Genetic relationship of milkfish (Chanos chanos) from Indonesia, the Philippines and Taiwan using mitochondrial cytochrome b sequences

Adiputra, Yudha Trinoegraha; Hsu, Te‐Hua; Gwo, Jin‐Chywan

doi:10.1111/j.1439-0426.2010.01629.x

Cited by 7 publications

(4 citation statements)

References 13 publications

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“…Similar milkfish stocks in the Philippines and in West Java, Indonesia, earlier reported by Adiputra, Hsu, and Gwo (), where milkfish stocks from Taiwan, Indonesia and the Philippines were compared and based on mitochondrial cytochrome b sequence variation, two clades of milkfish populations were noted to exist. The first clade had stocks from representative sites in Taiwan, Indonesia and the Philippines while the other clade comprised only of Indonesian stocks.…”

Section: Discussionsupporting

confidence: 73%

“…Adiputra et al. () hypothesized that ocean currents, depending on the direction, can either enhance genetic similarities/differences among Indonesian milkfish stocks from those coming from the Philippines and Taiwan. In the present study, the Indonesian stock came from West Java and the assumption is that the hatchery where the fry were produced were from breeders on‐grown from wild juveniles collected proximal to or in the Java Sea.…”

Section: Discussionmentioning

confidence: 99%

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Genetic assessment of milkfish (Chanos chanos Forsskal) stocks based on novel short tandem repeats for marker-aided broodstock management

et al. 2018

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Milkfish hatchery broodstock are either from on‐grown wild‐caught or hatchery‐produced fry/juveniles. To determine if a marker‐assisted management scheme can be formulated for improved milkfish hatchery production, milkfish stocks were genetically characterized using nine novel short tandem repeats or microsatellites. Eight wild‐bred Philippine stocks (CLA, CUR, CAM, SIH, SBH‐I1, HH, PAL and ZH‐P0), four hatchery‐bred stocks (SBH‐I2, SBH‐D, BoH and ZH‐F1), two farm stocks of known mixed lineages (SPH and BDH) and one Indonesian hatchery‐bred stock (WJH) were assessed. WJH was included since milkfish fingerlings from Indonesia reared in Philippine farms could be developed into future broodstock. Mean allelic richness (Ar) was highest in wild‐bred stocks (9.5) and lowest in hatchery‐bred spawners (9.1). Mean expected heterozygosities (He) were relatively similar in all stocks with wild‐bred stocks slightly higher (0.67) than the others. An analysis of molecular variance indicated significant yet low genetic differentiation among stocks (FST = 0.013; p = .000) where variation (98.6%) was explained by intra‐stock differences. In some of the domesticated stocks, reductions in mean allelic richness were observed in first generation hatchery broodstock (e.g. ZH‐F1; Ar = 8.3), compared with their founder stock (e.g. ZH‐P0; Ar = 9.4). The Indonesian stock was similar to local wild‐bred stocks based on genetic variability indices; thus, it might be likely that the local stocks’ fitness traits could be comparable with the imported milkfish stock which has been perceived to be better. The quality of locally available farmed milkfish and prospects of formulating a broodstock management scheme for the production of good quality milkfish seedstock are herewith discussed.

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Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Genetic assessment of milkfish (Chanos chanos Forsskal) stocks based on novel short tandem repeats for marker-aided broodstock management

et al. 2018

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“…Milkfish genetic variations have been previously investigated in the Pacific Ocean from the Philippines to Hawaii using isozymes and PCR-RFLP (Winans, 1980;Ravago-Gotanco & Juinio-Meñez, 2004). Other studies utilized, namely, the use of: (a) mitochondrial cytochrome b sequences to determine the genetic relationships among milkfish from Indonesia, the Philippines, and Taiwan (Adiputra et al, 2011); (b) amplified fragment length polymorphism (AFLP) in Indonesian stocks (Adiputra et al, 2012); (c) microsatellite markers of milkfish in the Philippines which were characterized using novel short tandem repeats (Santos et al, 2015;Romana-Eguia et al, 2018); (d) the mtDNA control region and cytochrome b genes in the Philippines and Indonesia (Santos et al, 2019); and (e) ATPase 6/8 genes in India (SriHari et al, 2019). This research is the first attempt to compare the genetic diversity of milkfish in Vietnam and also is the first study to use the COI marker for genetic assessment in milkfish.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Chanos Chanos (Forsskål, 1775) from Natural Populations in Vietnam

Trang

Ngân

et al. 2022

vjas

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The genetic diversity of five natural populations of milkfish (Chanos chanos) collected in Nghe An, Quang Binh, Binh Dinh, Phu Yen, Khanh Hoa provinces in Vietnam was examined using COI gene sequence analysis. Twelve haplotypes were noted from a total of 50 sequences along with 12 variable sites and 6 parsimony informative sites. The Quang Binh milkfish population had the highest haplotype (0.889 ± 0.060) and nucleotide diversities (0.00301 ± 0.00049). Overall, haplotype and nucleotide diversities were 0.804 ± 0.036 and 0.00212 ± 0.00026, respectively. Genetic differentiation (FST) was high between the milkfish populations of Nghe An – Quang Binh (0.21744) and Nghe An - Phu Yen (0.26215). Haplotype network analysis indicated that milkfish populations shared common haplotypes and each population had its own private haplotypes. Population structure and demographic expansion were not evident for all populations except for Quang Binh. This is the first principal endeavor to understand genetic information of milkfish in Vietnam, thereby providing information for scientists, managers, and the general public to establish timely strategies to explore, protect, and develop milkfish genetic resources in the future.

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“…Catfishes of these genera are consumed by humans and have a high economic value when prepared as smoked fish. The research on cytochrome b in Indonesia has been carried out on Chanos chanos (Adiputra et al 2011), Puntius cf. binotatus (Karlina et al 2016), Osphronemus goramy (Nugroho et al 2019), Bagridae, Pangasiidae and Ariidae (Megarani et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene

et al. 2020

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Abstract. Elvyra R, Solihin DD, Affandi R, Junior MZ, Suhendra M. 2020. Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene. Biodiversitas 21: 3539-3546. The study of molecular characteristics and phylogenetic relationships among silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) is very scarce. Existing data are mostly based on morphological characters. Genetic markers among Kryptopterus, Ompok, and Phalacronotus can be analyzed by exploring the nucleotide and amino acid sequences of the mitochondrial cytochrome b gene region (906 base pairs). This study aims to identify molecular characteristics and phylogenetic relationships of silurid catfishes from the Kampar River based on the cytochrome b gene. This research examined 14 silurids of four species from three genera in the Kampar River of Indonesia. Molecular phylogenetic trees were constructed using the neighbor-joining method. This study revealed that three amino acid sites can be used as specific genetic markers for characterizing Kryptopterus limpok. They are E (glutamic acid) at site 123, V (valine) at site 155, and M (methionine) at site 156. Two amino acid sites can be used as specific genetic markers of Ompok spp., A (alanine) at site 201 for O. hypophthalmus, and S (serine) at site 282 for O. eugeneiatus. Two amino acid sites, I (isoleucine) at site 197 and L (leucine) at site 284, can be used to identify Phalacronotus apogon from the Kampar River, Indonesia. The phylogram results based on genetic distance (p-distance) from nucleotide cytochrome b sequences generally showed that intraspecies of K. limpok, O. eugeneiatus, O. hypophthalmus and P. apogon from the Kampar River formed relationship groups within each species supported by high bootstrap values. Additionally, based on genetic distance, K. limpok data from the Kampar River samples and GenBank formed one relationship group within species of K. limpok with a high bootstrap value. This study proves that cytochrome b gene can be used to identify molecular characteristics and phylogenetic relationships of K. limpok, O. eugeneiatus, O. hypophthalmus, and P. apogon from the Kampar River, Indonesia.

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Genetic relationship of milkfish (Chanos chanos) from Indonesia, the Philippines and Taiwan using mitochondrial cytochrome b sequences

Cited by 7 publications

References 13 publications

Genetic assessment of milkfish (Chanos chanos Forsskal) stocks based on novel short tandem repeats for marker-aided broodstock management

Genetic assessment of milkfish (Chanos chanos Forsskal) stocks based on novel short tandem repeats for marker-aided broodstock management

Genetic Diversity of Chanos Chanos (Forsskål, 1775) from Natural Populations in Vietnam

Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene

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