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Expression analysis of miR160a and its target auxin response factor genes reveals a possible role in response to graft incompatibility in tomato (Solanum lycopersicum L.)

agricultural-science
biotechnology
genetics
molecular-biology
plant-science

Abstract

Background. Graft incompatibility represents a major barrier to the widespread adoption of grafting in tomato production. Grafting incompatibility can be detected through various physiological, biochemical, and metabolic markers, but these markers vary with graft combinations, soil conditions, and environmental factors, making graft incompatibility detection highly challenging. Thus, a deeper understanding of the molecular processes is needed to identify compatible graft combinations by targeting genes that hinder graft union formation. The regulatory interaction between miR160a and auxin response factor (ARF) genes may represent a key molecular mechanism underlying graft incompatibility in tomato. MiR160a, a highly conserved microRNA, regulates auxin response factor (ARF) genes that are vital for revascularization at the graft union.

Methods. To better understand the underlying genetic mechanisms related to graft incompatibility, the present study quantified the expression of miRNA160a from tomato (sly-miR160a) and its regulatory genes, Solyc11g069500.2.1 ( SlARF10 ), Solyc09g007810.3.1 ( SlARF16 ), and Solyc11g013480.2.1 ( SlARF17 ) in self-grafted, intraspecific, and interspecific grafted seedlings of tomato at 4, 8, and 16 days after grafting through qRT-PCR.

Results. The gene expression data revealed a strong regulatory response to graft compatibility: The interspecific graft (R/PP; Roma scion/ pepper rootstock) exhibited high miR160a expression and suppressed ARF gene expression, indicating stress-related gene silencing, likely contributing to reduced graft compatibility. In contrast, intraspecific (R/SR; Roma scion/ super red rootstock) and self-grafts (R/R) showed the opposite pattern, low sly-miR160a and high ARF expression, suggesting a more favorable auxin-regulated environment for successful graft union and vascular development. The molecular data are consistent with survival percentage and yield analysis, where intraspecific grafts (R/SR) produced a significantly increased number of fruit and overall fruit yield as compared to self-grafts (R/R) and non-grafted (NG) controls.

Conclusions. These findings identify the sly-miR160a-ARF pathway as a promising molecular target, where suppression of miR160a–ARF activity through RNA-based sprays or transient gene silencing approaches could facilitate graft union formation and enhance compatibility in tomato. Further, the sly-miR160a-ARF pathway could act as a biomarker for early detection of graft incompatibility to select compatible genotypes in rootstock breeding programs.

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