Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.

The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like 'Triplex affinity capture' did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a 'Sequential Reverse Genome Walking (SRGW)' strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace 'local b' as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar 'Kuching' with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper.

Genotypic diversity among 46 isolates of Sclerospora graminicola collected from seven states in India during 1992-2005 was determined through pathotyping and AFLP analysis. A high level of variation was observed among the isolates for downy mildew incidence, latent period and virulence index. Based on the reaction on a set of nine pearl millet lines, 46 isolates were classified in 21 pathotypes. Quantitative differences in virulence levels of the test isolates were assessed by calculating the virulence index (disease incidence 6 latent period 7 1 ). A dendrogram generated by the average linkage cluster analysis of virulence index clustered the 46 isolates into eight groups. Regionspecific grouping of five isolates from Gujarat and six from Rajasthan was observed within two distinct groups. Temporal variation was also observed among the isolates collected from the same location and same host over the years. A total of 297 bands were scored following selective amplification with three primer combinations E-TT/M-CAG, E-AT/M-CAG and E-TG/M-CAT and all of them were polymorphic. Cluster analysis of AFLP data clustered the test isolates into seven groups. Analysis of molecular variance indicated that variation in the S. graminicola populations was largely due to differences among the isolates within the states.

Participatory rural appraisal was undertaken in 70 villages in India and Nepal, covering 1185 farmers to generate baseline information on the current plant protection practices. The study revealed that 93% of the farmers in India and 90% in Nepal had adopted chemical control for the management of various insect pests in different crops; however, less than 20% of the farmers expressed confidence on their efficacy. In India, 52% of farmers get their plant protection advice from pesticide dealers, while in Nepal, the majority of the farmers (69%) make their plant protection decisions through agricultural officers. A majority of the farmers (73% in India and 86% in Nepal) initiate the plant protection based on the first appearance of the pest, irrespective of their population, crop stage and their damage relationships. About 50% of the farmers in India and 20% in Nepal were not using any protective clothing while spraying. Health problems associated with the application of plant protection chemicals were reported by farmers. The cost of plant protection on various crops ranged from 7 to 40% of the total crop production cost. Though integrated pest management (IPM) has been advocated for the past two decades, only 32% in India and 20% in Nepal were aware of IPM practices. IPM implementation in selected villages brought a 20 -65% reduction in pesticide use in different crops. The vegetable samples analysed for pesticide residues revealed the presence of residues.

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