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Genome-wide SSR marker development in oil palm by Illumina HiSeq for parental selection

Published online by Cambridge University Press:  22 April 2015

Puntaree Taeprayoon ,
Patcharin Tanya ,
Yang Jae Kang ,
Anek Limsrivilai ,
Suk-Ha Lee  and
Peerasak Srinives
Puntaree Taeprayoon
Affiliation:
Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom73140, Thailand
Patcharin Tanya*
Affiliation:
Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom73140, Thailand
Yang Jae Kang
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul151-921, Republic of Korea
Anek Limsrivilai
Affiliation:
Golden Tenera Limited Partnership, Krabi81000, Thailand
Suk-Ha Lee*
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul151-921, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul151-921, Republic of Korea
Peerasak Srinives
Affiliation:
Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom73140, Thailand
*
*Corresponding authors. E-mail: altanya55@yahoo.com; sukhalee@snu.ac.kr
*Corresponding authors. E-mail: altanya55@yahoo.com; sukhalee@snu.ac.kr
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Abstract

Next-generation sequencing is a new technique for plant genome sequencing at a large scale that is faster and cheaper than previous sequencing technologies. The present work reports the development of new polymorphic simple sequence repeat (SSR) markers in oil palm (Elaeis guineensis Jacq.) using Illumina HiSeq sequencing data. More than 39 Gb (total 39,086,646,904 bases) was generated from the selected oil palm clone, D4. After de novo assembly, a total of 130,840 potential SSRs were identified. For SSR validation, 144 out of 762 SSR primer pairs were designed, including tri-nucleotide motifs, from the D4 contigs. Using 11 lines from three different clones of oil palm, 61 SSR primers revealed polymorphic alleles and high average polymorphic information content (PIC) values. Cluster analysis separated all oil palm plants into three clusters: clones A, B and C. These identified genome-wide SSR markers will enrich current genomic resources of the oil palm crop.

Keywords

Elaeis guineensisnext-generation sequencingoil palmSSR
Type
Short Communication
Information
Plant Genetic Resources , Volume 14 , Issue 2 , June 2016 , pp. 157 - 160
Copyright
Copyright © NIAB 2015 

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