Plants. 2024; 13(1):134. https://doi.org/10.3390/plants13010134

Chicago/Turabian Style

Ding, Xiaowen, Jubin Shi, Jinxin Gui, Huang Zhou, Yuntao Yan, Xiaoya Zhu, Binying Xie, Xionglun Liu, and Jiwai He. 2024. "Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study" Plants 13, no. 1: 134. https://doi.org/10.3390/plants13010134

APA Style

Ding, X., Shi, J., Gui, J., Zhou, H., Yan, Y., Zhu, X., Xie, B., Liu, X., & He, J. (2024). Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. Plants, 13(1), 134. https://doi.org/10.3390/plants13010134

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Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

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