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

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 data-bases 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.Peer reviewe

Symptoms observed in common bean plants in La Compañia, Nicaragua.

<p>(a), Stunting of the plant, malformation and blistering of leaves. (b), Mild epinasty and vein reversion. (c), Green-yellow chlorosis. (d), Green-yellow mosaic.</p

Detection of PvEV-1 by RT-PCR in common beans in Tanzania.

<p>In the list below, landraces are marked with asterisk (*). Other samples represent improved varieties (origin of samples shown in parenthesis). Lane labelled ‘M’ represents a O'GeneRuler 1 kb Plus DNA ladder. The expected size of PCR products was 374 bp. Lanes 1, ‘Njugu’* (Southern Highlands zone); 2, ‘pooled RNA’ (Southern Highlands zone); 3, ‘pooled RNA’ (Eastern zone); 4, ‘pooled RNA’ (Northern zone); 5, ‘Rosekoko’/’Lyamungu 85’ (Eastern zone); 6, ‘Salundi’ (Southern Highlands zone); 7, ‘E 36’ (Southern Highlands zone); 8, ‘Msafiri’* (Southern Highlands zone); 9, ‘Msafiri’* (Eastern zone); and 10, ‘Mshindi’ (Eastern zone).</p

Conserved domains in the polyprotein encoded by PvEV-1 and PvEV-2 from Nicaragua.

<p>Numbers indicate the residues defining the conserved domains. Hel-1, helicase; CPS, putative capsular polysaccharide synthase; UGT, UDP-glycosyltransferase; RdRp, RNA-dependant RNA polymerase; and MTR, methyltransferase.</p

Viruses detected in the pools of common bean samples from Nicaragua (NI) and Tanzania (TZ) by VirusDetect.

<p>Viruses detected in the pools of common bean samples from Nicaragua (NI) and Tanzania (TZ) by VirusDetect.</p

Identification of PvEV-2 in the sample pool HXH8 from the Southern Highland zone of Tanzania based on small-RNA deep sequencing.

<p>(a), Viral contigs (red bars) mapped to the sequence of PvEV-2-Okada (AB719398) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178242#pone.0178242.ref025" target="_blank">25</a>] using VirusDetect [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178242#pone.0178242.ref051" target="_blank">51</a>]. Each nucleotide in the contigs was covered by siRNA reads at least 5 times. (b) The 21- to 24-nt reads mapped to the sequence of PvEV-2. The <i>x</i> axis and the scale below the figure depict the viral genome and nucleotide positions, respectively. The <i>y</i> axis indicates the number of siRNA reads derived from the coding strand (blue bars above the <i>x</i> axis) and complementary strand (red bars below the <i>x</i> axis).</p