in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)

Microsatellites are an important class of molecular markers having wide application in genetic research. Development of microsatellites using conventional methods is laborious and expensive. Alternatively, in silicoapproach can be followed to detect simple sequence repeats (SSRs) from expressed sequ...

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Autores principales:	V Radhika, C Aswath, D C Lakshman Reddy, Shweta ., A Bhardwaj
Formato:	article
Lenguaje:	EN
Publicado:	Society for Promotion of Horticulture - Indian Institute of Horticultural Research 2011
Materias:	anthurium araceae expressed sequence tag (est) microsatellite simple sequence repeat (ssr) Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/96ddbf0a24184fe398d6d442f06f46ed
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id	oai:doaj.org-article:96ddbf0a24184fe398d6d442f06f46ed
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spelling	oai:doaj.org-article:96ddbf0a24184fe398d6d442f06f46ed2021-12-02T11:18:49Zin Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)0973-354X2582-4899https://doaj.org/article/96ddbf0a24184fe398d6d442f06f46ed2011-06-01T00:00:00Zhttps://jhs.iihr.res.in/index.php/jhs/article/view/439https://doaj.org/toc/0973-354Xhttps://doaj.org/toc/2582-4899Microsatellites are an important class of molecular markers having wide application in genetic research. Development of microsatellites using conventional methods is laborious and expensive. Alternatively, in silicoapproach can be followed to detect simple sequence repeats (SSRs) from expressed sequence tags (ESTs) available in public biological databases. The in silico developed EST-SSRs have been found to be transferrable across species and genera. A study was undertaken to mine simple sequence repeats (SSRs) from the expressed sequence tags (ESTs) of arum lily, Zantedeschia aethiopica, belongs to the family Araceae. A total of 4283 ESTs of Zantedeschia aethiopica, downloaded from dbEST of NCBI, were pre-processed and subjected to clustering and assembly. In all, 1968 clusters (800 contigs and 1168 singletons) were obtained, resulting in 54 % reduction in ESTs. In addition, 1936 SSRs were obtained, which included 617 mono, 101 di-, 201 tri-, 80 tetra-, 23 penta- and 898 hexa-nucleotide repeats. The plant has an abundance of 0.70 SSRs/ kb. We designed 1091 primers for these SSRs. A few in silico designed SSR primers were tested for polymorphism in Anthurium, belonging to the Araceae family, resulting in 40% amplification success.V RadhikaC AswathD C Lakshman ReddyShweta .A BhardwajSociety for Promotion of Horticulture - Indian Institute of Horticultural Researcharticleanthuriumaraceaeexpressed sequence tag (est)microsatellitesimple sequence repeat (ssr)Plant cultureSB1-1110ENJournal of Horticultural Sciences, Vol 6, Iss 1, Pp 37-40 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	anthurium araceae expressed sequence tag (est) microsatellite simple sequence repeat (ssr) Plant culture SB1-1110
spellingShingle	anthurium araceae expressed sequence tag (est) microsatellite simple sequence repeat (ssr) Plant culture SB1-1110 V Radhika C Aswath D C Lakshman Reddy Shweta . A Bhardwaj in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
description	Microsatellites are an important class of molecular markers having wide application in genetic research. Development of microsatellites using conventional methods is laborious and expensive. Alternatively, in silicoapproach can be followed to detect simple sequence repeats (SSRs) from expressed sequence tags (ESTs) available in public biological databases. The in silico developed EST-SSRs have been found to be transferrable across species and genera. A study was undertaken to mine simple sequence repeats (SSRs) from the expressed sequence tags (ESTs) of arum lily, Zantedeschia aethiopica, belongs to the family Araceae. A total of 4283 ESTs of Zantedeschia aethiopica, downloaded from dbEST of NCBI, were pre-processed and subjected to clustering and assembly. In all, 1968 clusters (800 contigs and 1168 singletons) were obtained, resulting in 54 % reduction in ESTs. In addition, 1936 SSRs were obtained, which included 617 mono, 101 di-, 201 tri-, 80 tetra-, 23 penta- and 898 hexa-nucleotide repeats. The plant has an abundance of 0.70 SSRs/ kb. We designed 1091 primers for these SSRs. A few in silico designed SSR primers were tested for polymorphism in Anthurium, belonging to the Araceae family, resulting in 40% amplification success.
format	article
author	V Radhika C Aswath D C Lakshman Reddy Shweta . A Bhardwaj
author_facet	V Radhika C Aswath D C Lakshman Reddy Shweta . A Bhardwaj
author_sort	V Radhika
title	in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
title_short	in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
title_full	in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
title_fullStr	in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
title_full_unstemmed	in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)
title_sort	in silico microsatellite development in arum lily (zantedeschia aethiopica)
publisher	Society for Promotion of Horticulture - Indian Institute of Horticultural Research
publishDate	2011
url	https://doaj.org/article/96ddbf0a24184fe398d6d442f06f46ed
work_keys_str_mv	AT vradhika insilicomicrosatellitedevelopmentinarumlilyzantedeschiaaethiopica AT caswath insilicomicrosatellitedevelopmentinarumlilyzantedeschiaaethiopica AT dclakshmanreddy insilicomicrosatellitedevelopmentinarumlilyzantedeschiaaethiopica AT shweta insilicomicrosatellitedevelopmentinarumlilyzantedeschiaaethiopica AT abhardwaj insilicomicrosatellitedevelopmentinarumlilyzantedeschiaaethiopica
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in Silico Microsatellite Development in Arum Lily (Zantedeschia aethiopica)

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