Advances in Rice Coleoptile Elongation: Implications for Direct-Seeded Rice Adaptation

doi:10.1016/j.rsci.2026.02.004

Abstract

Abstract:

The rice coleoptile, a key protective structure during seed development, is crucial for safeguarding the plumule and facilitating seed germination. It plays a pivotal role in seedling emergence from soil, with its elongation characteristics being particularly important in direct-seeding systems. Coleoptile elongation is a complex biological process coordinately regulated by environmental factors, genetic background, plant hormones, and other signaling molecules, all of which interact to modulate elongation dynamics. This review systematically summarizes the mechanisms underlying coleoptile elongation, explores the regulatory roles of environmental and physiological factors, and synthesizes recent research progress on the identification of coleoptile-related QTLs, gene mining, and molecular regulatory mechanisms. Furthermore, we discuss the potential applications of coleoptile research in rice genetic improvement, aiming to provide a theoretical basis and novel insights for leveraging coleoptile traits in future breeding strategies.

Key words: rice, coleoptile, gene mining, breeding application

Fan Honghuan, Song Jian, Tang Liqun, Wang Junmin, Sheng Zhonghua, Jiao Guiai, Tang Shaoqing, Hu Shikai, Hu Peisong. Advances in Rice Coleoptile Elongation: Implications for Direct-Seeded Rice Adaptation[J]. Rice Science, 2026, 33(3): 327-339.

Figures/Tables 5

Fig. 1. Schematic diagram of rice coleoptile structure.

Fig. 2 Related QTLs controlling coleoptile elongation in rice. GWAS, Genome-wide association study.

Fig. 3. Distribution of mapped QTLs for controlling coleoptile length on rice chromosomes. These QTLs detected by genome-wide association studies (GWAS) span relatively long physical intervals (represented by the grey segments on the chromosomes), and their positions are indicated by the physical location of the peak single nucleotide polymorphism within the QTL interval.

Table 1. Genes regulating coleoptile elongation in rice.

Gene	Chromosome	Phenotype	Method	Population/Genetic material	Reference
GY1	1	Coleoptile length	Map-based cloning	gy1 mutant and TN1 F₂population	Xiong et al, 2017
OsFLZ18	6	Coleoptile length	Map-based cloning	432 rice varieties	Ma et al, 2021
OsTPP7	9	Coleoptile length	Map-based cloning	KHO and IR64 NILs	Kretzschmar et al, 2015
OsEE1	10	Coleoptile length	GWAS	591 rice accessions	Li et al, 2025
OsCIPK15	11	Germination rate, coleoptile length	Gene knockout	Nipponbare	Ye et al, 2018
OsGF14h	11	Germination rate, coleoptile length	GWAS	WR04-6 and Qishanzhan RILs	Sun et al, 2022
OsUGT75A	11	Coleoptile length	GWAS	245 rice varieties	He et al, 2023

Fig. 4. Model of anaerobic germination mechanisms in rice. Orange arrows indicate activating effects, blue arrows represent inhibition, green arrows show the direction of metabolic reactions. orange dashed arrows indicate modest promotion, and black arrows denote common regulatory patterns. while solid and dashed black lines illustrate the outcomes of the respective pathways. The red crosses represent inhibition or suppression of the corresponding pathways or gene expression.JA, Jasmonic acid; ABA, Abscisic Acid; IAA, Indole-3-acetic acid; SA, Salicylic acid; ETH, Ethylene; GA, Gibberellin; T6P, Trehalose-6-phosphate; PDC, Pyruvate decarboxylase; ADH, Alcohol dehydrogenase; UDP, Uridine diphosphate; ARF, Auxin response factor; TIR, Toll/Interleukin-1 receptor; PP2C, Protein phosphatase 2C; GAMYB, Gibberellin-induced MYB transcription factor; MYBS1, MYB-related protein S1.

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