Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania
May
Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania
Noora Nordenstedt 0 1
Delfia Marcenaro 0 1
Daudi Chilagane 1
Beatrice Mwaipopo 1
Minna-Liisa RajamaÈki 0 1
Susan Nchimbi-Msolla 1
Paul J. R. Njau 1
Deusdedith R. Mbanzibwa 1
Jari P. T. Valkonen 0 1
0 Department of Agricultural Sciences, University of Helsinki , Helsinki , Finland , 2 Nicaraguan Institute of Agricultural Technology (CNIAB-INTA), Managua, Nicaragua, 3 Sokoine University of Agriculture , Morogoro , Tanzania , 4 Mikocheni Agricultural Research Institute , Dar es Salaam , Tanzania
1 Editor: Ulrich Melcher, Oklahoma State University , UNITED STATES
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.
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Data Availability Statement: The small-RNA
sequencing libraries and assembled contigs of viral
sequences are available in European Nucleotide
Archive (ENA) under the project (study accession)
PRJEB19286.
Foreign Affairs of Finland (grants 36419901,
HEL67338-129 and 36421515 to J. Valkonen),
Ministry of Agriculture and Forestry, Finland (grant
2221/03.01.02/2015 to J. Valkonen), and European
Cooperation in Science and Technology (FA COST
Action FA1407), none of which had any role in data
collection or analysis, decision to publish, or
manuscript preparation. The Nicaraguan Institute
of Agricultural Technology (INTA) and Mikocheni
Agricultural Research Institute, Tanzania, financially
supported the collection of research material but
had no role in decision to publish or manuscript
preparation.
Introduction
Common bean (Phaseolus vulgaris L.; Fabaceae; referred to as CB here) is an annual legume
that was domesticated independently in Mesoamerica (Central America) and the Andes over
7000 years ago [
1
]. Today CB is grown worldwide and is a vital source of nutrition in many
developing countries. In Nicaragua (Central America) and Tanzania (eastern Africa), for
example, CB is the second most important source of dietary protein and starch after maize
[
2,3,4,5
]. However, in both countries the yields of CB are rather poor and can vary greatly
owing to pests, diseases, weeds, weather and edaphic constraints. In this regard, better-yielding
and well-adapted CB cultivars are being bred and introduced to improve yields [
4,6,7,8
].
Seedborne pathogens, including certain viruses, have great potential to reduce growth and
yield of food crops because they interfere with plant growth from the beginning [
9,10
]. The
seedborne viruses known to infect CB crops in Nicaragua include Bean common mosaic virus
(BCMV, genus Potyvirus; Potyviridae) [11] and Southern bean mosaic virus (genus Sobemovirus)
[
12,13
]. Other seedborne viruses of CB, such as Bean common mosaic necrosis virus (BCMNV;
genus Potyvirus) [
14,15
] and Cucumber mosaic virus (CMV) [
16
], have been reported elsewhere
in Mesoamerica. In Tanzania, BCMV and BCMNV occur in CB and forage legumes [
17,18
],
and CB is also sometimes infected with Cowpea mild mottle virus (CPMMV; genus Carlavirus)
[19]. Besides seeds, vectors such as aphids (e.g., BCMV, BCMNV, CMV), whiteflies ( (...truncated)