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Utilization of COI Marker for Species Identification and Population Delineation of White Shrimp in the Demak Waters, Indonesia

ILMU KELAUTAN: Indonesian Journal of Marine Sciences · Vol. 31 No. 1 (2026) · hlm. 37–48

DOI
10.14710/ik.ijms.31.1.37-48
ISSN
2406-7598, 0853-7291
Terbit
2026-03-01
Penerbit
Marine Science Department Diponegoro University
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-sa/4.0

Abstrak

White shrimp is one of the largest artisanal capture fisheries commodities in Demak. The utilization of these shrimps often overlooks their species category as they are mostly white in appearance. Growing trend of shrimp fishing may affect shrimp management due to population declination to the genetic level since the genetic data are insufficient. Hence, we aim to identify and study the genetic diversity of white shrimp caught in Demak Waters to provide an overview as a reference for fishery improvement project. A random purposive sampling method was used to collect a total of 90 white shrimp specimens from four fishing grounds (Babalan, Gojoyo, Menco, and Seklenting) in the Demak Waters. Specimens were extracted using Chelex 10%, amplified using PCR, and sequenced by the Sanger method based on the mtDNA COI gene. This research revealed the presence of five species of white shrimp: Penaeus merguiensis, Fenneropenaeus penicillatus, Penaeus vannamei, Metapenaeus brevicornis, and Metapenaeus ensis. The genetic diversity studies were continued using the Penaeus merguiensis species only. The results showed 17 haplotypes with a genetic diversity (Hd) of 0.6936 and a nucleotide diversity of 0.00108, which express moderate genetic diversity. Population analysis using Analysis of Molecular Variance (AMOVA) indicated a non-significant difference between the four study populations (panmictic population) with an FST value of 0.00756 (P-value < 0.05). Based on these results, an adequate management of stock is important. For instance, an open-closed season is needed in order to sustain and reduce capture pressure on the white shrimp population in Demak waters.

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  • Diponegoro University
  • University of the Ryukyus
  • University of Bangka Belitung
  • Universitas PGRI Ronggolawe
  • Artha Wacana Christian University
  • Tropical Biosphere Research Center, University of the Ryukyus
  • University of Tasmania
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Rekan penulisOrganisasiArtikel bersama
Ambariyanto AmbariyantoDiponegoro University7
Nining NursalimDiponegoro University6
Agus SabdonoDiponegoro University5
Elis IndrayantiDiponegoro University4
Munasik MunasikDiponegoro University4
Subagiyo SubagiyoDiponegoro University3
Ni Kadek Dita CahyaniDiponegoro University3
Ita WidowatiDiponegoro University3
Umbu Domu WoraDiponegoro University3
Fanny Iriany GinzelArtha Wacana Christian University3
Norma AfiatiDiponegoro University2
Mu’alimah HudatwiUniversity of Bangka Belitung2
Michio HidakaUniversity of the Ryukyus2
Dwi HaryantiDiponegoro University2
Marita Ika JoesidawatiUniversitas PGRI Ronggolawe2
Chrisna Adhi SuryonoDiponegoro University2
EKA MAYA KURNIASIHUniversity of the Ryukyus2
Retno HartatiDiponegoro University2
Dwi HaryantiDiponegoro University1
Mila Amelia Nur AzizahDiponegoro University1
Ranjeet BhagooliDiponegoro University1
Mea PradnawatiDiponegoro University1
Raden ArioDiponegoro University1
Suryono SuryonoDiponegoro University1
Ibnu PratiktoDiponegoro University1
Nur Taufiq-SpjDiponegoro University1
Syahrial Varrel CanavaroDiponegoro University1
Tiara AnggitaDiponegoro University1
Bayu Kreshna Adhitya SumartoTropical Biosphere Research Center, University of the Ryukyus1
Justin CullenUniversity of Tasmania1
Muhammad DailamiUniversity of Brawijaya1
Ni Putu Dian PertiwiUniversitas Pendidikan Ganesha1
Andrianus SembiringAfiliasi tidak diketahui1
Aji Wahyu AnggoroAfiliasi tidak diketahui1

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Sumber metadata: OAI-PMH (metadata jurnal) http://ejournal.undip.ac.id/index.php/ijms/oai, pertama di-harvest 8 Nov 2026, terakhir terlihat 8 Nov 2026.
Metadata asli (oai_dc) 
<oai_dc:dc xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/  http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
	<dc:title xml:lang="en-US">Utilization of COI Marker for Species Identification and Population Delineation of White Shrimp in the Demak Waters, Indonesia</dc:title>
	<dc:creator>Karosekali, Jasiel Junior</dc:creator>
	<dc:creator>Kholilah, Nenik</dc:creator>
	<dc:creator>Syam, Almay Atsiil Harits</dc:creator>
	<dc:creator>Subagiyo, Subagiyo</dc:creator>
	<dc:creator>Wijayanti, Diah Permata</dc:creator>
	<dc:creator>Bachtiar, Muggi</dc:creator>
	<dc:subject xml:lang="en-US">COI; Demak Waters; DNA Barcoding; Haplotypes; White Shrimp</dc:subject>
	<dc:description xml:lang="en-US">White shrimp is one of the largest artisanal capture fisheries commodities in Demak. The utilization of these shrimps often overlooks their species category as they are mostly white in appearance. Growing trend of shrimp fishing may affect shrimp management due to population declination to the genetic level since the genetic data are insufficient. Hence, we aim to identify and study the genetic diversity of white shrimp caught in Demak Waters to provide an overview as a reference for fishery improvement project. A random purposive sampling method was used to collect a total of 90 white shrimp specimens from four fishing grounds (Babalan, Gojoyo, Menco, and Seklenting) in the Demak Waters. Specimens were extracted using Chelex 10%, amplified using PCR, and sequenced by the Sanger method based on the mtDNA COI gene. This research revealed the presence of five species of white shrimp: Penaeus merguiensis, Fenneropenaeus penicillatus, Penaeus vannamei, Metapenaeus brevicornis, and Metapenaeus ensis. The genetic diversity studies were continued using the Penaeus merguiensis species only. The results showed 17 haplotypes with a genetic diversity (Hd) of 0.6936 and a nucleotide diversity of 0.00108, which express moderate genetic diversity. Population analysis using Analysis of Molecular Variance (AMOVA) indicated a non-significant difference between the four study populations (panmictic population) with an FST value of 0.00756 (P-value &lt; 0.05). Based on these results, an adequate management of stock is important. For instance, an open-closed season is needed in order to sustain and reduce capture pressure on the white shrimp population in Demak waters.</dc:description>
	<dc:publisher xml:lang="en-US">Marine Science Department Diponegoro University</dc:publisher>
	<dc:date>2026-03-01</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:type xml:lang="en-US"></dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://ejournal.undip.ac.id/index.php/ijms/article/view/70764</dc:identifier>
	<dc:identifier>10.14710/ik.ijms.31.1.37-48</dc:identifier>
	<dc:source xml:lang="en-US">ILMU KELAUTAN: Indonesian Journal of Marine Sciences; Vol 31, No 1 (2026): Ilmu Kelautan; 37-48</dc:source>
	<dc:source>2406-7598</dc:source>
	<dc:source>0853-7291</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://ejournal.undip.ac.id/index.php/ijms/article/view/70764/pdf</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2026 ILMU KELAUTAN: Indonesian Journal of Marine Sciences</dc:rights>
	<dc:rights xml:lang="en-US">https://creativecommons.org/licenses/by-sa/4.0</dc:rights>
</oai_dc:dc>