Papaya ringspot virus (PRSV) causes the Papaya ringspot disease. Virus-host interactions appear to play a significant role in the replication, pathogenesis, and infection caused by the PRSV. PRSV coat protein is likely to be involved in the processes of RNA replication, aphid transmission, and cell-to-cell movement, which is closely related to the host cell proteins resulting in a PRSV infection. To identify the host proteins that interact with the CP in vitro, immune precipitation, insolution trypsin digestion, and LC-MS/MS were performed. Twenty-three identified proteins that interacted with the CP are involved in cellular metabolism, transcription, signal, translation, carbohydrate metabolism, protein metabolism, stress response, photosynthesis, nucleotide metabolism, respiration, and lipid metabolism processes. The search tool for interactions of chemicals (STITCH) results show that SWP (an RNA polymerase II transcription mediator) and MPPBETA (Mitochondrial processing peptidase) are involved in known plant defense mechanisms including transcription factors, cell division, hormones, stress, mitochondrial electron transferase, respiration, and proteasome. Therefore, analyzing virus-host protein interactions at a molecular level is important to build a better understanding of the virus replication mechanism and cellular responses mounted against viruses by the host defense system.

Background Sri Lankan cassava mosaic virus (SLCMV) is a plant virus causing significant economic losses throughout Southeast Asia. While proteomics has the potential to identify molecular markers that could assist the breeding of virus resistant cultivars, the effects of SLCMV infection in cassava have not been previously explored in detail. Results Liquid Chromatography-Tandem Mass Spectrometry (LC/MS–MS) was used to identify differentially expressed proteins in SLCMV infected leaves, and qPCR was used to confirm changes at mRNA levels. LC/MS–MS identified 1,813 proteins, including 479 and 408 proteins that were upregulated in SLCMV-infected and healthy cassava plants respectively, while 109 proteins were detected in both samples. Most of the identified proteins were involved in biosynthetic processes (29.8%), cellular processes (20.9%), and metabolism (18.4%). Transport proteins, stress response molecules, and proteins involved in signal transduction, plant defense responses, photosynthesis, and cellular respiration, although present, only represented a relatively small subset of the detected differences. RT-qPCR confirmed the upregulation of WRKY 77 (A0A140H8T1), WRKY 83 (A0A140H8T7), NAC 6 (A0A0M4G3M4), NAC 35 (A0A0M5JAB4), NAC 22 (A0A0M5J8Q6), NAC 54 (A0A0M4FSG8), NAC 70 (A0A0M4FEU9), MYB (A0A2C9VER9 and A0A2C9VME6), bHLH (A0A2C9UNL9 and A0A2C9WBZ1) transcription factors. Additional upregulated transcripts included receptors, such as receptor-like serine/threonine-protein kinase (RSTK) (A0A2C9UPE4), Toll/interleukin-1 receptor (TIR) (A0A2C9V5Q3), leucine rich repeat N-terminal domain (LRRNT_2) (A0A2C9VHG8), and cupin (A0A199UBY6). These molecules participate in innate immunity, plant defense mechanisms, and responses to biotic stress and to phytohormones. Conclusions We detected 1,813 differentially expressed proteins infected cassava plants, of which 479 were selectively upregulated. These could be classified into three main biological functional groups, with roles in gene regulation, plant defense mechanisms, and stress responses. These results will help identify key proteins affected by SLCMV infection in cassava plants.

The major flaw of cassava is its indigenous cyanide. Traditional breeding program for diminishing cyanide in cassava take a long waiting time for harvesting cassava tubers to assess cyanide content. Genetic markers are useful for selection of good agricultural traits, which also applied in low-cyanide cassava breeding programs by detecting gene associate with cyanide content in cassava. Therefore, the objective of this study was to develop SNP markers to detect low cyanide trait in cassava. Genotype analysis was carried out using Genotyping by Sequencing (GBS) technology assembling with phenotype analysis. Then, the SNP markers associated with cyanide content were found. Afterward, the primers of SNP marker associated with cyanide content 2 positions were developed using tetra-primer ARMS-PCR techniques. S16_640082 and S16_735381 SNP markers on chromosome 16 showed potential ability of the selection of cassava varieties with cyanide content less than 250 mg HCN/kg fresh weight. The selection accuracy of S16_640082 and S16_735381 SNP markers was 73.33 and 76.64 %, respectively. These markers could be used in marker assisted selection (MAS) in cassava seedling. It substantially reduces cassava breeding programs cost and time. HIGHLIGHTS The major flaw of cassava is its indigenous cyanide. Up to our knowledge, there is rarely report on SNP marker related to cyanide content in Thai cassava population By performing genome wide association mapping (GWAS) to characterize the genome position related to HCN, 2 novel SNP markers associated with cyanide content were found The primers to detect the SNP markers were developed using tetra-primer ARMS-PCR techniques The markers showed ability of the selection of cassava varieties with cyanide content less than 250 mg HCN/kg fresh weight GRAPHICAL ABSTRACT

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