Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing

ABSTRACT The petiole of Colocasia gigantea (Blume) Schott is an important agricultural and biological organ, which contains high dietary fiber, pyridoxine, and nicotinamide. However, available genomic resources of C. gigantea are scarce, and this restricts further genetic diversity research, linkage...

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Autores principales:	Liu,Yujing, Guo,Yu, Xing,Deke, Long,Chunlin
Lenguaje:	English
Publicado:	Instituto de Investigaciones Agropecuarias, INIA 2018
Materias:	Microsatellite markers 454 sequencing
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392018000100023
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spelling	oai:scielo:S0718-583920180001000232018-04-25Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencingLiu,YujingGuo,YuXing,DekeLong,Chunlin Microsatellite markers 454 sequencing ABSTRACT The petiole of Colocasia gigantea (Blume) Schott is an important agricultural and biological organ, which contains high dietary fiber, pyridoxine, and nicotinamide. However, available genomic resources of C. gigantea are scarce, and this restricts further genetic diversity research, linkage map construction, and marker-assisted selection in C. gigantea. A large-scale genomic DNA study of C. gigantea was conducted using the 454 sequencing technology to develop simple sequence repeats (SSRs). We identified 31 069 putative genomic C. gigantea SSRs, and 100 primers were randomly selected to validate their usefulness in 10 C. gigantea samples. The specificity of six primers yielded amplification products with expected sizes and exhibited polymorphism. The number of alleles per locus ranged from 3 to 7 alleles and the polymorphic information content (PIC) ranged from 0.561 to 0.756. The newly developed SSRs in this study should be useful tools for assessing genetic diversity, understanding population structure, and conserving and using C. gigantea effectively.info:eu-repo/semantics/openAccessInstituto de Investigaciones Agropecuarias, INIAChilean journal of agricultural research v.78 n.1 20182018-03-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392018000100023en10.4067/S0718-58392018000100023
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Microsatellite markers 454 sequencing
spellingShingle	Microsatellite markers 454 sequencing Liu,Yujing Guo,Yu Xing,Deke Long,Chunlin Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
description	ABSTRACT The petiole of Colocasia gigantea (Blume) Schott is an important agricultural and biological organ, which contains high dietary fiber, pyridoxine, and nicotinamide. However, available genomic resources of C. gigantea are scarce, and this restricts further genetic diversity research, linkage map construction, and marker-assisted selection in C. gigantea. A large-scale genomic DNA study of C. gigantea was conducted using the 454 sequencing technology to develop simple sequence repeats (SSRs). We identified 31 069 putative genomic C. gigantea SSRs, and 100 primers were randomly selected to validate their usefulness in 10 C. gigantea samples. The specificity of six primers yielded amplification products with expected sizes and exhibited polymorphism. The number of alleles per locus ranged from 3 to 7 alleles and the polymorphic information content (PIC) ranged from 0.561 to 0.756. The newly developed SSRs in this study should be useful tools for assessing genetic diversity, understanding population structure, and conserving and using C. gigantea effectively.
author	Liu,Yujing Guo,Yu Xing,Deke Long,Chunlin
author_facet	Liu,Yujing Guo,Yu Xing,Deke Long,Chunlin
author_sort	Liu,Yujing
title	Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
title_short	Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
title_full	Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
title_fullStr	Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
title_full_unstemmed	Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing
title_sort	development and characterization of genomic simple sequence repeats for colocasia gigantea (blume) schott using 454 sequencing
publisher	Instituto de Investigaciones Agropecuarias, INIA
publishDate	2018
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-58392018000100023
work_keys_str_mv	AT liuyujing developmentandcharacterizationofgenomicsimplesequencerepeatsforcolocasiagiganteablumeschottusing454sequencing AT guoyu developmentandcharacterizationofgenomicsimplesequencerepeatsforcolocasiagiganteablumeschottusing454sequencing AT xingdeke developmentandcharacterizationofgenomicsimplesequencerepeatsforcolocasiagiganteablumeschottusing454sequencing AT longchunlin developmentandcharacterizationofgenomicsimplesequencerepeatsforcolocasiagiganteablumeschottusing454sequencing
_version_	1714205374722080768

Development and characterization of genomic simple sequence repeats for Colocasia gigantea (Blume) Schott using 454 sequencing

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