Advances in Life Sciences 5(18), Print : ISSN 2278-3849, 7965-7969, 2016
Sugarcane Germplasm Database (SGDB): An Approach For Identifying Genotypes of Diversified Uses K. PRAVEEN1, M. HEMANTH KUMAR2 AND A. UMAMAHESHWARI3 1
Dept. of Genetics and Plant Breeding, S.V. Agricultural College, Tirupati Institute of Frontier Technology, Regional Agricultural Research Station, Tirupati, Andhra Pradesh 517502. 3 Dept. of Bioinformatics, SVIMS, Tirupati. email:
[email protected] ;
[email protected] 2
ABSTRACT Sugarcane Germplasm Database (SGDB) was developed for 45 descriptors on 131 germplasm accessions using MySQL 5.6 server, Dreamweaver web design tool, JAVA programming language and Apache Tomcat server to rationalize storage, retrieve, update, query and report data for multiuser environment. The information included data on the 131 genotypes with 27 Distinct, Uniform and Stable (DUS) descriptors as described in PPV & FRA, India, 18 agronomic and quality descriptors and pictures in JPeG format on the most distinctive features. Based on the characters required for diversified uses of sugarcane an exercise was made to group the 131 genotypes for the most important morphological and agronomic characters. The advance search engine on all the webpages was intended to search the genetic stocks for a combination of characters. Selection of genotypes for diversified uses such as commercial cane cultivation for cane and CCS yield, for cogeneration and for ethanol production was made easy by using this database. Key words Sugarcane Germplasm Database Sugarcane (Saccharum spp.) is an important food crop of the tropics and subtropics accounting for 62 per cent of world sugar production. With the ever increasing demand for sugar and its byproducts due to rise in population and increasing trends in per capita consumption due to improving living standards and to meet the ever present competition from other food crops, productivity of the crop per unit area has to be increased. Sugarcane is being utilized for diversified uses such as commercial cane cultivation for cane and CCS yield, for cogeneration and for ethanol production. Germplasm is the basic material for selection and improvement of sugarcane through breeding to meet the needs of the world’s rapidly rising population by producing variety with diversified uses. Selection of germplasm accessions for a combination of economically important traits becomes cumbersome when the number of accessions is more. Parental selection to make a cross for the development of more than two traits takes time in conventional method of selection. To overcome the foresaid constraints a database was constructed to rationalize storage, retrieve, manipulate, query, data report in a multiuser environment and to improve accessibility to breeding stocks. The database was utilized for selection of
the genotypes having required characteristics to incorporate in breeding programmes in ecofriendly environment.
MATERIALS AND METHODS Data recorded on 131 sugarcane genotypes (Figure 4) maintained at ARS, Perumallapalle, Tirupati for 27 DUS descriptors (as per PPV&FRA, India Guidelines, 2005) and 18 agronomic and quality characters (Figure 5) during different growth stages of the crop served as data set to build the database. The data were collected on all the ranges in each character and were recorded in alphabetical and numerical forms. Sugarcane Germplasm Database (SGDB) was developed in HPZ800 workstation environment, with 12 Intel Xeon processor, 12 GB RAM, NVidia Graphics card, 1TB Hard and Windows 8 operating system. MySQL 5.6 server, Dreamweaver CS6 web design tool, JAVA script and Apache Tomcat server 6.0 were installed in the specified workstation to develop the Sugarcane Germplasm Database (SGDB). Adobe Photoshop and Macro media flash player were installed for quality image and interactive movie hosting in SGDB. Rao et al. (2007) reported that new multipurpose cane varieties with very high fibre content was found to produce more biomass per hectare and a wide range of brix values when compared to the traditional sugarcane varieties. High fibre multipurpose cane varieties with acceptable levels of fermentable sugars would extend the supply of bagasse and contribute to fuel ethanol production. In order to support cogeneration and ethanol production there is need for developing varieties capable of high biomass with high fibre content and higher total sugars (Govindaraj, 2009). Radhamani et al. (2012) concluded that a variety meant for ethanol production should have high total and fermentable sugars in juice coupled with high cane yield and also the high fibre sugarcane clones with optimum sugar and yield could be exploited for co-generation by using the fibre and trash as well as ethanol production directly from juice. An overview of the literature revealed that the genotypes selected should be erect in stool habit, with absence of leaf hairiness, narrow to medium leaf blade width, weak adherence of leaf sheath, medium to thick internode diameter, medium to high NMC per stool, without splits on internodes, small to medium sized bud, smooth rind surface, absence of pithiness, medium to tall cane height, absence
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of flowering, single cane weight of >1.5 kg, sucrose > 18 per cent, brix >20 per cent, CCS >12 per cent, purity >85 per cent, cane yield >100 t ha-1 and CCS yield of >12 t ha-1. An exercise was made to group the 131 germplasm accessions for the most important morphological and agronomic characters using SGDB. A large number of accessions were identified for each group of important characters. They may be utilized for direct commercial cultivation or may be used as parents in hybridization programmes for improvement of a combination of characters or utilized for diversified uses such as commercial cane cultivation for cane and CCS yield, for cogeneration and for ethanol production.
RESULTS AND DISCUSSION Sugarcane Germplasm Database (SGDB) was developed for 45 descriptors (Figure 5) on 131 germplasm accessions (Figure 4) using MySQL 5.6 server, Dreamweaver web design tool, JAVA programming language and Apache Tomcat server (Figure 1). It was made user friendly by providing self explanatory command buttons for navigation through the database. Access from one form to the other and to the information contained in the forms was established using relational softwares. Provision for uploading of additional information/data/pictures was made. SGDB would enable breeders to gain autonomy in data mining and management, replacing to a certain extent the use of records and accession registers. The four main databases viz., morphological, agronomic, quality, pest and disease reaction descriptors were redesigned and regrouped under one single database, the genetic stocks. By typing the name of the descriptor in the search engine for genetic stocks on all the pages, a main menu containing the list of descriptors will be displayed. A click on the descriptor gives the variations of descriptors. By clicking on the variations of descriptors a new page containing the list of genetic stocks possessing the characters will be visualized (Figure 2). The advance search engine on all the pages was intended to search the genetic stocks for a combination of characters (Figure 3). By using these search engines 131 sugarcane accessions were classified and grouped into distinct classes suitable to diversified uses such as commercial cane cultivation for cane and CCS yield, for cogeneration and for ethanol production (Table 1). Apart from cane and CCS yields, high sucrose percentage, absence of leaf sheath hairiness, easy or medium detrashing, small to medium sized bud, absence of splits, absence of pithiness and absence of flowering are the important characters which decide the acceptance of farmers for commercial cultivation of a variety. By using the database the genotypes viz., 2003T129, 2005T16, 2005T50, 86V96, 2003T123, 95V74, 2006T36 and 2006T3 were found to possess all these characters that are considered for promotion of varieties for improving cane and CCS production. Similarly high fibre percentage, low sucrose percentage, low CCS percentage
and high cane yield are the important characters for a genotype suitable for cogeneration, pulp and paper making (Govindaraj, 2009). It was observed that the genotypes 85R186, 97R383, BO91, 93R113, 97R7, 83V288, 97R424, 2000A213, 2002V2, 94A73 and 2005T89 possess the aforesaid characters and can be considered as high biomass types useful for cogeneration, pulp and paper making. A variety suitable for production of biofuel, ethanol should have high juice extraction percentage, high cane yield, high sucrose percentage, high CCS yield, absence or sparse leaf sheath hairiness, easy or medium detrashing, small to medium sized bud, absence of pithiness and absence of flowering (Radhamani et al., 2012). By this database the genotypes viz., 2006T3, 2005T50, 93A145, 97R272, Co1148, 87A298, 2005T52 and 2004T68 can be considered for production of ethanol as they have all the characters contributing to high ethanol production. Considerable number of quality databases devoted to crops that allow access to users through GUI (Graphical User Interface) were developed during the last decade (Kumudini et al., 2013; Singh et al., 2013; Scaria et al., 2011; Aravind et al., 2011; Amar et al., 2011; Jayashree and Hoisington, 2010 and Villordon et al., 2010). Among them a few were devoted to germplasm collection and characterization. ‘Bean Genes’ is a database consisting of Phaseolus and Vigna species germplasm (http:// beangenes.cws.ndsu.nodak.edu/). The ‘Grain genes’ database stores information on genetic and taxonomic data of sugarcane, wheat, rye, barley, oats and their relatives (http://wheat.pw.Usda.gov/GG2/index.html). ‘DEBDOM’ is a database encompassing the banana diversity of Manipur (http://isbd.gov.in/debdom/). ‘InDiaMed’ is a comprehensive database of Indian Medicinal plants for diabetes (http://www.indiamed.info). The Sugarcane Germplasm Database (SGDB) developed was not made as an open access. It was meant for sugarcane crop improvement in designated research stations of ANGRAU. Databases for restricted users/for a specific institute were also developed by a number of researchers for different crops. Mundil et al. (2005) developed PBMIS, a relational database and PBDB, a menu driven application to improve the utilization and management of sugarcane germplasm at Mauritius Sugar Industry Research Institute with emphasis on the germplasm and hybridization components. A few other databases on sugarcane were also developed on similar lines (Raboin and Hont, 2001; Altoveros and Quilloy, 2002; Ruiz et al., 2004 and Hamelin et al., 2012.) The database, SGDB, can be used as a platform for the sugarcane characterization, conservation, utilization and documentation. It was developed to allow the researchers to access, mine, retrieve, update, edit, transfer and integrate data with ease and for selection fo genotypes possessing group of characteristics for diversified uses. Data security was provided and data entry is password protected. It was not made as an open access database till complete saturation of all the forms.
PRAVEEN et al., Sugarcane Germplasm Database (SGDB): An Approach For Identifying Genotypes of Diversified Uses 7967
Fig. 1. Home page
Fig. 2. Page containing the list of genetic stocks selected for a descriptor
Fig. 3. Advanced search engine page containing the list of characters used for combination selection of genetic stocks
Fig. 4. Genetic stock page depicting the number and names of sugarcane accessions of ARS, Perumallapalle
Fig. 5. Morphological, agronomic and quality descriptors page along with pictures
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Table 1. Group of genotypes for combination of economic traits using SGDB
S. No.
Combination of characters
Genotypes
Diversified uses
2003T129, 2005T16, 2005T50, 86V96, 2003T123, 95V74, 2006T36, 2006T3.
Useful for commercial cane cultivation by farmers for cane and CCS yields.
85R186, 97R383, BO91, 93R113, 97R7, 83V288, 97R424, 2000A213, 2002V2, 94A73, 2005T89.
High biomass types useful for cogeneration and paper making.
2006T3, 2005T50, 93A145, 97R272, Co1148, 87A298, 2005T52, 2004T68
Useful for ethanol production.
High yield High sucrose % High CCS yield Absence of leaf sheath hairiness 1
Easy / medium detrashing Small/ medium bud size Absence of splits Absence of pithiness Absence of flowering High fibre %
2
Low sucrose % Low CCS % High yield High juice extraction percentage High cane yield High sucrose % High CCS yield
3
Absence or sparse leaf sheath hairiness Easy/medium detrashing Small/medium bud size Absence of pithiness Absence of flowering
LITERATURE CITED Altoveros, N.C and Quilloy, R.B. 2002.Sugarcane Variety Improvement in Southeast Asia and the Pacific for Enhanced and Sustainable Productivity-Germplasm Component.IPB-CAUPLB and PHILSURIN Experiment Station.
“Breeding sugarcane for use in sugar-industrial complex”, SBI Coimbatore: 148-162. Hamelin, C., Sempere, G., Jouffe, V and Ruiz, M. 2012. TropGeneDB, the multi-tropical crop information system updated and extended.Nucleic Acids Research.1–4.
Amar, J.N., Samuel, B.T., Chongtham, R., Kalita, J.,Khanikar, C., LipeeBoruah, Khan, M.L and Sureshkumar, S.S. 2011.Documentation, identification and development of a database on bananaresources of Ne India (Musanei). Proceeding of Silver Jubilee Symposium on Bioinformatics – BTISNET in India (1986 2011), Centre for Bioinformatics, Pondicherry University.pp. 74.
Jayashree, B and Hoisington, D. 2010. Bioinformatics Tools for Crop Research and Breeding.Molecular techniques in crop improvement, Springer Science + Business Media:97-115.
Aravind, G.K.,Sushil, M.K., Usha, T.,Chatterjee, S., Asim, B.K.,Bhujangrao, B., Nagaveni and Arnab, S. 2011. Bambooinfoline: A database for North Bengal bamboos. Proceeding of Silver Jubilee Symposium onBioinformatics – BTISNET in India(1986 2011), Centre for Bioinformatics, Pondicherry University.pp. 116.
Mundil, D., Ramdoyal, K., Rivet, L., Ng See Cheong, F.M and Chintaram, E. 2005.Information Technology as a Tool to Improve the Utilisation and Management of Sugar Cane Germplasm at the MSIRI.MAS, Food and Agricultural Research Council, Reduit, Mauritius.111-118.
Govindaraj, P. 2009. Breeding varieties for cogeneration and ethanol production. ICAR International Training programme on
Kumudini, T., Rayabarapu, N., Moosa, S., Talla, V., Bhyravbhatla, B and Rao, S. 2013. InDiaMed: A comprehensive database of Indian medicinal plants for diabetes. Open access Journal, Bioinformation. 9(5):378-380.
Raboin, L.M and Hont, D.A. 2001. A sugarcane genetic database. Proceedings of the 75th Annual Congress of the South African Sugar Technologists Association, Durban, South Africa, 31 July-
PRAVEEN et al., Sugarcane Germplasm Database (SGDB): An Approach For Identifying Genotypes of Diversified Uses 7969 3 August 2001.Published as CD.
D364-D367.
Radhamani, R., Rakkiyappan, P., Kannan, R., Eyalarasan., K and Karthikeyan, K. 2012. Ethanol Production of Some Promising Commercial Sugarcane Varieties for Ecofriendly use of Ethanol as an Automobile Fuel. International Journal of Science & Emerging Technologies. 4(5): 18-180.
Scaria, R., Jose, E., Shidhi, P. R and Keshavachandran, R. 2011. MEDBASE: A Database on Medicinal Plants in Kerala. Proceeding of Silver Jubilee Symposium on Bioinformatics – BTISNET in India (1986 2011), Centre for Bioinformatics, Pondicherry University. pp:51.
Rao, P.S., Davis, H and Simpson, C. 2007. New sugarcane varieties and year round sugar and ethanol production with bagasse based cogeneration in Barbados and Guyana. XXVI Congress, International Society of Sugarcane Technologists, ICC, Durban, South Africa.1169-1176.
Singh, W.A., Gopalrao, S.B., Gourshyam, T., Handique, P.J and Devi, H.S. 2013.DEBDOM: Database exploring banana diversity of Manipur. Open access Journal, Bioinformation. 9(5):270-273.
Ruiz, M., Rouard, M., Raboin, L.M., Lartaud, M., Lagoda, P and Courtois, B. 2004.TropGENE-DB, a multi-tropical crop information system. Database issue Nucleic Acids Research. 32:
Villordon, A., Gichuki, S., Kulembeka, H., Jeremiah, S.C and LaBonte, D. 2010.Development of a Web-Accessible GIS database as a tool for SweetpotatoGermplasm Collection activities in East Africa. Horticultural Science. 45:153.
Received on 16-09-2016
Accepted on 22-09-2016
