Transcriptome analysis of resistant cotton germplasm responding to reniform nematodes

Authors: Feng, Chunda; Stetina, Salliana - Sally; Erpelding, John

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2024
Publication Date: 3/26/2024
Citation: Feng, C., Stetina, S.R., Erpelding, J.E. 2024. Transcriptome analysis of resistant cotton germplasm responding to reniform nematodes. Plants. 13:958. https://doi.org/10.3390/plants13070958.
DOI: https://doi.org/10.3390/plants13070958

Interpretive Summary: Reniform nematode is an increasing threat to the U.S. cotton production, which causes hundreds of millions of dollars in loss annually. Current management approaches using chemical control and crop rotation are not sustainable or effective, and growing resistant cultivars is the most economical and effective way to control this important parasite. However, resistance to reniform nematode has not been found in the widely grown Upland cotton but found in its relative species such as Sea Island cotton and Asiatic cotton. Two resistant lines each of Sea Island cotton and Asiatic cotton were used to study the gene expressions five and nine days after inoculation with reniform nematodes. Differentially expressed genes (DEGs) were identified by comparing the gene expression levels to their non-inoculated counterparts. Two DEGs conferring resistance to root-knot nematodes were identified. Some other DEGs were identified that have potential roles in plant defense. The findings in this research will aid other scientists in understanding the mechanisms of resistance and help to develop molecular markers for resistance genes, which would be eventually beneficial for the development of resistant cultivars for cotton growers.

Technical Abstract: Reniform nematode (Rotylenchulus reniformis) is an important microparasite for Upland cotton (Gossypium hirsutum L.) production. Growing resistant cultivars is the most economical management method, but only a few G. barbadense genotypes and some diploid Gossypium species confer high levels of resistance. This study conducted a transcriptome analysis of resistant genotypes to identify genes involved in host plant defense. Seedlings of G. arboreum accessions PI 529728 (A2-100) and PI 615699 (A2-190), and G. barbadense genotypes PI 608139 (GB 713) and PI 163608 (TX 110) were inoculated with the reniform nematode population MSRR04 and root samples were collected on the fifth (D5) and nineth (D9) day after inoculation. Differentially expressed genes (DEGs) were identified by comparing root transcriptomes from inoculated with non-inoculated plants. Accessions A2-100 and A2-190 showed 52 and 29 DEGs on D5, respectively, with 14 DEGs in common, and 18 DEGs for A2-100 and 11 DEGs for A2-190 on chromosome 5. On D9, four DEGs were found in A2-100 and two DEGs in A2-190. For GB 713, 52 and 43 DEGs and for TX 110, 29 and 117 DEGs were observed on D5 and D9, respectively. Six DEGs were common at the two sampling times for these genotypes. Some DEGs were identified as Meloidogyne-induced cotton (MIC) 3 and 4, resistance gene analogs, or receptor-like proteins. Other DEGs have potential roles in plant defense, such as peroxidases, programmed cell death, pathogenesis related proteins, and systemic acquired resistance. Further research on these DEGs will aid in understanding the mechanisms of resistance to explore new applications for the development of resistant cultivars