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Int. J. Mol. Sci. 2017, 18(12), 2523; https://doi.org/10.3390/ijms18122523

Whole-Genome Re-Alignment Facilitates Development of Specific Molecular Markers for Races 1 and 4 of Xanthomonas campestris pv. campestris, the Cause of Black Rot Disease in Brassica oleracea

1
Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon 57922, Korea
2
School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick CV35 9EF, UK
*
Authors to whom correspondence should be addressed.
Received: 4 November 2017 / Revised: 20 November 2017 / Accepted: 21 November 2017 / Published: 24 November 2017
(This article belongs to the Section Molecular Plant Sciences)
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Abstract

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops. In this study, a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X. campestris pv. incanae (Xci), X. campestris pv. raphani (Xcr) and X. euvesicatoria (Xev) were aligned to identify variable regions among races. To develop specific markers for races 1 and 4, primers were developed from a region where sequences were dissimilar in other races. Sequence-characterized amplified regions (SCAR) and insertion or deletion of bases (InDel) were used to develop each specific set of primers. The specificity of the selected primers was confirmed by PCR tests using genomic DNA of seven different Xcc races, two strains of X. campestris pathovars and other species of bacteria. Bacterial samples of the races 1 and 4 isolates were collected from artificially inoculated cabbage leaves to conduct bio-PCR. Bio-PCR successfully detected the two Xcc isolates. By using our race-specific markers, a potential race 1 strain from the existing Korean Xcc collection was identified. The Xcc race 1 and 4-specific markers developed in this study are novel and can potentially be used for rapid detection of Xcc races through PCR. View Full-Text
Keywords: black rot; Xanthomonas campestris pv. campestris; races; PCR; SCAR; InDel; cabbage black rot; Xanthomonas campestris pv. campestris; races; PCR; SCAR; InDel; cabbage
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Rubel, M.H.; Robin, A.H.K.; Natarajan, S.; Vicente, J.G.; Kim, H.-T.; Park, J.-I.; Nou, I.-S. Whole-Genome Re-Alignment Facilitates Development of Specific Molecular Markers for Races 1 and 4 of Xanthomonas campestris pv. campestris, the Cause of Black Rot Disease in Brassica oleracea. Int. J. Mol. Sci. 2017, 18, 2523.

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