Occurrence, distribution, and genetic diversity of faba bean viruses in China

Abstract

With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.

Keywords: China; distribution; faba bean; genetic diversity; incidence; small RNA sequencing; viruses.

FIGURE 1

Leaf samples were collected from faba plants displaying major virus-like symptoms. Major symptoms include (A) shrinkage and wilting, (B) mosaic, (C) shrinkage and mosaic, (D) dwarfing and chlorosis, and (E) chlorosis, leaf curling, and dwarfing.

FIGURE 2

Symptomatic faba bean leaf samples were collected from fields near cities within Jiangsu, Anhui, Gansu, Sichuan, Yunnan, Guangxi, Hubei, and Chongqing (GS, Dingxi; CD, Chengdu; KM, Kunming; DL, Dali; WH, Wuhan; CQ, Chongqing; GX, Nanning; TL, Tongling; LH, Liuhe; QJ, Qujing; HF, Hefei; LS, Lishui; NT, Nantong).

FIGURE 3

PCR validation for the presence of nine viruses in faba bean leaf samples. The sizes of virus-specific bands were as follows: BYMV, 400 bp; VCV, 1,500 bp; SMV, 400 bp; BCMV, 500 bp; PSbMV, 400 bp; BWYV, 550 bp; CMV, 400 bp; MDV, 900 bp; BBWV, 1,500 bp.

FIGURE 4

Prevalence and distribution of faba bean viruses in 13 predominant growing regions. (A) Incidences (infected samples/total samples) of BYMV, VCV, SMV, BCMV, PSbMV, BWYV, CMV, MDV, and BBWV. (B) Heat map of BYMV, VCV, SMV, BCMV, PSbMV, BWYV, CMV, MDV, and BBWV incidences (infected samples/total samples per year) between 2019 and 2021. Red represents a high incidence and blue represents a low one. (C) Heat map of BYMV, VCV, SMV, BCMV, PSbMV, BWYV, CMV, MDV, and BBWV incidences (infected samples/total samples per region) between regions (WH, Wuhan; LH, Liuhe; TL, Tongling; LS, Lishui; QJ, Qujing; CQ, Chongqing; GX, Nanning; NT, Nantong; CD, Chengdu; DL, Dali; KM, Kunming; GS, Dingxi; HF, Hefei). Red represents a high incidence and blue represents a low one.

FIGURE 5

Faba bean samples infected with multiple viruses. (A) Intersections of all nine viruses. (B) Heat map of mixed virus infections (mixed-infection sample/total samples per region) in various regions (HF, Hefei; LH, Liuhe; GS, Dingxi; DL, Dali; LS, Lishui; CD, Chengdu; NT, Nantong; KM, Kunming; WH, Wuhan; CQ, Chongqing; GX, Nanning; QJ, Qujing; TL, Tongling). Red represents a high incidence and blue represents a low one.

FIGURE 6

Neighbor-joining phylogenetic tree based on BYMV CP nucleotide sequences obtained from isolates collected from different hosts and regions. Red diamond marks indicate novel sequences obtained in this study.

FIGURE 7

Sequence demarcation tool analysis of BYMV CP sequences. (A) Color-coded pairwise identity matrix generated from BYMV CP sequences. Each colored cell represents a percentage identity score between two sequences (B) Pairwise identity frequency distribution plot of BYMV CP sequences.

FIGURE 8

Amino acid sequence comparison of the BYMV CP N-terminal. Sequence alignment was achieved using the MUSCLE method by Jalview software. Conserved amino acids are highlighted with different colors according to the ClustaLx code. The red box signifies the NAG motif.