Begomoviruses (Family-Geminiviridae) are plant infecting single stranded DNA viruses known to evolve very fast. Here, we have analysed the DNA-A sequences of 302 begomoviruses reported as 'type isolates' from different countries following the list of International Committee on Taxonomy of Viruses till 2017. Phylogenetic analysis was performed which revealed two major evolutionarily distinct groups namely Old World (OW) and New World (NW) viruses. Our work present evidence that cp gene has varied degree of diversification among the viruses reported from NW and OW. The NW viruses are more conserved in their cp gene sequences than that of OW viruses irrespective of host plant families. Further analysis reveals that cp gene differs in its recombination pattern among OW and NW viruses whereas rep gene is highly recombination prone in both OW and NW viruses. The sequence conservation in cp gene in NW viruses is a result of meagre recombination and subsequent low substitution rate in comparison to OW viruses. Our results demonstrated that the cp gene in NW viruses is less likely to possess nuclear localisation sequences than OW cp gene.Further we present evidence that the NW-cp is under the influence of strong purifying selection. We propose that the precoat protein (pcp) gene present exclusively in the 5' of cp gene in OW viruses is highly diversified and strong positive selection working on pcp gene might be attributing largely to the diversity of OW-cp gene.
Indigenous folk rice cultivars often possess remarkable but unrevealed potential in terms of nutritional attributes and biotic stress tolerance. The unique cooking qualities and blissful aroma of many of these landraces make it an attractive low-cost alternative to high priced Basmati rice. Sub-Himalayan Terai region is bestowed with great agrobiodiversity in traditional heirloom rice cultivars. In the present study, ninety-nine folk rice cultivars from these regions were collected, purified and characterized for morphological and yield traits. Based on traditional importance and presence of aroma, thirty-five genotypes were selected and analyzed for genetic diversity using micro-satellite marker system. The genotypes were found to be genetically distinct and of high nutritive value. The resistant starch content, amylose content, glycemic index and antioxidant potential of these genotypes represented wide variability and ‘Kataribhog’, ‘Sadanunia’, ‘Chakhao’ etc. were identified as promising genotypes in terms of different nutritional attributes. These cultivars were screened further for resistance against blast disease in field trials and cultivars like ‘Sadanunia’, ‘T4M-3-5’, ‘Chakhao Sampark’ were found to be highly resistant to the blast disease whereas ‘Kalonunia’, ‘Gobindabhog’, ‘Konkanijoha’ were found to be highly susceptible. Principal Component analysis divided the genotypes in distinct groups for nutritional potential and blast tolerance. The resistant and susceptible genotypes were screened for the presence of the blast resistant pi genes and association analysis was performed with disease tolerance. Finally, a logistic model based on phenotypic traits for prediction of the blast susceptibility of the genotypes is proposed with more than 80% accuracy.
Chilli leaf curl virus is one of the most devastating virus infecting chilli crops in India. Management of chilli leaf curl disease largely relies on early detection and quantification of the virus. In the present study different Open Reading Frames from chilli leaf curl virus from sub-Himalayan Terai region were cloned, sequenced and submitted in NCBI database with accession number MN851261, MN857412, and MN857413. Comparison of these gene sequences with previously reports revealed that chilli leaf curl virus coochbehar strain exhibits 90–92% similarity with tomato leaf curl joydebpur virus and pepper leaf curl Bangladesh virus. Using these sequence primers were designed from the unique AV2 region of the chilli leaf curl virus coochbehar strain and a SYBR based Rapid Real-time Viral Load estimation (ReViLeR) technique was developed to quantify the virus directly from extracts of infected leaf samples. Seventeen chilli genotypes were evaluated for virus accumulation with ‘ReViLeR’ method after challenge inoculation with chilli leaf curl virus. Traditional landraces like Chuapara, Line boya and White chilli were found to have highest viral titer (36659, 22909 and 25195 viral copies per genomic unit (GU) respectively). On the other hand, from the genotypes like Micro, Pusa Sadabahar, Dalle Khursani no virus was detected. Higher viral load in the susceptible genotypes manifested severe leaf curl symptoms whereas resistant genotypes with no detectable viral load remained healthy. The sensitivity of the newly developed ReViLeR technique was found up to 83% in rapid detection of chilli leaf curl virus.
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