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Screening of polymorphic microsatellite markers from the whole-genome sequences of nipa (Nypa fruticans Wurmb.)

Published online by Cambridge University Press:  31 May 2021

Junaldo A. Mantiquilla ,
Merlene E. Elumba ,
Meng-Shin Shiao  and
Yu-Chung Chiang Open the ORCID record for Yu-Chung Chiang [Opens in a new window]
Junaldo A. Mantiquilla
Affiliation:
Department of Biological Sciences, National Sun Yat-sen University, No. 70 Lienhai Road, Kaohsiung80424, Taiwan Department of Biological Sciences and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Mintal, Davao City8022, Philippines
Merlene E. Elumba
Affiliation:
Department of Biological Sciences and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Mintal, Davao City8022, Philippines
Meng-Shin Shiao
Affiliation:
Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok10400, Thailand
Yu-Chung Chiang*
Affiliation:
Department of Biological Sciences, National Sun Yat-sen University, No. 70 Lienhai Road, Kaohsiung80424, Taiwan Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung807, Taiwan
*
*Corresponding author. E-mail: yuchung@mail.nsysu.edu.tw
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Abstract

Nipa (Nypa fruticans Wurmb.), aside from being part of the mangrove forest ecosystem that has been under assault at an alarming rate, lacks information on its genetic variation at the population level for conservation planning purposes. Microsatellites, or simple sequence repeats (SSRs), are molecular markers employed to detect genetic variations in population studies. Here, the primers for this palm were identified through whole-genome sequencing using the Illumina® Sequencing Technology platform. Over half (52.4%) of SSRs consisted of mononucleotide repeats, whereas the remainder mostly consisted of dinucleotide (22.7%) and trinucleotide (22.4%) repeats. The frequencies of longer repeats (tetranucleotides, pentanucleotides and hexanucleotides) were exceptionally rare (2.5%). At least 18 out of 75 genomic loci were polymorphic, based on 37 randomly selected samples assayed for screening. Polymorphic loci (P) reached a mean of 72% across the Indo-West Pacific region. Estimates of genetic diversity showed a lower mean observed heterozygosity (Ho) (0.195) than expected (He) (0.316), suggesting evolutionary forces were acting across nipa populations. The fixation (F) index (0.388) supported this result, which indicates considerable genetic differentiation among populations in the region. An average of 2.111 alleles (Na) was obtained. In conclusion, these microsatellite markers are promising tools for genetic evaluation of nipa populations to facilitate characterization of this species in its distribution range.

Keywords

genetic diversitymicrosatellitesNypa fruticans Wurmbpolymorphic loci
Type
Short Communication
Information
Plant Genetic Resources , Volume 19 , Issue 4 , August 2021 , pp. 316 - 319
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

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