A short review on the identification of ABCDE genes in monocot plants

Soorya S, Swapna TS, Sabu KK. 2022. A short review on the identification of ABCDE genes in monocot plants. Journal of Tropical Life Science 12(3): 423 – 433.

https://doi.org/10.11594/jtls.12.03.15

One of the most important divisions in the plant kingdom is the monocotyledon division of angiosperms. More than 60,000 monocot spp. have been identified, the majority of which are economically important, such as the Poaceae, Orchidaceae, Arecaceae, Liliaceae, and certain other families. The involvement of the ABCDE model of floral organ determination during flower development is a growing area of research in the field of molecular biology due to the diversity in the floral morphology of monocots. The MADS-box gene family is a large molecular transcript family that helps identifies specific proteins involved in floral development. It is classified into several classes based on its function. The review aimed to evaluate the significance of ABCDE genes for floral development and subsequent organ identification, which have been discovered in a range of monocot plants, as well as the functions of these genes in determining the sex of dioecious plants. We sought to summarise the MADS-box gene responsible for flower initiation and floral whorl differentiation reported in economically valuable monocotyledonous plants.

Genetic diversity and structure revealed by genomic microsatellite markers in Centella asiatica (L.) Urb., a plant with medicinal potential

 Abstract

Background: Around the world, medicinal plants are utilised for various purposes. Centella asiatica is one of the important medicinal plants widely used in many medicinal systems. Nevertheless, analysis of the genetic diversity would pave the way for its most suitable utilisation.

Methods and results: The present study analyses the genetic diversity and structure of eighty C. asiatica accessions collected from the southern states of India, using ten genomic microsatellite markers. The mean Nei’s gene diversity (0.46) indicates considerable genetic diversity. Analysis of molecular variance (82.48%) exhibited significant genetic variance between samples within the population. The cluster analysis brought out the structure of the analysed populations as three subpopulations based on the genetic differentiation.

Conclusions: The study showed significant intra-population variation, predominant inbreeding and population differentiation in C. asiatica. The findings will help better understanding of the genetic structure and gene pool of the plant.

Full article link: https://rdcu.be/cAvFI

Genetic resources of Asian Palmyrah palm (Borassus flabellifer L.): A comprehensive review on diversity, characterization and utilization

Asian palmyrah palm (Borassus flabellifer L.) is a multipurpose, economically important tree widely distributed in the Indian subcontinent and Southeast Asia. The multifaceted uses (~800 uses) of the tree as food, wood and medicine make it a viable industrial crop. However, the dioecious nature of the tree coupled with long juvenile phase (12–20 years to initiate flowering), long stature and considerable variations in the productivity of male and female trees necessitates the application of new biotechnological tools for crop improvement. This review provides comprehensive information on the extent of genetic diversity of the crop, problems associated with palmyrah cultivation along with its multifaceted application and research gaps to be addressed for the effective utilization and conservation of palmyrah palm genetic resources.

Siju S. and K. K. Sabu. 2021. Genetic resources of Asian Palmyrah palm (Borassus flabellifer L.): A comprehensive review on diversity, characterization and utilization. Plant Genetic Resources. Published online: 08 January 2021. https://doi.org/10.1017/S1479262120000477

Sakthipriya M., S. S. Vishnu, S. Sujith, P. Rajeesh Kumar, and K. K. Sabu. 2018. Analysis of genetic diversity of Centella asiatica using SSR markers. International Journal of Applied Sciences and Biotechnology Vol 6(2): 103-109. http://dx.doi.org/10.3126/ijasbt.v6i2.19583

Abstract
Genetic diversity represents the heritable variation within and between populations of organisms. A better understanding of genetic diversity and its distribution is essential for its conservation and use. In this study the genetic diversity analysis was performed in 30 accessions of Centella asiatica (L.) Urb. using 10 SSR markers. C. asiatica is a tropical medicinal plant from Apiaceae family native to Southeast Asian countries. It is among the top herbs in the category of anti-aging and CNS drugs used worldwide. The whole plant and aerial parts are used widely in traditional and alternative medicines due to its ample pharmacological activities. The molecular screening through microsatellite markers showed low polymorphism (0.019) between the samples analyzed. Further studies, including the effect of environmental factors, genetic composition or possibility of inbreeding, are required to analyze the probable reason for the low variability exists in the species.

Int. J. Appl. Sci. Biotechnol. Vol 6(2): 103-109

Keywords: Centella asiatica; genetic diversity; SSR; microsatellites; medicinal plant

Assessment of genomic diversity in cardamom by flow cytometry, cytological studies and ISSR analysis

Intraspecific variations in cardamom (Elettaria cardamomum Maton): Assessment of genomic diversity by flow cytometry, cytological studies and ISSR analysis

Article in SpringerPlus 5(1) · September 2016
DOI: 10.1186/s40064-016-3226-x

Background
The main goal of the work was to analyse intraspecific variation in Elettaria cardamomum Maton (cardamom) using genome size, cytological studies and molecular marker data. Nuclear DNA content and molecular marker details furnish data on genome size and genetic diversity respectively among the studied accessions and both complement each other for evolutionary and taxonomic studies.

Results
The relative 2C genome size and total number of base pairs of cardamom was determined through flow cytometric analysis using propidium iodide staining. The nuclear DNA content was estimated in various sections of the species representing individuals from wild and cultivar genotypes following Zea mays L. CE-777 (2C = 5.43 pg) as internal reference standard. Chromosome number from growing root tip was examined following standard protocols. Twenty-six ISSR primers that generated polymorphic bands were used for genetic diversity analysis of the thirty accessions of cardamom. Estimated nuclear 2C DNA content ranged from 2.57 to 3.22 pg demonstrating 1.25-fold variation. The mean amount of 2C nuclear DNA of the cardamom was calculated as 2.87 pg which is equivalent of 2806 Mbp as the diploid genome size. The chromosome number was found to be 2n = 48. Among the thirty accessions of cardamom studied using ISSR markers, C53 (feral from Bonacaud) showed a very prominent level of genetic diversity and was lowest for C96 (Avinash-I, a released variety from Indian Institute of Spices Research, Kozhikode).

Conclusion
These analyses revealed the existence of genetic variability within the studied cardamom accessions. The plant specimens also differed significantly in their genome size. However, the genetic variability parameters did not show any correlation with genome size.

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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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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).

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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