Tuesday, November 29, 2011

The History of DNA Barcoding (Video)

A DNA barcode is a DNA sequence that uniquely identifies each species of living thing. Dr. Mark Stoeckle from The Rockefeller University talks about the history of DNA barcoding, from the first paper published in 2003 to the international consortium of researchers that exists today.
DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species. Applications include, for example, identifying a plant even when flowers or fruit are not available, identifying insect larvae (which typically have fewer diagnostic characters than adults), identifying products in commerce (for example, herbal supplements or wood), etc. It differs from molecular phylogeny in that the main goal is not to determine classification but to identify an unknown sample in terms of a known classification. Here is the WIKI page on DNA barcoding: http://en.wikipedia.org/wiki/DNA_Barcoding

Friday, March 25, 2011

Vacancy of a Junior Research Fellow (JRF) position

Project: Genetic studies on selected rattan palms (Calamus sp.) using microsatellite markers

Essential qualification: First class M.Sc. in Botany/Biotechnology
Desirable qualification: Research experience in Plant Molecular Biology

The last date prescribed was 11th April 2011 [Closed].

Please email your CV for information about conducting MSc Projects/Dissertations and PhD programmes.

Friday, March 11, 2011

Genetic studies in rattan palms (Calamus sp.) using SSR markers

Natural variation is essential for conservation and utilization of plant genetic resources. Human interference on forests may cause depletion of natural genetic variation in the gene pool and even to genetic erosion of certain species. Rattans are one such species currently under crisis due to over-exploitation. They represent high value non-wood forest produce primarily used for making furniture, handicraft items and an important raw material in the cottage industry which contributes significantly in rural economy. There are about 1 lakh people in Kerala living out of this valuable resource. However, number of small scale industrial (SSI) units depending on these forest produce are decreasing drastically.  Besides, over exploitation of the rattans has exerted severe pressure on existing populations and sometimes resulted in loss of genetic diversity.
There are about 600 rattan species in 13 genera globally and 51 species in 4 genera in India, of which 75% are endemic and 40.5% threatened. The Western Ghats region of India is rich in species diversity of rattans with one genus, viz. Calamus having 27 species of which 21 are identified.
Presently associated (as Principal Investigator) to a research project on ‘Genetic studies on selected rattan palms (Calamus sp.) using microsatellite markers’.

Objectives of the project are to collect natural populations of the selected rattan palms, viz. C. brandisii, C. gamblei, C. nagabettai, C. thwaitesii, C. travancoricus and C. hookerianus and analyze genetic diversity, population structure and differentiation using SSR markers.

The project is being funded by Kerala Biotechnology Commission/KSCSTE.

Genetic diversity in bamboo germplasm in TBGRI using ISSR markers

Bambusetum in Tropical Botanic Garden & Research Institute (TBGRI) has 660 accessions of Bamboos belonging to 60 species spread across 12 hectares of land area. The collection includes species mainly from the Western Ghats, north-eastern region of India, South East Asia and a few cultivated ones. 

Inter-single sequence repeat (ISSR) markers were used as a tool to analyze natural genetic variations within 10 bamboo species (Bambusa balcooa, B. bambos, B. tulda, B. vulgaris, Cephalostachyum pergracile, Dendrocalamus brandisii, D. giganteus, D. hamiltonii, D. strictus and Ochlandra travancorica) were collected from TBGRI bamboosetum.

Genetic analysis revealed high level of natural genetic variation between individuals in most of the bamboo species. 

Genetic Structure of Oryza rufipogon Griff. Natural Populations

Genetic Structure of Oryza rufipogon Griff. Natural Populations in Malaysia: Implications for Conservation and Genetic Introgression of Cultivated Rice

Thirty polymorphic Oryza sativa microsatellite loci (SSRs) were used to study population genetic structure of O. rufipogon Griff. natural populations in Malaysia. A total of 445 alleles were detected with an average of 14.8 alleles per locus in 176 individuals of O. rufipogon sampled from the states of Penang, Kedah, Kelantan and Terengganu where the natural populations are still found. The Kelantan population in the northeast of Peninsular Malaysia had the highest level of genetic diversity as measured by the mean number of alleles per locus, Aa=7.67, average number of effective alleles, Ae=5.50, percentage of polymorphic loci, P=100%, observed heterozygosity, Ho=0.631 and expected heterozygosity, He=0.798. In contrast, the Terengganu population in the east showed the lowest level of genetic diversity measured by the same criteria (Aa=4.23, Ae=2.10, P= 100%, Ho=0.549 and He=0.449). Model–based clustering analysis using the STRUCTURE 2.2 program placed all the individuals into 12 clusters that corresponded to the geographic sampling locations. Neighbour-joining tree was constructed based on Nei’s genetic distance to further assess the genetic structure of the O. rufipogon individuals, showed good agreement (93.8%) with the model-based cluster analysis. However, the neighbour-joining tree identified subpopulations that STRUCTURE could not identify. The classification of individuals from the same populations under the same cluster supported the population differentiation. These two analyses seemed to indicate expansion of populations from the northeast of Peninsular Malaysia (Tumpat, Pasir Mas and Kota Bahru, Kelantan) not only to the immediate south of the region i.e. Terengganu but also into the northwest (i.e. Penang and Kedah) with the former being more recent. Oryza rufipogon accession IRGC105491 and O. sativa ssp. indica cultivar MR219, which were included in this study for comparisons with the local wild rice accessions, indicated that introgression of cultivated rice could change genetic composition and affect the population genetic structure of wild rice. This possibility should be carefully considered in plans to conserve this wild rice.

Published in:
Tropical Plant Biol. (2010) 3:227–239

Development and evaluation of advanced backcross families of rice for agronomically important traits

Wild relatives of crop species may contain trait-enhancing genes. Our studies showed that grain yield in cultivated rice can be increased significantly using the genes found in common wild rice. Advanced backcross progenies (Oryza rufipogon IRGC105491 x O. sativa cv. MR219) exhibited higher values for most of the yield and yield-related traits analyzed in comparison to the cultivated parent, MR219. About 10% of the BC2F2 families exhibited 33.5% higher grain yield per plant in comparison to MR219. Even though there was an increase in empty grains per panicle, number of tillers per plant also increased considerably (41.5%). This resulted in higher grain yield per plant, which ranged from 52.4 to 77.5g for the selected families in contrast to 42.4g for MR219. Two families, viz., S163 and S165, were identified through GGE biplot analysis as most promising genotypes for cultivar development. The backcross families offer an efficient source of genetic diversity for future breeding programmes.

CITATION: Sabu, K.K., Abdullah, M.Z., Lim, L.S., Wickneswari, R. (2006). Development and evaluation of advanced backcross families of rice for agronomically important traits. Commun. Biometry Crop Sci. 1 (2), 111-123. 

Heritability and genetic variability in Oryza sativa x O. rufipogon cross

Analysis of heritability and genetic variability of agronomically important traits in Oryza sativa x O. rufipogon cross

Heritability is a measure of possible genetic advancement under selection. Estimation of variance components could imply partitioning of genetic variability over different sources of variation. This article describes statistical methods applied and some of the observations made on results of heritability and analysis of environmental variances of grain yield and related traits of progenies derived from a cross between wild and cultivated rice. The study shed light on the genetic information of grain yield and related traits such as their heritability, genetic and environmental effects in the F1 progenies of a cross between O. sativa and O. rufipogon. A considerable amount of additive genetic variation was found in these families. The traits with high heritability, considerable phenotypic correlation and low seasonal variability can be used in further improvement of the F1 progenies. The results obtained were highly promising and can be utilized to develop new rice cultivars.

Published in:
Agronomy Research 7(1), 97-102, 2009

Using SAS® procedures to estimate genetic variances and heritability in a rice cross

Heritability is a measure of possible genetic advancement under selection. Estimation of variance components could imply partitioning of genetic variability over different sources of variation. This article describes statistical methods applied and some of the observations made on results of heritability and genetic variance analysis of rice yield and related traits of progenies derived from a cross between wild and cultivated rice. A completely random model was used to perform analysis of variances employing PROC GLM. Parent-offspring regression coefficient was calculated using PROC REG. The parent-offspring regression can be greatly influenced by environments resulting in higher or lower trait expression in the offspring relative to the parents. Hence the data was standardized using PROC STANDARD and regression coefficients were recalculated. Variance components for the statistical design were estimated using PROC MIXED. Phenotypic correlations were analyzed by applying PROC CORR. Normal distribution and histograms of various traits were determined using PROC CAPABILITY. The results obtained were highly promising and can be utilized to develop new rice cultivars.

Presented at the 19th SUM forum, Kuala Lumpur Convention Centre, Malaysia

Postdoc research: Improvement of rice yield through molecular breeding

This research was conducted to identify possible trait enhancing quantitative trait loci (QTLs) from common wild rice, Oryza rufipogon. Two hundred and sixty-six BC2F2 families were developed from an interspecific cross between O. rufipogon accession no. IRGC 105491 and O. sativa cv. ‘MR219’during 2002-2003. Field evaluation of the BC2F2 families for 18 yield and yield related traits was carried out in 2004 at Malaysian Agricultural Research and Development Institute, Seberang Perai. Ninety three SSR (simple sequence repeat) markers were used to create a genetic linkage map spanning the twelve rice chromosomes. Ninety one QTLs were detected by means of marker regression with a significance level of p < 0.01. Among the putative QTLs, 21 were significant and 70 were suggestive. QTLs having favourable effects were noticed for days to heading (decrease heading period up to 6%), grain filling (increased filled grains plant-1 up to 12%), grain yield (increased grain yield plant-1 up to 10%), resistance to bacterial leaf blight (increased resistance by 13%), and tolerance to brown planthopper infection (increased tolerance by 40%). Quantitative data analysis suggests that about 10% of the total of 266 BC2F2 families demonstrated nearly 27% higher yield potential in comparison to the parental cultivar ‘MR219’. This increase is mostly due to higher tillering ability which is characteristic of O. rufipogon. These families also showed a considerable increase in tolerance against bacterial leaf blight and brown plant hopper infestation. The selected BC2F2 families can offer an efficient source of genetic diversity for future breeding programmes. The study concludes that even though wild rice is inferior to most of the agronomic traits, they could positively contribute to the overall yield enhancement in cultivated rice.

Application of molecular markers for the analysis of genetic diversity and systematics


Analysis of genetic diversity is carried out using a variety of tools and techniques, however due to its accuracy, the use of molecular markers find much popularity. Such studies often hold diverse applications in the fields of utilisation of genetic resources, molecular taxonomy and conservation of biological materials. There are many reports available which deal with the use of protein/DNA markers in edible mushrooms. Oyster mushrooms (Pleurotus sp.) are one of the popular edible mushrooms in the tropics thoroughly studied mainly to scrutinise speculated position of many species and genotypic classes. The present review discusses on the application of isozyme and RAPD markers for the analysis of genetic diversity and systematics of Pleurotus sp.

Published in:
In Frontiers of Fungal Diversity in India (Prof. Kamal Festschrift)/Ed. By G.P. Rao, C. Manoharachari, D.J. Bhat. Lucknow, International, Xxiv, 906 P.

The use of RAPD in assessing genetic variability in Andrographis paniculata Nees

RAPD analysis was done to determine intraspecific variability in Andrographis paniculata, a popular antipyretic and hepatoprotective drug used in traditional medicine in India. The accessions collected from parts of India and southeast Asia on molecular analysis revealed moderate variation within the species. Similarity measurement using UPGMA followed by cluster analysis resulted in 5 major groups based on geographical distribution that generally reflected expected trends between the genotypes. There were also important exceptions like AP48, an accession from Thailand showing close resemblance to AP38 collected from Tamil Nadu and AP29 from Assam significantly diverse from the rest of the native genotypes. The results indicated that RAPD could be effectively used for genetic diversity analysis in wild species of prospective value as it is reliable, rapid and superior to those based on pedigree information.

Published in:
Current Science (Bangalore) 76: 833-835

Active principle content and isozymes of Andrographis paniculata Nees (Kalmegh)

Germplasm collection of Andrographis paniculata Nees (Kalmegh), a medicinal herb endowed with curative properties against a variety of ailments, was carried out from various parts of south Asia. The germplasm was reared in a field plot under identical conditions and then seeds were collected and used for the present study. Seed progenies of 15 accessions were analysed at 15 loci representing 8 enzyme systems. On an average 5.4 loci (36.00%) were found to be polymorphic (P) and mean observed number of alleles per locus (A) was 1.41. Average observed heterozygocity (Ho) was 0.406 and expected value (He) was 0.233 showing moderate level of genetic variation among different accessions. Product synthesis did not correlate with allelic variations in any of the accessions but an accession AP36 accumulating significant concentration (1.47% dry weight) of andrographolide in the leaves may be potentially useful for breeding and cultivar development.

Published in:
Journal of Medicinal and Aromatic Plant Sciences 23 (2001) 637-647.

Genetic variation in south Indian populations of Phyllanthus amarus Schum. & Thonn. (Euphorbiaceae), assessed using isozymes

Fifteen populations of Phyllanthus amarus from different parts of southern India were subjected to assessment of genetic diversity using isozymes. Analyses include electrophoretic separation of isozymes, scoring of active loci and genetic data analysis using POPGENE®. The six isozymes scored for a total of 14 loci with an overall polymorphism of 48.57%. Mean observed number of alleles was 1.56 and gene diversity index averaged to 0.39. In general, our studies reveal the existence of intraspecific genetic variations in P. amarus. Considering the medicinal importance, possible negative influence of intraspecific variations in the maintenance of constancy of drugs prepared from this herb may be anticipated and hence caution must be exercised during product preparations. Besides, it is recommended that a concerted effort need to be undertaken to superimpose genetic and medicinal profile to identify putative populations for conservation as well as sustainable utilization.

Published in:
Proceedings of the Fifteenth Kerala Science Congress (03 – 17), 29-31 January 2003, Thiruvananthapuram, pp. 196-201

Variable Invariably: An introduction to intraspecific variations in Medicinal Plants

It is needless to say that variety is the spice of life, Nature has myriads of life forms on this planet among which variations are of ubiquitous occurrence. It is particularly so in the megacentres of diversity in the tropics which harbor approximately two-third of the biota and where many species of economic importance presumably had their origin. As a matter of fact, variations between individuals of the species (a group of closely related if not identical individuals which can exchange genes between each other) was observed over the millennia and were considered real ‘hotspots’ of evolution. The notion that no two individuals of a sexual progeny are 100% identical prevailed when methods of scientific scrutiny were not available. In 17th century when the concept of a species was poorly understood, the English naturalist John Ray (1628-1705) showed that within a species there might occur individuals different from the normal in one or more characters. Later Charles Darwin (1809- 1882) upgraded this concept into a supremo and effectively linked the variations with natural selection and origin of new species. An evolutionary biologist or a breeder, variations among plants and animals has always fascinated a mind of enquiry and helped to select a desirable variant or breed a new form of greater agronomic value. Traditional vaidyas and village doctors of yester years were no different. They collected herbs of certain morphological attributes (of flowers, fruits, leaves etc.) and preferred root drugs of specific colour, smell, size, fibrous content, itching quality etc. obviously within the species and from locations (habitats) known only to them.

Full Text

PhD Thesis: Intraspecific variations in Andrographis paniculata Nees

Abstract: For the biodiversity- rich developing countries in the tropics, chemical and genetic prospecting of their plant genetic resources is a priority area not only to fish out genotypes/molecules of potential economic importance but also to add value to them. The present study essentially directed towards this objective, involves analysis of intraspecific variations in Andrographis paniculata Nees [കിരിയാത്ത്] (Acanthaceae), an important medicinal plant of India, presumably having its centre of origin and diversity in southern India and Sri Lanka. Specifically, the study is directed to: (i) elucidate biology of A. paniculata by understanding distribution, habitat, phenology of flowering/fruiting, cytology, breeding system and seed dormancy/ germination of the species; (ii) quantify the amount of genetic variability within A. paniculata and its patterns of interpopulation differentiation; (iii) assess the significance of inbreeding and gene flow to the level and pattern of diversity presently observed in A. paniculata; (iv) test the hypothesis that genetic distance can be significantly correlated with geographical distance; (v) identify superior genotype(s) with increased biomass and product (andrographolide) synthesis; and (vi) suggest conservation and utilization/improvement strategy for the species based on the data generated. Studies on biology of the species revealed that the plant is naturally self-pollinating, but possibility for cross-pollination could not be entirely ruled out. Intraspecific variation of A. paniculata was analysed using quantitative traits, isozyme and random amplified polymorphic DNA (RAPD) markers. The three approaches differed in the amount of variation detected. Analysis of the ten morphological characters revealed considerable diversity at inter-population level. Variation in the active principle (andrographolide) content was moderate with maximum concentration on dry weight basis (1.47%) was recorded in a population from Tamil Nadu (AP36) with a mean value of 0.95%. Product concentration did not correlate with allelic variations in any of the populations but AP36, with the highest concentration (in the leaves) averaged through three generations may help development of a cultivar.

RAPD assay revealed the highest polymorphism among the three markers tested. Twentyfive random primers generated an average of 1.61 bands (alleles) per primer (locus) with a mean polymorphism of 0.71. Isozymes on the other hand were analysed at 15 loci representing 8 enzyme systems. On an average the mean observed number of alleles per locus was 1.37 and the proportion of polymorphic loci was 0.32. Genetic differentiation estimated by Nei's distances suggested a common gene pool for the populations collected from Kerala while those from Tamil Nadu and elsewhere from India revealed more divergence. More or less, exotic populations exhibited similarity to Tamil Nadu populations which may shed light on their origin. In general, the genetic clustering derived from isozyme and RAPD data was in agreement with the geographical locations/distances. Further analysis of the two natural populations (Sirumalai and Nallamalai) collected from geographically isolated areas using Nei's distance and fixation indices indicated substantial divergence at the sub population level. This pointed out varied drift and bottleneck effects and differential gene flow between them. Local isolation, either natural or artificial, also promotes divergence of the populations. Further more, the within- populations diversity was significantly different between populations, indicating that evolutionary potential is not evenly distributed amongst populations. Regarding conservation of representative populations of A. paniculata, caution must be exercised due to sizeable differentiation at the local and withinpopulation levels. For practical conservation purpose and maintenance of maximum genetic variation within existing populations, outright collection of all the plants before seed set in a given locality by the local plant collectors should be discouraged.

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