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Hendre P.S.,CSIR - Central Electrochemical Research Institute | Hendre P.S.,Life science and Technology Center | Aggarwal R.K.,CSIR - Central Electrochemical Research Institute
PLoS ONE | Year: 2014

Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic-/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study. © 2014 Hendre, Aggarwal.

Kamalakannan R.,Life science and Technology Center | Varghese M.,Life science and Technology Center | Suraj P.G.,Life science and Technology Center | Arutselvan T.,Life science and Technology Center
Journal of Forestry Research | Year: 2016

We evaluated a clone trial comprised of 20 ramets each of 40 Eucalyptus camaldulensis clones for growth and fertility at 4 years of age. The clones differed significantly in growth with 65–100 % survival in 38 clones while two clones had low survival (40 and 10 %). Fecundity was high and fertility variation low, as indicated by the sibling coefficient value (Ψ = 1.4) with 55 % of clones contributing 80 % of the fruits. Thinning strategies were considered to convert the clone trial to a clonal seed orchard and enhance both gain and diversity in seed crop. When clones were selected based on growth without considering fertility, truncation selection (to retain clones with higher DBH than the trial mean value) would give 8 % gain, but 59 % reduction in effective population size (Ne). Gain and predicted diversity (Ne) was highest when ramets were selected in linear proportion to the breeding value of each clone. Mass selection with the same intercept (for DBH) as truncation selection would give a moderate 3 % gain, but over two times higher predicted Ne than truncation selection. When fertility of retained trees was considered after thinning, mass selection would yield 52 % effective contribution from the orchard trees compared to only 30 % contribution from truncation selection and linear thinning. Higher representation of superior clones in linear thinning and mass selection would lead to greater fertility variation and over 30 % reduction in effective clone number (Nc) from that predicted (Ne, assuming equal fertility among ramets) before thinning. © 2015, Northeast Forestry University and Springer-Verlag Berlin Heidelberg.

Kullan A.R.K.,Life science and Technology Center | Kulkarni A.V.,Life science and Technology Center | Kumar R.S.,Life science and Technology Center | Rajkumar R.,Life science and Technology Center
Tree Genetics and Genomes | Year: 2016

Casuarina is a widely cultivated plantation tree species in coastal India, primarily due to its fast growth, high productivity and suitable for pulp and paper production. However, genetic studies of Casuarina have been hindered by lack of genomic resources and genetic markers. Knowledge of the genetic diversity and population structure of Casuarina germplasms will provide the basis for utilizing and improving resource in the breeding program. Keeping this in view, in the present study, we have identified a total of 11,503 simple sequence repeat (SSR) makers from 86,415 expressed sequence tags (ESTs) of Casuarina equisetifolia and C. junghuhniana after redundancy elimination. Dinucleotide repeats were the most abundant accounting for 72.5 % of all microsatellites, followed by trimer (23.4 %), hexamer (1.7 %), tetramer (1.5 %), and very few pentamer (0.6 %) repeats. Of these, 50 markers were used to estimate genetic diversity and population structure among 96 accessions of C. cunninghamiana and C. junghuhniana. EST-SSR markers revealed high level of polymorphism, detecting a total of 829 alleles with an average of 17 alleles per locus. Polymorphic information content (PIC) values ranged from 0.32 to 0.93, with an average of 0.78 per locus. The average observed (Ho) and expected heterozygosity (He) obtained was high and fairly similar in C. cunninghamiana and C. junghuhniana, thereby suggesting highly heterogeneous nature of Casuarina. Population structure using a Bayesian model-based clustering approach identified clear delineation between C. cunninghamiana and C junghuhniana. Further, these markers were also evaluated in four species of Casuarina confirming high rate of cross-species transferability. The results of this study can provide valuable insights for genetic and genomic research in Casuarina. © 2016, Springer-Verlag Berlin Heidelberg.

Sood S.,Life science and Technology Center | Dwivedi S.,Life science and Technology Center | Reddy T.V.,Life science and Technology Center | Prasanna P.S.,Life science and Technology Center | Sharma N.,Life science and Technology Center
Plant Breeding | Year: 2013

Production of doubled haploid plants through androgenesis in flue-cured Virginia (FCV) tobacco is a promising and convenient alternative to conventional selfing techniques for the generation of absolute homozygous lines. Here, we show a robust in vitro haploid and doubled haploid development protocol in FCV tobacco with major emphasis on improving the efficiency of chromosome doubling using in vitro colchicine treatment. We used five FCV tobacco hybrids for comparison of colchicine treatments. The anther culture response varied with developmental stages of the buds, and the highest response was observed in stage 2 buds. The effect of cold pretreatment was significant, and 4 days of pretreatment was optimum for gametic embryogenesis. Among the methods used for determining the ploidy status of plants, flow cytometry was found to be easy, fast and reliable for high-throughput screening of haploids. Doubled haploids regeneration percentage varied from 6.77 to 11.95 in in vivo treatment, while the range of variation was 22.11% to 28.40% in in vitro colchicine treatment. We observed a pronounced increase in plant survival and the proportion of doubled haploid plants in in vitro treatment compared with the standard in vivo approach. © 2013 Blackwell Verlag GmbH.

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