BackgroundDespite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.). The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS) markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species.ResultsConsidering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs) of tea (Camellia sinensis L.). A total of 109 (8.9%) unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%), tri (30.8%), tetra (6.6%), penta (7.5%) and few hexa (4.1%) nucleotide repeats. Among the dinucleotide repeats, (GA)n.(TC)n were most abundant (83.6%). Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5%) primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6%) were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO) characterization. Thirty six (60%) of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC) ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (HE) and observed (Ho) obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test for IAM and SMM models for the UGMS loci showed excess heterozygosity and did not show any bottleneck operating in the tea population.ConclusionUGMS markers identified and characterized in this study provided insight about the abundance and distribution of SSR in the expressed genome of C. sinensis. The identification and validation of 61 new UGMS markers will not only help in intra and inter specific genetic diversity assessment but also be enriching limited microsatellite markers resource in tea. Further, the use of these markers would reduce the cost and facilitate the gene mapping and marker-aided selection in tea. Since, 36 of these UGMS markers correspond to the Arabidopsis protein sequence data with known functions will offer the opportunity to investigate the consequences of SSR polymorphism on gene functions.

IMPF: 01.55The most important evolutionary event in the success of commercial tea cultivation outside China in ca. 30 countries came about by the origin of India hybrid tea in India, derived from the extensive spontaneous hybridization that took place between the Assam type tea growing in the forest regions of Assam, North-East India and China type tea introduced from China in ~1875 to many regions of North-East India. The release of an enormous pool of vigorous and highly variable plants of India hybrid tea in North-East India was a significant step forward for the origin and evolution of tea as a highly successful crop plant. The 1,644 accessions and clones of India hybrid tea, representatives of known 15 morphotypes, were screened by 412 AFLP markers amplified by 7 AFLP primer pair combinations. All the 412 genetic loci were polymorphic across the 1,644 accessions and clones. The analysis was done with distance (PCoA and NJ) methods, and the STRUCTURE (Bayesian) model. Both PCoA and NJ analysis clustered 1,644 tea accessions and clones into six major groups with one group in each, constituted mostly by China hybrid, Assam China hybrid and Assam hybrid morphotypes, of distinct genetic identity. No group was exclusive for any particular morphotype. The accessions and clones belonging to morphotypes, Assam type, Assam hybrid, China hybrid and China Cambod were distributed in all the groups. It is the Assam type/Assam hybrid morphotypes which exhibit much broader genetic variability than in China type/China hybrid/Cambod type/Cambod hybrid morphotypes. The STRUCTURE analysis inferred 16 populations (K = 16), for which the greatest values of probability were obtained. Nine of the 16 clusters were constituted by the tea accessions and clones of ?pure? ancestry. The remaining clusters were of ?mixed? ancestry. This analysis provides evidence that the accessions and clones of the same morphotype are not always of same genetic ancestry structure. The tea accessions and clones obtained from outside North-East India shared the same groups (distance method) and clusters (STRUCTURE model) which were constituted by North-East India accessions. The present study also demonstrates very narrow genetic diversity in the commercial tea clones vis-a-vis the profound genetic diversity existing in the tea accessions. These clones were distributed in hardly two of the six groups in NJ tree. The identified 105 core accessions and clones, capturing 98% diversity, have their origin from almost all groups/subgroups of NJ tree.Peer reviewe

Genetic based study provide emphasis on the population study of geographically isolated population, gene flow among them and evolutionary history of the species. In the present study, we aimed to detect the genetic variations in species of genus Schistura from Uttarakhand. Very little is known for the pattern of distribution and genetic diversity of the species of genus Schistura from the Garhwal and Kumaun region. Out of six primer only four primers were used to generate the fragments patterns from the samples collected. Polymorphism within and between the populations were assayed and total 60 bands were amplified ranging from 1-150 kb. Maximum number of bands was observed in Schistura montanus from the Srinagar, Garhwal and Uttarkashi regions. Total 60 bands were amplified in the all four primer with high percentage of polymorphic loci 50% Schistura montanus from Garhwal region and 28.8% in the S. montanus from the Kumaun region were observed. The level of heterozygosity were found 0.006-0.18 in the all three species. The percentage of polymorphism was 50% within the populations and high heterozygosity the sample of S. montanus when compared with other species. Observed pattern of RAPD markers reveals that the samples from the Garhwal region exhibit high diversity and used four primers are sufficient to distinguish the different population in the both region except the samples of the S. gangiticus of Garhwal region.

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