Rapidly evolving sex-specific sequences in Calamus travancoricus Bedd. ex. Becc. and Calamus nagbettai R.R.Fernald & Dey

Gene sequences mediating sexual reproduction are more divergent within and between closely related species. Microsatellite or simple sequence repeat (SSR) markers are valuable molecular tools for analysis of genetic variability, phylogeny, and also for identifying sex at seedling stage in dioecious plant species. Calamus travancoricus Bedd. ex. Becc. and Calamus nagbettai R.R.Fernald & Dey are economically important rattan species. The dioecious nature of the Calamus spp. limits its breeding and cultivation. The sex of rattans can only be identified after attaining reproductive maturity which ranges from 5 to 15 years. A study was carried out in this background and 9 putative sex-specific PCR products were identified as sex markers for C. travancoricus and C. nagbettai and sequenced by Sanger method. The sequence homology search revealed occurrence of identical sequences in many plant species across different families indicating the conserved nature of the sequences. However, these sequences were not present in opposite sex in the studied species, indicating divergent evolution favoring sex determination. Annotation of these sequences revealed that most of these are mediating sexual reproduction by and large. An adequate sex ratio is to be maintained for these dioecious palms in natural habitat for producing offsprings having equal gene complements for continual evolution and sustainable utilization. Developing scientific management strategies and improved utilization of canes could help to generate employment locally and thus contribute to the socioeconomics sustainably.

https://link.springer.com/article/10.1007%2Fs11295-017-1220-2

Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.)

Snake gourd is a natural antibiotic and the plant is commonly used in folk medicines throughout India. The present study was carried out using transcriptomic sequence of Trichosanthes kirilowii Maxim. for the development and validation of EST-SSR markers and EST sequences of T. dioica Roxb. for identification of EST-SNPs in T. cucumerina var. cucumerina L. A total of 382 primers were developed and out of which 58 were found to be suitable for genetic analysis. For experimental validation, 20 primers were randomly selected and amplified in T. cucumerina var. cucumerina and two related genera, viz. Coccinia grandis and Momordica charantia. It was found that 90% of the primers generated PCR products in T. cucumerina var. cucumerina and considerable cross generic amplification in M. charantia and C. grandis. Further, identification of EST-SNPs in T. cucumerina var. cucumerina was also carried out. The SNPs detected were converted to CAPS markers using the tool SNP2CAPS. The newly developed SSR and SNP markers offer novel additions to the genomic resources of this important medicinal herb for population studies, phylogenetics analyses and estimation of genetic diversity.

Citation: Silpa S, Shinsy M Y, Sabu K K. 2016. Development and validation of EST-SSR and identification of EST-SNP markers for snake gourd (Trichosanthes cucumerina var. cucumerina L.). Abrahamia 2: 51-56

Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

Elettaria cardamomum Maton is one of the most ancient and valuable spice crops. Cardamom is cultivated following intensive pesticide usage where alleles present in the wild cardamom genotypes could positively contribute towards genetic improvement of the cultivars. However, the genetic map or whole-genome sequence of E. cardamomum is not available and very limited information on simple sequence repeat (SSR) markers are publicly available. We have tested whether SSRs from Curcuma longa can be used to analyze genetic diversity E. cardamomum.

Int J Appl Sci Biotechnol, Vol 3(2): 188-192

N Anjali, Sowmya S Dharan, F Nadiya, K K Sabu

DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12380  

Keywords: EST-SSR; microsatellite; genetic diversity; Elettaria cardamomum; cardamom; marker development

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UKM Scientists Developed High Yielding Superior Red Rice

After seven years of research UKM’s scientists with the cooperation of MARDI’s research officers have successfully produced a variety of rice which not only can increase padi yield but also has properties with low gylcaemic index suitable for diabetics.

Its Plant Genetics and Biotechnology expert, from the Faculty of Science and Technology, Prof Dr. R. Wickneswari Ratnam assisted by some 14 other scientists from UKM, Malaysia Agricultural Research and Development Institute (MARDI), Universiti Putra Malaysia (UPM) , Malaysia Nuclear Agency (MNA) and UM had been doing research on this since 2002 and have succeeded in producing the new padi variant G33 named UKMRC9 which can increase local red rice production.

Prof Wickneswari described it as a superior red rice developed through conventional breeding involving controlled cross-breeding between cultivar MR219 and wild rice Oryza rufipogon. It involved the transfer of genes of the wild type to the common paddy produced by MARDI now extensively cultivated in the country.

She was assisted by Dr K K Sabu, Dr. Lim Li Sze, Dr. Atiqur Bhuiyan, Dr. Abdul Rahim Harun, En. Parviz Fasahat, Puan Ngu Mee Siing, En. Abdullah M Zain, Puan Site Zuraini Abdul Rahman, Dr. Narimah Md Kairudin, Dr. Tilakavati Karupiah, Prof. Aminah Abdullah, Dr. Kharidah Muhammad, Chua Khun Aik and Tan Choon Heen in planning and carrying out the seven years of research. Read full article.

Genetic diversity among cardamom germplasm accessions assessed by SSR and ISSR analysis

Abstract: Cardamom (Elettaria cardamom Maton; Zingiberacea), the ‘Queen of spices’ is one of the most important and highly priced spices. The important areas of cultivation in Kerala are Nelliampathy, Wynad and Idukki. The origin of cardamom is believed to be in the Western Ghats, where presumably rich and untapped genetic diversity of the cardamom still resides. Biodiversity present in the wild relatives of crop plants in Kerala have not yet been addressed properly (Nayar, 2011). The present study aims to collect and evaluate genetic diversity among wild cardamom populations in comparison to the cultivated counterparts.

Citation

Ashitha J P, Anija T A, Anjali, N and K K Sabu. 2013. Genetic diversity among cardamom germplasm accessions assessed by SSR and ISSR analysis. Proc of the 25th Kerala Science Congress held at Technopark at Thiruvananthapuram during 29th January to 1st February 2013, pp. 263-265 (03-27).

Link to Google Scholar citation

Association Mapping in Plants

Association (linkage disequilibrium [LD]) studies represent a novel powerful approach to evaluate candidate genes regulating plant phenotype and identify alleles of key interest at these genes. It is based on correlation between gene sequence and plant performance for target traits, and represent a powerful approach to evaluate candidate genes regulating the plant phenotype.

This new technique takes into account the thousands of genes to evaluate for QTL effect and is a more efficient approach that does not require generation of segregating populations/large numbers of progeny. As it can utilize all of the historic recombination events in a diverse population of individuals it can generate higher resolution genetic maps and, is needed to complement current map based cloning methods.

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

Abstract
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

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

APPLICATION OF MOLECULAR MARKERS FOR THE ANALYSIS OF GENETIC DIVERSITY AND SYSTEMATICS

Abstract
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.