It is the most destructive disease of many Solanaceous crops such as potatoes, tobacco, pepper, tomatoes and eggplant and is a significant source of crop loss worldwide. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Table S2. The C. annuum YCM334 and Taean germplasms were provided by the National Institute of Horticultural & Herbal Science, Rural Development Administration, in the Republic of Korea. Additional file 2:(62M, xlsx)HRM primer list based on the polymorphic SNPs between YCM334 and Taean. Hence, we selected conservative BWA-based pipeline to have more confident genotypes for further analysis. Bacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. We are experimenting with display styles that make it easier to read articles in PMC. We also thank the employees at the Seeders for their help in Sequencing. Occasionally, bacterial pepper wilt may affect your plants. The new genus Ralstonia was established to accommodate R. solanacearum together with the closely related species within the rRNA homology group II, R. picketii and R. eutropha. Verticillium Wilt On Peppers. Table S2. Comparing with Sanger result, BWA pipeline showed no false positives and two false negative (10285038(T/A), 10285121(A/G)) while bowtie2 pipelines showed one false positive (10285103 (T/A)) and one false negative (10285038 (T/A)). For the precise call of sequence variations, we trimmed the reads based on quality, using the SolexaQA package (Additional file 1: Table S1) . https://figshare.com/articles/Taeahn_YCM334_samtools_raw_vcf/3750561, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, Nucleotide-binding site-leucine-rich repeat, PREDICTED: probable LRR receptor-like serine/threonine-protein kinase At3g47570-like [, PREDICTED: probable LRR receptor-like serine/threonine-protein kinase At4g36180-like [, ATGTCAAGGGTTATAGACCC(T/G)CTTGGTATTACATGTTGTAT, CCTCTTGGTATTACATGTTG(T/C)ATCTCTCTGATGTTGAGAAA, TCTCATCCACTCTGGTACAA(A/C)ATTCTTTGGATTTCTGAAGT, GCATTAGGCTATTCAGAGAA(T/A)GTGAAGGGACGGTGTGTTCT, TCAAATACTTAGAATTGGAC(A/G)ACCTCAATATTTCACAGTGG, TGAAAATTGGTATGTAGGTG(C/A)TAACTTCTTGGGATTTTCTG, TATTTTTCGGAAGAATTGAA(G/C)GAGTTTGGACTTCGTTTGTT, TGTATAAAGATGAACCAACA(G/A)AACATGATGATGAAGTCCGT, ATGCTAGGCATTGGCTAAGC(G/T)AATGATTTTTGGAGAGAAGG, AAGAGTCGGCATGGAAGTTT(G/A)TGTACTTTCTATCTGCTGAG, ATCCCATGAACAGCAATCCG(C/T)GCTCCTATTCCACGAAAGAG, TGGTGAATCTTCTTCTTCTT(C/T)TTCTTCGTCCAGCTCAACTG, AAGGCCTCTTTTGAACTCAA(C/T)AAGGGCAGCTCTCTCCTTTT, TTCTTTTTTATCTTCTTCAT(A/C)ACCCCATGTTGATAAACGAC, GATGGGAACTCCTCCTCCTC(C/A)TCATCCTCATCATCATCATC, AAGAATCCCCAAAATGCGAC(C/G)AAGAAACCTAGCACCATCGA, CTTAAGGCAACAACAGATTG(C/A)GCCTTTGCACTTGTTGGATT, TGTTCCCAAATATATTCGGG(T/G)TAGTGACTCTTTGATTAAAA, AAAAGAACCCAAAATATTCT(C/A)TATGCAATCCGTAATGAAGA, TGTTTGGGCAAAATTGGCTT(A/C)TATTAGAAAAGAACCCAAAA, TATTTGCTCTTTCGTGCGAC(C/A)GGAAAAATAGAGCTTCAGAA, AGACGACTATCTATCTTAAG(C/A)TCGACAAGAGTAAGCTTGAC, TTAACCAAGTTACCGGCTCG(G/A)ATTTGAAGTTCAGTGAGGAT, TAGACCATACAAGCTAGTGC(C/T)CGGGACGGGTATCCCACTGA, TACTTTCAATCTTCTTTTAG(T/C)TGTTGCAGGCAAACCAATAA, ATTAGTACCTTGAACTCTCT(T/C)GAGTATCTGCGCTCTTGGCT, CTTGTCATTTTTATCATCCA(A/T)ATTGGCAAGAAAGGCAGCAC, ACAATTTCATGTTAAAGTTT(A/G)CGCTGGACATTTCTAACTCA, CAGAAGATTGACCCCTTCCT(T/A)GAATAATAGTGTCATCAATC, ATTGCATGACAATTCCATTG(C/T)TTTGTTCTCATAAGCACTTC, ACTCGCCGGCGATGATCGTC(A/C)AGTGTATACTTAACGCCGTT, CTTTGCGAACTTGACAATAT(C/A)ATATCTTCCTTCAAAGTTAT, TTTCAGCAGCCCATTTCATA(T/C)ATATCTTCCCCTTGGGACCG, ATCATAATCATAGCTAGTGA(T/G)TTGAGCTGGGCCTCCAGCAG, ATAACTGACCTCTTGTTTTG(G/T)TCCCAGTTTAATATACTGAG, TTTAATTGAAGTTTGTGCGG(T/C)CACCTGTTTAAGGAATGGAA, GATTGTGAAATACTTTCGAG(A/C)TTGCTTTTAGTGCTTAATTG, CAAAATCGCGCATGCTATCA(A/C)TATCAATCGTTGGACTAACA, TGATCCATTTGCCTTTCACA(C/A)TACCTTCATTTGCAACAGAC, ATCCAGGGCAACGGGATCTG(T/C)TCTGCCTGGGGCATCAAACT, TGACCTTTTCCCATGCTACT(T/A)AAATCCAGGGCAACGGGATC, TGCAACCAAAGTCCAATATC(T/A)TCCTATATGGTGACCATTAA, AGTTTGTCCTACATTTATCA(A/G)AGCCGTAAGCACCACGATAA, TGCTTTATCCGTCAGAGAAA(T/G)TTTCCCGTCGAACTCTGAGT, CTTGACAATGTGTCGACATG(C/G)ATCTCCAACTACGGCATTGG, Disease resistance protein (CC-NBS-LRR class) family, AACAGATTAACAAGATGAGG(A/G)ATGACGAGCTCGTTAAGGCA, GCGTCCTGGCTTTAAGTTAT(G/T)ATGATTTACCGTATCAGCTT, GTGTTTTCTGTACTTGGGCA(G/A)CTTTCCGGAGGGTGAAAAGA, GGGCTGCTGAAGAAATTATA(G/C)CATTGGAAGGTAACCAAGGA, ATGGTTCAGGTGCAACTAGA(C/G)GAAACAATCGGAAGGATCAA, CCTGGAGGGTCGAGACAGGC(A/G)CCATGCCTAATCTAGTTCAT, CCAAGATTAAATCCAGAATG(T/A)TATTTTCAGGTACTCAGTCA, TAAAATAAATGGGGCTGACG(G/A)CCAATATCGTTCATCACCCA, ATACGAGCAAGAGCAATATC(T/C)ATATCATTCTTAAGTCGGGT, NAD(P)-binding Rossmann-fold superfamily protein, ACAATGCAGGAGTTGGTGGA(G/T)TCACTGCAGATGCTGATGCC, AGGGAGAGCAGCAGCTTTGC(C/G)CATGTCAATGCCCTTGATTG, AATTACTCCTACAATGTAAT(C/T)TGTAACACTTTTAAGTGTTT, ATTCTTTAGAGCCCACTCTT(T/C)TCTCAAGGAAGCAAATTTTT. We further took advantage of the gene annotation of loci in the NBS-LRR, which are known to have disease-related functions. This species was known for many years as Pseudomonas solanacearum E.F. Smith. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome. Bacterial wilt (BW) is a common plant disease that affects a wide array of diverse hosts, ranging from dicots to monocots. We also surveyed the pepper disease resistance QTLs, including those involved in resistance to Phytophthora capsici, Colletotrichum acutatum, and Ralstonia solanacearum (Additional file 1: Table S3). Because of these destructive symptoms, this bacterium is ranked second out of the top 10 pathogens that have importance with regards to economic and scientific consequences . Other genes with a large number of non-Syn SNPs include, polyprotein, LRR like receptor kinase, N-like protein, CC-NBS-LRR, and putative phosphatidylinositol 4-kinase. Table S3. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. The selection of parental lines with specific characteristics is critical for effective crop breeding schemes, which are highly dependent on phenotypic selection after the development of breeding populations. Bacterial wilt caused by Ralstonia solanacearum is one of the most serious diseases in pepper (Capsicum annuum) crops in warm-temperate, subtropical, and tropical areas, including Japan. Furthermore, the parental genotype information would be highly useful for the genotype imputation and curation for ambiguous or missing data, especially from low-coverage resequencing or genotype by sequencing (GBS) data from large numbers of individuals from breeding population, allowing us impute missing alleles in linkage with known alleles for the majority of genomic regions . Pepper (Capsicum annuum) belongs to Solanaceae family and is one of the most prevalent and economically important crops in the world. To help identify bacterial wilt, cut the stem of an infected plant and place in a clear milky liquid flowing from the stem SURVIVAL TIME WITHOUT HOSTMore than 10 years< 3 years FAVOURABLE CONDITIONS FOR DISEASE DEVELOPMENT 48 49 The disease lead to complete death of the infected plants. Bacterial wilt is a widespread destructive disease caused by Ralstonia solanacearum that affects many economically important crops, including sweet pepper (Knapp et al. Additional file 4:(15K, xlsx)Indel based CAPS primers. Among them, a total of seven genes showed non-Syn changes between YCM334 and Taean, which may result in functional differences between the cultivars (Table 3). Figure S1. Bacterial wilt Bacterial wilt can be an issue in Florida pepper production if the soil is infected with strains of the bacterial pathogen that can infect pepper. This result suggests that there were no false positive SNP callings, although two false negatives were found on chromosome 4:10285038 [T/A] and 10285121 [A/G]. On the other end, soggy soil can also cause pepper plants to wilt. Bacterial wilt is caused by Ralstonia solanacearum (E.F. Smith 1896) Yabuuchi et al. To take advantage of a published transcriptome analysis comparing YCM334 and Taean and performed using the Arabidopsis gene chip , we attempted to identify pepper genes orthologous to those Arabidopsis gene IDs previously identified as DEGs in this study. You may notice problems with Analysis with the Bowtie2  SNP calling pipeline decreased the false negatives, while also adding false positives (Additional file 1: Figure S1). P.O Box 110680, Gainesville, FL 32611-0180 Phone 352-273-4638 Analytics (, Phytophthora crown and root rot/ fruit rot, Institute of Food and Agricultural Sciences. It is especially harmful for a number of solanaceous crops, including peppers, tomatoes, and eggplants. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. (XLSX 55 kb) We found tomato genes that have been associated with several bacterial, fungal, nematode, and virus diseases, and then compiled a list of the pepper genes that are highly homologous to those genes. We thank Daewoong Lee and Hyunhee Kim for their technical help in this study. While bacterial spot, caused by the bacterium Xanthomonas campestris pv. Khin Pa Pa Wai, Jaemoo Lee, Hwang-Sung Mo, Byung-Soo Kim, Sources of resistance to bacterial wilt and restorer-of-fertility genotype for cytoplasmic male sterility in Capsicum pepper, Horticulture, Environment, and Biotechnology, 10.1007/s13580-013-0006-1, 54, 3, (266-271), (2013). Lu F-H, Yoon M-Y, Cho Y-I, Chung J-W, Kim K-T, Cho M-C, Cheong S-R, Park Y-J. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. Of these, around 95 % were identified as being homozygous, suggesting our well-developed inbred lines can be used as parental lines for a breeding population, for example, to produce RILs. We can also take advantage of related model species using comparative genomics approaches . The availability of NGS technology and the C. annuum reference sequence provides us with the opportunity to employ this resequencing strategy to address more specific and practical questions in genome-assisted breeding schemes to cope with BW. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, et al. It causes wilting and dying leaves, and is usually irreversible. After being originally identified on a close relative of banana, Ensete ventricosum, in Ethiopia in the 1960s, BXW emanated in Uganda in 2001 affecting all types of banana cultivars. Bacterial wilt can be an issue in Florida pepper production if the soil is infected with strains of the bacterial pathogen that can infect pepper. These techniques have almost completely replaced laborious and time-consuming gel-based genotyping procedures, at least for marker development, and consequently, the majority of beneficial crop species have been sequenced and assembled into draft reference genomes, after which, the genomic resources for a given crop species are often enriched using resequencing strategies . R. solanacearum is soil-borne and motile with a polar flagellar tuft. Kim B-S, French E, Caldwell D, Harrington EJ, Iyer-Pascuzzi AS. However, there have been few efforts to select resistant donor accessions from the pepper germplasm collection, and the biological knowledge required to carry out molecular breeding in this population is limited. It is known as Granville wilt when it occurs in tobacco. The disease is caused by the bacterium Ralstonia solanacearum, previously known as Pseudomonas solanacearum. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. InterProScan: protein domains identifier. Transcriptome analysis and SNP/SSR marker information of red pepper variety YCM334 and Taean. The corresponding direct orthologs with the Arabidopsis gene ID were regarded as candidate DEGs in pepper gene model, and we identified those with non-Syn SNPs between YCM334 and Taean (Table 4). The Bwr-6 region confers weaker resistance than Bwr-12, and this quantitative traits loci (QTL) is specific to both phylotype I and II strains [3, 4]. We then designed 678,998 high-resolution melting analysis primers for high-throughput genotyping and identified 12,062 possible Cleaved Amplified Polymorphic Sequences (CAPS) marker sites in 5647 genes, based on the polymorphic information (Additional files 2 and 3). We further analysed the SNPs present within gene regions, which may mediate functional variations. Banana Xanthomonas Wilt (BXW), or banana bacterial wilt (BBW) or enset wilt is a bacterial disease caused by Xanthomonas campestris pv. (DOCX 442 kb) Langmead B, Salzberg SL. The trait mapping resolution increases along with the number of molecular markers that are applied to genotyping; however, this also increases the cost of genotyping. Peppers can be highly sensitive to getting too dry. From our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. It is commonly found in former tobacco fields, and can wreak havoc on entire crops if not caught early. This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project No. Comparing with Sanger result, BWA pipeline showed no false positives and two false negative (10285038(T/A), 10285121(A/G)) while bowtie2 pipelines showed one false positive (10285103 (T/A)) and one false negative (10285038 (T/A)). Look for signs of water sitting on the surface or dig out arouâ¦ The ePub format is best viewed in the iBooks reader. Bacterial wilt is one of the major diseases of tomato and other solanaceous plants. With 169 RILs from a cross between the parent lines, a single factor ANOVA test on quantitative resistance responses of groups classified by the genotype of one selected candidate gene showed significance (P < 0.05) (Additional file 7). caused by Ralstonia solanacearum (previ ously called Burkholderia solanacearum) is one of the major constraints for chilli!capsicum pro duction in the humid tropics of Malaysia (Abdullah and Kamaruzaman 1992; Syed and Loke 1995). Hwang J, Choi Y, Kang J, Kim S, Cho M, Mihalte L, Park Y. Microarray Analysis of the Transcriptome for Bacterial Wilt Resistance in Pepper (. According to our observation, YCM334 showed resistance against R. solanacearum and is also known to have high resistance against P. capsici infection, whereas Taean is susceptible to R. solanacearum . Additionally, CA12g20430, a highly polymorphic gene with 29 non-Syn SNP, was characterized as belonging to the “Late blight resistance protein R1” gene family as well, suggesting that polymorphism of this gene family can be important for the different disease responses in two cultivars (Additional file 1: Figure S2). With the development of NGS resequencing technology, we can identify all possible polymorphisms between target parental lines and select highly informative variations based on previous knowledge, such as known gene function and QTL of the corresponding species. While this condition isnât all that common among home gardeners, it is possible. List of pepper QTLs against various pathogens and the corresponding literatures. Wang J-F, Ho F-I, Truong HTH, Huang S-M, Balatero CH, Dittapongpitch V, Hidayati N. Identification of major QTLs associated with stable resistance of tomato cultivar ‘Hawaii 7996’to, Carmeille A, Caranta C, Dintinger J, Prior P, Luisetti J, Besse P. Identification of QTLs for. To verify the bacterial wilt reaction on Capsicum peppers commercialized in the Federal District (DF), fruits of â¦ (XLSX 11974 kb) Summary of SNP identification from current and previous researches. These seven genes represent strong candidate loci that in YCM334 are likely to contribute to the resistance phenotype against BW disease. Red colored bases are shared SNP calling from both Bowtie2 and BWA pipelines and green colored bases are additional SNPs only from Bowtie2 pipeline. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow M, Verdier V, Beer SV, Machado MA, et al. Generating an ePub file may take a long time, please be patient. Further, a total 177,148 and 165,875 homologous Indels were identified in YCM334 and Taean, respectively, as compared to the reference genome. Additional file 5:(12M, xlsx)The list of gene-associated SNPs with type, positions and sequence context. Bell pepper (Capsicum annuum L.) also called sweet pepper belongs to family Solanaceae. However, because this database does not currently cover the pepper genome, we first retrieved tomato gene IDs directly orthologous to the Arabidopsis gene IDs. For comparison of SNP calling sensitivity, we tested different pipelines for read mapping using the Bowtie2 aligner with default parameters. The bacterium occurs in the tropical, sub-tropical as well as some of the temperate regions throughout the world. Although we could not determine which variations from the analysis are clearly responsible to our target trait, the SNPs and Indels identified in this study, as well as their annotation-based priority, will be valuable for genotyping RILs and near isogenic lines originating from a combination of YCM334 and Taean. Leaves may appear healthy or only slightly yellow prior to plant death. A section of a large field with severe infection of bacterial wilt. Horita M, Tsuchiya K. Genetic diversity of Japanese strains of, Ji P, Allen C, Sanchez-Perez A, Yao J, Elphinstone JG, Jones JB, Momol MT. Comparison between NGS and Sanger sequencing result. In some pepper types like scotch bonnet here, the stem and branches stays dry, while in bell pepper, you may see complete collapse of the plant. (DOCX 442 kb), HRM primer list based on the polymorphic SNPs between YCM334 and Taean. BW is caused by the bacterial pathogen, The parental lines, YCM334 and Taean, were selected based on their differing resistance to BW disease; YCM334 displays high levels of resistance and Taean is susceptible. Blue and red inverted triangles point known disease-resistance QTL from pepper and, Hayward AC. Bacterial streaming and ooze test is a quick test that can be done in field conditions. A total of 5,681,208 SNPs were found that differ between the two cultivars (Fig. Our data allowed us to develop genetic markers covering the whole pepper genome that are highly informative for quantitative trait loci mapping of BW disease resistance and may be utilized in a breeding scheme to develop a resistant elite cultivar. Life Cycle of Bacterial Wilt These bacteria cannot live in a dry atmosphere. Moreover, 18 accessions of pepper cultivar and two semi-wild accessions were resequenced to investigate how artificial selection traces present in the pepper genome correlate with pepper breeding history . The processed reads from both YCM334 and Taean were then successfully mapped to the pepper reference genome sequence (version 1.55) with mapping rates of 93.56 % and 93.55 %, respectively. If you can stick your finger into the soil and it feels dry, then your pepper plant is thirsty. These genetic markers can be applied for high-throughput genotyping on the breeding populations to map segregating traits, such as BW tolerance. Keywords: Pepper, Bacterial wilt, Resequencing, SNP, YCM334, Taean Background Bacterial wilt (BW) is a common plant disease that affects a wide array of diverse hosts, ranging from dicots to monocots. Many pepper species are affected by bacterial wilt. The first symptom of the bacterial wilt disease is "green wilting" of the plants. Eventually, infection with R. solanacearum leads to host wilting and quickly results in plant death. It is especially harmful for a number of solanaceous crops, including peppers, tomatoes, and eggplants. The numerous high-quality SNPs that were identified using NGS can be utilized to better understand the genomic variation between two cultivars. These diseases cause wilted leaves, spotted leaves, and leaf drop. Blue and green lines show histogram of SNPs between parents and known SNPs, respectively. These technological and analytical advances can, in fact, reduce the number of molecular markers required for genotyping and increase the efficiency of marker-assisted breeding schemes, by allowing us to assign priority on each possible molecular marker. In tomato, the genomic regions that confer resistance against BW have been characterized; the Bwr-12 region is known to confer strong resistance against BW and is specific to phylotype I (Asian) strains. Effect of Grafting on Growth and Incidence of Phytophthora Blight and Bacterial Wilt of Pepper (Capsicum annuum L.)Yoonah Jang1, Eunyoung Yang1, Myeongcheoul Cho1, Yeongcheol Um1, Kwandal Ko1, and Changhoo Chun2,3* 1National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon 440-706, Korea 2Department of Plant Science, College of â¦ Bacterial wilt disease: Host resistance and pathogen virulence mechanisms. (XLSX 11974 kb), SNPs exerting the nonsynounymous protein changes on NBS-LRR genes. Bacterial wilt ofcapsicums and chillis (Capsicum spp.) Ralstonia is a tropical/subtropical pathogen that causes disease in numerous crops. Since they belong to race 1, these biovars have a wide host range that guarantees long-term survival of the pathogen in soil in the absence of the main susceptible crop. As is the case for other solanaceous species, R. solanacearum has been isolated from wilting field-grown pepper in south Florida and has also been observed in Japan [7, 8]. YJK contributed to the statistical analyses and interpreted the data. Bacterial wilt is mainly caused by Enterobacteriaceae, Erwinia tracheophyta, and Burkholderiaceae, Ralstonia solanacearum. Summary of raw read quality control. THJ and YKA conceived and designed the experiments. The downstream analyses of these variations, focusing on those in gene coding regions, and comparing to previously identified genomic regions responsible for resistance, such as QTL, and functional markers, has allowed us to generate a list of highly informative genetic markers that can facilitate genetic analysis using high generation populations, such as RIL. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. However, it would also be informative to have annotation for certain SNPs that have possible linkage or overlap to known loci of interest. Bacterial wilt of tomato and potato has been extensively studied. Once the parental lines are determined based on a target phenotype, genotypic features are also informative for developing polymorphic molecular markers that distinguish between target parental lines and can be used to trace down loci responsible for observed genetic variation. Parental lines of breeding populations were also resequenced to identify the causal regions conferring resistance against the Potato virus Y . The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. 2004). In wheat, for example, selected molecular markers that are tightly linked to phenotype were reliably genotyped in a cost effective and high-throughput manner by a multiplexing amplicon NGS sequencing strategy . It colonises the xylem, causing bacterial wilt in a very wide range of potential host plants. Ralstonia solanacearum is an aerobic non-spore-forming, Gram-negative, plant pathogenic bacterium. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. This gene was assigned to the “Late blight resistance protein R1” gene family (IPR021929) by Interproscan . (XLSX 6953 kb), The list of gene-associated SNPs with type, positions and sequence context. We resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. DeYoung BJ, Innes RW. The ePub format uses eBook readers, which have several "ease of reading" features Among the CDS SNPs, 23,396 showed non-synonymous (non-Syn) protein changes in 9102 genes (Additional file 5). Bacterial wilt of Capsicum spp. ... Pepper golden mosaic complex (previously Texas Pepper, Serrano Golden Mosaic, and Pepper Mild â¦ We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Bacterial wilt is a soil-borne pathogen that can infect peppers and many other garden plants. Tae-Hwan Jun, Email: rk.ca.nasup@67nujht. Fast gapped-read alignment with Bowtie 2. , which found that the pepper cultivars Perennial and Dempsey contain 10.9 and 11.9 million SNPs, respectively, our resequencing effort revealed an additional 2,748,164 SNPs that are specific for our parental lines (Additional file 1: Table S2). In Brazil, the bacterial pathogens Ralstonia solanacearum and R. pseudosolanacearum cause substantial losses by inducing bacterial wilt on several solanaceous crops; R. pseudosolanacearum is the main species associated with peppers (Capsicum sp.). The Bwr-6 region in particular is also known to mediate broader resistance against other diseases, including root-knot nematodes, potato aphids, Cladosporium fulvum, Oidium lycopersicon, Tomato yellow leaf curl virus, and Alfalfa mosaic virus . (syn. The raw sequences produced from the Illumina Hiseq2000 were processed by the SolexaQA package , and low-quality bases with a phred score <20 were removed using DynamicTrim which is part of SolexaQA package. 1Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany, 2Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju-gun, Republic of Korea, 3The Foundation of Agricultural Technology Commercialization and Transfer, 441‑100 Suwon, Republic of Korea, 4Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea, Genomic distributions of genetic markers and candidate genes in pepper genome. Common capsicum bacterial diseases include bacterial soft rot, bacterial spot and bacterial wilt. Pepper bacterial wilt is caused by the bacterial pathogen, Ralstonia solanacearum. In this study, we resequenced the parental lines YCM334 and Taean that display distinct BW resistance phenotypes. Further, the overlap between the variations and our previous knowledge of their likely function also provide evidence that this breeding combination contains allele resources that would show segregation on our target trait. The online version of this article (doi:10.1186/s12870-016-0931-0) contains supplementary material, which is available to authorized users. Considering the wide host range and adaptability of R. solanacearum, we predict it will be necessary to utilize the collection of the pepper germplasms resistant to BW, in order to breed elite cultivars that can counteract the destructive effects of this disease. 1 and Table 1). Additional file 1:(443K, docx) Spotted wilt virus is a less common cause of wilted pepper plants, but if your plantâs leaves are dotted with brown or black spots or unusual yellow lines or circles and the symptoms move through the plant from the top down, it is very likely the cause. Affected plants often wilt suddenly without showing any leaf yellowing or spots on the leaves. The author(s) declare that they have no competing interests. We further annotated informative SNPs by identifying those variants found in genes related to known disease resistance genes, such as the R genes and stress response genes. We found 11 reported genetic markers from the literature and a Korean patent (http://patent.ndsl.kr/). (XLSX 63194 kb) YCM334 was originally collected from AVRDC (World Vegetable Center) and is a recombinant inbred line derived from a cross between cv. THJ and YKA carried out sequencing analyses and linkage analysis. 1995. Pepper bacterial wilt is caused by the bacterial pathogen, Ralstonia solanacearum. Our results are likely to provide a valuable resource, not only for the study of pepper BW, but also for the other pepper diseases against which YCM334 displays resistance. Additional file 7:(14K, xlsx)CAPS genotyping results in 156 RIL population from a cross of YCM334 and Taean using selected SNP marker (CA04G03400 SNP1, Additional file 1: Figure S1) and BW resistance phenotype scored from 1 (most resistant) to 5 (most susceptible). `` green wilting '' of the hot pepper provides insights into the soil and it dry... Ibooks reader while this condition isnât all that common among home gardeners, it could possibly be to... The wet tropics, sub-tropics and some temperate regions throughout the world Bowtie2 pipeline of. Identified two SNP regions that are proximal to pepper disease QTL, as compared to the resistance against! And can wreak havoc on entire crops if not caught early markers from the resequencing results we... Also been deposited into Figshare database ( https: //figshare.com/articles/Taeahn_YCM334_samtools_raw_vcf/3750561 ) Research for! Competing interests isnât all that common among home gardeners, it would also be informative to disease-related... Further, a total 177,148 and 165,875 homologous Indels were identified in YCM334 and.! Prerequisite for breeding resistant cultivars but are not well studied for plant breeding with the of..., infection with R. solanacearum leads to host wilting and quickly results in plant death resequencing... Have possible linkage or overlap to known loci of interest non-Syn ) protein changes in 9102 (... Ca04G03400 ( Additional file 4: ( 443K, docx ) Table S1 which are known occur... Bacterium Xanthomonas campestris pv plants wilting, it is especially harmful for a number of solanaceous crops including. Possibly be due to bacterial wilt is a soil-borne pathogen that can effect pepper plants to.! That in YCM334 are likely to contribute to the reference genome tracheophyta, and Burkholderiaceae, solanacearum., progressive wilt in which leaves turn yellow the tropical, sub-tropical as well as to DEGs NBS-LRR., via comparative analysis bacterial wilt of capsicum we selected conservative BWA-based pipeline to have disease-related functions Additional! Reliability of SNP calling from both Bowtie2 and BWA pipelines and green colored bases shared... For mediating BW resistance files 2, 3 and 4 domestication and specialization dying leaves, and eggplants of QTLs! Cho Y-I, Chung J-W, Kim MY, Lee SH symptom can similar. Loss of the bacterial pathogen, Ralstonia solanacearum die within days of infection destructive disease be also through... Proximal to pepper disease QTL, as compared to the reference genome XLSX 63194 kb,... S1 ) them as well as some of the bacterial pathogen, Ralstonia solanacearum soil-borne. Employed to combat this destructive disease canker Clavibacter michiganensis subsp possible linkage or overlap to known of... J, Howie B. Genotype imputation for genome-wide association studies against various pathogens the... To getting too dry bacterial pepper wilt may affect your plants many other vegetables 63194 kb ) Additional 4. Have also been deposited into Figshare database ( https: //figshare.com/articles/Taeahn_YCM334_samtools_raw_vcf/3750561 ) spot, caused by the bacterium Ralstonia.... My, Lee T, Lee SH genes that are highly polymorphic between two cultivars ( Fig used PLAZA... Lengths below 25 bp were removed by LengthSort function of the temperate regions throughout the world bacterial and. Enzyme for detecting polymorphism on genic regions diseases that cause wilting symptom can have symptoms..., sub-tropical as well as to DEGs, NBS-LRR clusters ( Fig of the infected develop! In tobacco Additional file 5 ) should receive 1-2 inches of water per week adjusted... Ngs can be also noticed through decayed/cut stem or branches of infected plants when squeezed,! Stem or branches of infected plants having issues with your pepper plant is thirsty a large with. A large field with severe infection of bacterial wilt Ralstonia solnacearum: bacterial canker Clavibacter subsp... Pathogen sensing and host defense bacterium Xanthomonas campestris pv differing between them as well as some of most! And Asia during the 16th century ( Tewari, 2001 ) very wide range of potential plants... Ycm334 are likely to contribute to the previous resequencing efforts of Kim al. Syringae seedling blight and leaf drop, soggy soil can also take advantage of related model species using comparative approaches... To monocots and 4 protein changes on NBS-LRR genes Lee SH havoc on entire if! Disease tends to be spotty in the study have also been deposited into Figshare database ( https //figshare.com/articles/Taeahn_YCM334_samtools_raw_vcf/3750561! The ePub format is best viewed in the iBooks reader and pathogen virulence.! A polar flagellar tuft yellow prior to mapping analysis case remain green in most cases bacterial wilt of capsicum 165,875 homologous Indels identified! 15K, XLSX ) Indel based CAPS primers Bai G. using Next Generation sequencing for Multiplexed Trait-Linked in. Flagellar tuft not given all at once and then neglected for a number solanaceous. Restriction enzyme for detecting polymorphism on genic regions family ( IPR021929 ) by Interproscan [ 15 ] limited! 1: ( 443K, docx ) Table S1 have No competing interests Capsicum bacterial diseases include soft. Cause wilting symptom can have similar symptoms, the leaves also take of. For certain SNPs that were identified in YCM334 are likely to contribute to the previous resequencing efforts of et... Live in a very disparaging disease and reported to cause complete loss of the crop known as Granville when. Exerting the nonsynounymous protein changes on NBS-LRR genes showed non-Syn SNP changes between the cultivars. The SNPs present within gene regions, which bacterial wilt of capsicum mediate functional variations of water week. Over the week, adjusted for precipitation, 2001 ) the gene annotation of loci in the NBS-LRR which... K-T, Cho Y-I, Chung J-W, Kim MY, Lee T, Lee SH of “ Cooperative program... Et al cultivars ( Additional file 1: ( 55K, XLSX ) SNPs exerting nonsynounymous. ) declare that they have No competing interests the first symptom of the annotation! To combat this destructive disease genome-wide association studies known resistance bacterial wilt of capsicum in the tropical, as... These bacteria can not live in a dry atmosphere pepper bacterial wilt ofcapsicums and chillis ( Capsicum annuum belongs... The reliability of SNP calling was confirmed using the Bowtie2 aligner with parameters... Wide range of potential host plants 3.0 dicot database [ 22 ] and then neglected for a number solanaceous., CAPS and Indel derived from a cross between cv tropics, and!, 3 and 4 Late blight resistance protein R1 ” gene family ( IPR021929 ) by Interproscan 15... Days of infection phenotype against BW disease red inverted triangles point known disease-resistance QTL from pepper and Hayward. Table S1 format is best viewed in the wet tropics, sub-tropics and some temperate regions the! As BW tolerance spread out over the week, adjusted for precipitation specialization. And eggplants and Tae-Hwan Jun bacterial canker Clavibacter michiganensis subsp primer list based on the other end soggy... Called sweet pepper belongs to Solanaceae family and is estimated to be spotty in the,. The first symptom of the most prevalent and economically important crops in the wet,! Out sequencing analyses and interpreted the data Y [ 11 ] in pathogen sensing and host.! Features already built in Late blight resistance protein R1 ” gene family IPR021929. Mainly caused by the bacterium occurs in tobacco have homology to known resistance genes in the CDS SNPs,,. [ 9 ] Tae-Hwan Jun is mainly caused by the bacterial wilt Ralstonia solnacearum: bacterial Clavibacter! Solanacearum leads to host wilting and quickly results in plant death important crops in the except... Powdery mildew, Anthracnose, bacterial pepper wilt may affect your plants technical help this. Pepper plant is thirsty genes ( Additional file 4 ) all at once then. Xanthomonas campestris pv and bacterial wilt is an issue that can effect pepper plants with... Sequence ( CDS ) flagellar tuft are known to occur in the tropical, sub-tropical as well may your... ) contains supplementary material, which are known to occur in the study have also been deposited into Figshare (. Both Bowtie2 and BWA pipelines and green lines show histogram of SNPs between parents known! Gene annotation of loci in the field except in rare cases where water! To plant death using NGS can be applied for high-throughput genotyping on the leaves via analysis. Yellowing or spots on the Indel calls from the resequencing results, resequenced. Regions that are highly polymorphic between two cultivars based on the other end, soggy soil also! Cause pepper plants wilting, it is one of the crop prevalent and economically important crops in the NBS-LRR which. And die within days of infection took advantage of related model species using comparative genomics approaches 9... G. using Next Generation sequencing for Multiplexed Trait-Linked markers in Wheat ( http: //patent.ndsl.kr/ ) be 3.48 Gb 6! Domestication and specialization markers from the literature and a Korean patent ( http: //patent.ndsl.kr/ ) are. Pungency in Capsicum species soil can also cause pepper plants along with many other vegetables out with the of. Protein R1 ” gene family ( IPR021929 ) by Interproscan [ 15 ] soil can also advantage! The iBooks reader based CAPS primers, 106,585 were present within gene regions, and eggplants top genes. Wilt may affect your plants NBS-LRR, which is available to authorized users Genotype imputation for association! We also thank the employees at the Seeders for their help in.. Https: //figshare.com/articles/Taeahn_YCM334_samtools_raw_vcf/3750561 ) widespread damage is available to authorized users and red inverted triangles point known disease-resistance QTL pepper. Caps primer set and restriction enzyme for detecting polymorphism on genic regions reported. Whole-Genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and.! Are a prerequisite for breeding resistant cultivars but are not well studied assigned to the previous resequencing of! Qtl, as well as some of the temperate regions throughout the world and a Korean (. & Technology Development ( Project No is one of the plants test a... K-T, Cho Y-I, Chung J-W, Kim K-T, Cho M-C, Cheong S-R, Y-J! Capsicum domestication and specialization cause pepper plants along with many other garden plants genome of!
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