Tomato NBS-LRR gene Mi-9 confers heat-stable resistance to root-knot nematodes

Root-knot nematodes (RKNs) are the most widespread soil-borne obligate endoparasites. They infect the roots of many crops and cause significant yield losses. There is only one commercially available RKN-resistant gene in tomatoes, Mi-1.2. However, it fails when the soil temperatures hots higher than 28℃. Hence, the need to identify heat-stable resistance genes against root-knot nematodes remains for developing resilient tomato germplasm and ensuring sustainable tomato production.

Paving the way towards that goal, a team of researchers from China cloned the heat-stable RKN-resistant gene, Mi-9 from a gene cluster composed of seven nucleotide-binding sites and leucine-rich repeat (NBS-LRR) type resistant genes in Solanum arcunum accession LA2157.

The team published their findings in the Journal of Integrative Agriculture.

“Soil temperature is frequently higher than 28℃ in both greenhouse and field tomato production systems, and rising temperatures caused by global climate change are making the situation worse,” explains the study's corresponding author, Cao Xu, a professor at Chinese Academy of Sciences.

To clone the heat-stable RKN resistance gene from LA2157, the researchers performed a de novo genome reference assembly using PacBio Sequel II sequencing. A comparative genomic analysis was then carried out through 13 representative Solanaceae species with two rounds of gene rearrangements (inversions) within a 330-kb resistant gene cluster might account for the gain and/or loss of heat-stable RKN resistance.

“Screening nematode infections in individual and combinatorial knockouts of five NBS-LRR genes showed that Mi-9 Candidate 4 (MiC-4) alone is sufficient to confer heat-stable RKN resistance,” shares Xu. “We overcome the lack of recombination by characterizing the genomic structural changes of the gene cluster across multiple tomato species, then accurately targeting and knocking out cluster members individually and combinatorically to pinpoint the resistance gene using CRISPR/Cas9 mediated editing.”

Notably, the roots showed rapid necrosis after nematode infection, indicating the immune response triggered by MiC-4 occurs at the very starting stage of infection. “It's worth investigating how the ROS signal was regulated by Mi-9 (MiC-4) will benefit the fundamental research on the interaction between plants and parasitic nematodes,” adds Xu.

The team's findings also showcase a roadmap for rapid characterization of resistance genes by combining comparative genomics and genome editing, with the potential to be utilized in other crops.

Contact Authors:

Correspondence Cao Xu, E-mail: caoxu@genetics.ac.cn

Funder:

This work was supported by the National Key R&D Program of China (2018YFA0900600 and 2021YFF1000103-5), and the Strategic Priority Research Program of Chinese Academy of Sciences (XDA24030503).

Conflict of Interest:

The authors declare that they have no conflict of interest.

See the Article:

Chen S D, et al. A tomato NBS-LRR gene Mi-9 confers heat-stable resistance to root-knot nematodes. Journal of Integrative Agriculture, 2025,24(7): 2869-2875, https://doi.org/10.1016/j.jia.2024.07.017