New Disease Reports (2005) 13, 10.

First report of molecular detection of an Aster yellows phytoplasma (Candidatus Phytoplasma asteris) isolate infecting chilli (Capsicum annuum) in India

M.S. Khan and S.K. Raj*


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Accepted: 28 May 2005

Chilli (Capsicum annuum; family Solanaceae) is an important spice crop, being cultivated over large areas in Asia, Africa, South and Central America, parts of USA and Southern Europe. India is the largest chilli producer in the world, producing 1.2 million tonnes of dry chilli, from an area of about 880,000 hectares. During the winter of 2004, a severe phytoplasma-like disease of chilli was noticed in the Bahraich district of Uttar Pradesh with a low incidence (ca. 5% of plots showed some infection). The symptom of the disease consisted of shortening of leaves, petioles & internodes and crowding of leaves and stunting of whole plant (Fig. 1).

For molecular detection of the causal pathogen, the total DNA of plant samples with or without symptoms was isolated using the protocol of Ahrens & Seemüller, 1992. Direct PCR was carried out using the universal 16S rDNA-specific primers P1/P6 (Deng & Hiruki, 1991), which resulted in the production of a ~1.5 kb product from diseased samples but not symptomless ones. Nested-PCR was further performed with primers R16F2n/R16R2 (Gundersen & Lee, 1996) which gave an amplicon of the expected size ~1.2 kb DNA. This product was cloned, sequenced and the data deposited in Genbank (Accession DQ343288). A blast search revealed the highest level of sequence identities (98%) with 16SrI Aster yellows group members, such as Barley deformation phytoplasma (AY734453), Aster yellows phytoplasma (AY665676), Valeriana yellows phytoplasma (AY102274), Onion yellows phytoplasma (AP006628) and Silene virescence phytoplasma (AY744070).

Previously a phytoplasma associated with chilli little leaf disease has been detected in India by graft transmission and electron microscopy (Singh & Singh 2000), but the causal pathogen was not characterised at the molecular level. To our knowledge, this is the first report of molecular detection of an isolate of Aster yellows phytoplasma (Candidatus Phytoplasma asteris) infecting chilli in India.

Figure 1: Diseased chilli plant showing phytoplasma-like symptoms
Figure 1: Diseased chilli plant showing phytoplasma-like symptoms


  1. Ahrens U, Seemüller E, 1992. Detection of DNA of plant pathogenic mycoplasma like organism by a polymerase chain reaction that amplifies a sequence of the 16S rRNA gene. Phytopathology 82, 828-832.
  2. Deng S, Hiruki D, 1991. Amplification of 16S rRNA genes from culturable and nonculturable mollicutes. Journal of Microbiological Methods 14, 53-61.
  3. Gundersen DE, Lee IM, 1996. Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia Mediterranea 35, 144-151.
  4. Singh D, Singh SJ, 2000. Chilli little leaf - a new phytoplasma disease in India. Indian Phytopathology 53, 309-310

This report was formally published in Plant Pathology

©2005 The Authors