First Report of Sweet potato badnavirus A in China

Abstract

HomePlant DiseaseVol. 100, No. 4First Report of Sweet potato badnavirus A in China PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Sweet potato badnavirus A in ChinaY.-H. Qin, X.-C. Li, Z.-C. Zhang, Q. Qiao, D.-S. Zhang, Y.-J. Wang, Y.-T. Tian, and S. WangY.-H. QinSearch for more papers by this author, X.-C. LiSearch for more papers by this author, Z.-C. ZhangSearch for more papers by this author, Q. QiaoSearch for more papers by this author, D.-S. ZhangSearch for more papers by this author, Y.-J. WangSearch for more papers by this author, Y.-T. TianSearch for more papers by this author, and S. WangSearch for more papers by this authorAffiliationsAuthors and Affiliations Y.-H. Qin X.-C. Li Z.-C. Zhang Q. Qiao D.-S. Zhang Y.-J. Wang Y.-T. Tian S. Wang , Institute of Plant Protection, Henan Academy of Agricultural Sciences; and Henan Key Laboratory of Crop Pest Control; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China. Published Online:5 Feb 2016https://doi.org/10.1094/PDIS-09-15-1081-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Sweet potato badnavirus A (SPBV-A) belongs to the genus Badnavirus of the family Caulimoviridae; thus far, this virus has been detected in sweet potato (Ipomoea batatas) in Peru (Kreuze et al. 2009) and Tanzania (Mbanzibwa et al. 2011). A survey was conducted from 2013 to 2015 to determine the incidence of SPBV-A in China. A total of 200 sweet potato samples showing vein clearing were collected from 16 provinces in China. Total nucleic acids were extracted from these samples using Universal Genomic DNA Extraction Kit Ver. 3.0 (TaKaRa, Dalian, China) in accordance with the manufacturer’s protocol. The partial polyprotein gene sequences of SPBV-A were amplified through PCR with the primer pairs BadnaBKF (5′-CAAATTAGGAGGCAGATAAATG-3′) and BadnaBSR (5′-GGTCTTCTTATGTTCCACCTT-3′) (Mbanzibwa et al. 2011). The expected 861-bp amplicons were amplified from 34 samples. PCR products were cloned into the pMD19-T vector (TaKaRa, Dalian, China) and then sequenced. The sequences were compared with those in GenBank using BLAST. Sequences in the 861-bp DNA fragment of the 34 samples (GenBank Accession Nos. KT448732 to KT448765) share 87.6 to 96.7% identity to the nucleotide sequence of the polyprotein gene of SPBV-A (Accession No. FJ560943); the result also revealed that the nucleotide sequences were 88.6 to 100% identical to each other. SPBV-A was detected in 34 of the 200 samples, and the positive rate was 17%. SPBV-A was distributed in Jilin, Shandong, Hebei, Shanxi, Shaanxi, Henan, Anhui, Guangxi, Fujian, Jiangsu, Chongqing, and Sichuan provinces in China. The total RNA of the 3 samples obtained from the positive sweet potato samples were randomly extracted from 0.1 g of fresh leaves by using the Total Plant RNA Extraction Miniprep System (Sangon, Shanghai, China) to confirm SPBV-A infection in China. Deep sequencing was conducted using Illumina Solexa 2000 (Beijing Berry Genomics Co., Ltd., Beijing). The pooled RNA (10 μg) was subjected to small RNA deep sequencing, and the results revealed 11,638,346 reads and 418,980,456 bases. The sequences were assembled with SOAPdenovo2 (http://soap.genomics.org.cn/soapdenovo.html) software with these settings: −k = 15, −d = 1, −R = 21, and −m = 21. The assembly generated gene fragments specific to 14 kinds of viruses, including Sweet potato feathery mottle virus, Sweet potato virus C, Sweet potato badnavirus B, Sweet potato badnavirus A, Sweet potato virus G, Sweet potato virus 2, Sweet potato leaf curl Georgia virus, Sweet potato chlorotic stunt virus, Sweet potato leaf curl virus, Sweet potato leaf curl Canary virus, Sweet potato leaf curl Bengal virus, Sweet potato leaf curl Lanzarote virus, Sweet potato leaf curl Uganda virus, and Sweet potato gold vein associated virus. The 370- and 358-bp SPBV-A genomic sequences were assembled from these three samples and then compared with the sequences of SPBV-A in GenBank. The finding also revealed nucleotide sequence identities of 87% and 89% to the SPBV-A sequence (Accession No. FJ560943), respectively, confirming the presence of SPBV-A in these three samples. Two sweet potato vine cuttings selected from the positive samples were grafted onto Ipomoea setosa, a universal plant indicator of sweet potato viruses (Schaefers and Terry 1976). At 3 to 4 weeks postinoculation, the graft-inoculated I. setosa plants exhibited leaf mosaic symptoms. The SPBV-A infection of the indicators was confirmed through PCR and sequencing. To our knowledge, this is the first report of SPBV-A on sweet potato in China. This study adds to the understanding of the presence and genetic diversity of this virus in China; further study into the damage and management strategy of this virus is required.