Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania

Abstract

Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30–36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21–24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9–99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.

Molecular detection and characterisation of black raspberry necrosis virus and raspberry bushy dwarf virus isolates in wild raspberries

“…Samples from raspberry plants numbers 1, 6, 26, 28 and 32 (Table ) were analysed for the presence of virus‐derived siRNAs as described (Kreuze et al ., ; Massart et al ., ; Nordenstedt et al ., ). Virus‐derived siRNAs are generated by RNA interference (also called RNA silencing), which is one of the natural antiviral responses in plant cells (Ratcliff et al ., ; Deleris et al ., ; Baulcombe, ).…”

“…Work was started by testing five randomly picked wild raspberries that had virus‐like symptoms and represented our three designated locations. RNA extracted from those five plants was pooled, and both the plant‐ and virus‐derived small interfering RNAs (siRNAs; length 21–24 nucleotides, nt) were sequenced because this approach allows detection of a wide range of unrelated plant viruses simultaneously (Kreuze et al ., ; Massart et al ., ; Nordenstedt et al ., ). Samples were also subjected to PCR with subsequent sequencing of the products, which confirmed the presence of RBDV and BRNV in wild raspberries in Finland.…”

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

“…HTS of small RNAs from leaves sampled, this time, from fields across Tanzania followed by data analysis also performed using VirusDetect led to the detection of several viruses belonging to eleven genera. Apart from the cryptic viruses and CPMMV detected by Nordenstedt et al [ 92 ], BCMNV, BCMV, CABMV, SBMV, CMV, ToLCU-related begomovirus and related umbraviruses were detected.…”

“…Seed-borne pathogens, including certain viruses, have great potential to reduce growth and yield of common bean because they interfere with plant growth from the beginning [ 92 ]. Against that background, seed-borne viruses were surveyed in common bean varieties, landraces and improved common bean varieties that are grown in Tanzania.…”

“…CPMMV was the only pathogenic virus identified among two other non-pathogenic viruses namely PvEV-1 and PvEV-2. These endornaviruses had not been previously detected on the African continent [ 92 ].…”