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Fulltext A preliminary study of genetic differentiation of two important cultured oyster species, Crassostrea iredalei and C. belcheri in Malaysia based on cytochrome oxidase I (COI) gene

Suzana M., Siti Azizah M. N., Devakie, M. N.

Buletin Persatuan Genetik Malaysia, 2009;14(1):14-17.
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This paper reports on a preliminary genetic investigation of two commercially cultured oyster species, white and black scar oysters, Crassostrea belcheri and C. iredalei, respectively. A total
of 68 individuals from three different areas in Malaysia namely a C. belcheri sample from Semporna (Sabah) and two populations of C. iredalei from Trai (Sabah) and Setiu (Terengganu) were
collected and analysed based on sequence analysis of cytochrome oxidase subunit I (COI). Alignment of COI gene was done using Alignment Explorer/CLUSTAL in Mega4.1. Genetic distances
within and between populations were calculated using Kimura 2-parameter. Phylogenetic dendograms were generated by Neighbour-Joining (NJ) and Maximum Parsimony (MP) methods.
The ingroup taxa were divided into two main clusters separating C. iredalei and C. belcheri with 99% bootstrap value. The two C. iredalei populations were homogeneous suggesting high
connectivity in the South China Sea for this species. The common central haplotype in the minimum spanning networks programme is believed to be the ancestral variant for the two species. The
findings from this study provides important baseline data for the aquaculture, management and monitoring of cultured populations of the oyster species.
Preliminary studies on cryopreservation of snakehead (Channa striata) embryos

Mohd Sharifuddin M, Siti Azizah MN

Cryobiology, 2014 Aug;69(1):1-9.
PMID: 24726775 DOI: 10.1016/j.cryobiol.2014.04.001

This paper reports the findings of the ongoing studies on cryopreservation of the snakehead, Channa striata embryos. The specific objective of this study was to collect data on the sensitivity of C. striata embryo hatching rate to low temperatures at two different developmental stages in the presence of four different cryoprotectants. Embryos at morula and heartbeat stages were selected and incubated in 1M dimethyl sulfoxide (Me2SO), 1M ethylene glycol (EG), 1M methanol (MeOH) and 0.1M sucrose solutions at different temperatures for a period of time. Embryos were kept at 24 °C (control), 15 °C, 4 °C and -2 °C for 5 min, 1h and 3h. Following these treatments, the embryos were then transferred into a 24 °C water bath until hatch to evaluate the hatching rate. The results showed that there was a significant decrease of hatching rate in both developmental stages following exposure to 4 °C and -2 °C at 1h and 3h exposure in each treatment. Heartbeat stage was more tolerant against chilling at -2 °C for 3h exposure in Me2SO followed by MeOH, sucrose and EG. Further studies will be conducted to find the best method to preserve embryos for long term storage.
Isolation of microsatellites in the bighead catfish, Clarias macrocephalus and cross-amplification in selected Clarias species

Nazia AK, Siti Azizah MN

Mol Biol Rep, 2014 Mar;41(3):1207-13.
PMID: 24381108 DOI: 10.1007/s11033-013-2965-9

The present study documents the isolation of eight polymorphic microsatellite markers from the bighead catfish, Clarias macrocephalus and cross-amplification in two other catfish species. The number of alleles per locus in C. macrocephalus ranged from 2 to 21. The most polymorphic locus was NCm-G12 with 21 alleles while the least polymorphic locus was NCm-H2 with only two alleles. Locus NCm-F8 significantly deviated from Hardy-Weinberg equilibrium (P value <0.05) after Bonferroni correction. Linkage disequilibrium was non-significant in all loci comparisons. The observed and expected heterozygosities varied from 0.033 to 0.967 and from 0.033 to 0.942, respectively. Mean polymorphic information content for the eight loci was 0.765. Cross-amplification was successfully performed with two other catfish species, C. batrachus and C. meladerma for all eight loci. Locus NCm-D8 was monomorphic in both species while NCm-F8 was monomorphic only in C. batrachus. These newly developed markers would be useful for better management and conservation of the economically important C. macrocephalus species.
Fulltext Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene

Chee SY, Devakie MN, Siti Azizah MN

Genet. Mol. Res., 2011;10(2):1237-44.
PMID: 21732288 DOI: 10.4238/vol10-2gmr1104

Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T. granosa to distinguish it from other related species found in other parts of the world and to create a DNA database for the species. An approximately 585-nucleotide fragment of the mitochondrial DNA (cytochrome oxidase I, COI) was sequenced for 150 individual cockles, representing 10 populations: three from the north, four from the central part and three from the southern part of peninsular Malaysia. Phylogenetic analyses of the resulting dataset yielded tree topologies that not only showed the relationship between T. granosa and its closest relatives but its position in the evolutionary tree. Three mitochondrial clades were evident, each containing an individual genus. Using the mutation rate of the COI gene, the divergence time between T. granosa and its closest related species was estimated to be 460 thousand years ago. This study provides a phylogenetic framework for this ecologically prominent and commercially important cockle species.
Fulltext Remarkably low genetic variation but high population differentiation in the climbing perch, Anabas testudineus (Anabantidae), based on the mtDNA control region

Jamsari AF, Muchlisin ZA, Musri M, Siti Azizah MN

Genet. Mol. Res., 2010;9(3):1836-43.
PMID: 20845309 DOI: 10.4238/vol9-3gmr933

Anabas testudineus (Anabantidae) is an important food fish in Southeast Asia. We analyzed the mitochondrial DNA control region sequence data to evaluate the genetic variability and population structure of this species. Sixty specimens were collected from four populations in Sumatra and two populations in Peninsular Malaysia. We found a very low level of genetic variability, with five of the six populations exhibiting total absence of genetic variation. Based on analysis of molecular variance, 84.72% of the total variation was among populations and 15.28% within populations. A geographical division based on FST values indicated highly significant genetic differentiation among populations from the four drainage systems: Aceh, Sumatra Utara, Pulau Pinang, and Terengganu (FST ranging from 0.633 to 1.000). No phylogeographic relationships among populations were detected, despite the generation of four distinct clades in a neighbor-joining phylogenetic tree.
Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia

Tan MP, Jamsari AF, Siti Azizah MN

J Fish Biol, 2016 May;88(5):1932-48.
PMID: 27027270 DOI: 10.1111/jfb.12956

Genetic variability and differences in wild striped snakehead Channa striata from Malaysia were analysed by genotyping nine novel nuclear microsatellite loci. Analysis revealed moderate-to-high genetic diversity in most of the populations, indicative of large effective population sizes. The highly diversified populations are admixed populations and, therefore, can be recommended as potential candidates for selective breeding and conservation since they each contain most of the alleles found in their particular region. Three homogenous groups of the wild populations were identified, apparently separated by effective barriers, in accordance with contemporary drainage patterns. The highest population pairwise FST found between members of the same group reflects the ancient population connectivity; yet prolonged geographical isolation resulted in adaptation of alleles to local contemporary environmental change. A significant relationship between genetic distance and geographical isolation was observed (r = 0·644, P < 0·01). Anthropogenic perturbations indicated apparent genetic proximity between distant populations.
Morphological variation between isolates of the nematode Haemonchus contortus from sheep and goat populations in Malaysia and Yemen

Gharamah AA, Rahman WA, Siti Azizah MN

J Helminthol, 2014 Mar;88(1):82-8.
PMID: 23176779 DOI: 10.1017/S0022149X12000776

Haemonchus contortus is a highly pathogenic nematode parasite of sheep and goats. This work was conducted to investigate the population and host variations of the parasitic nematode H. contortus of sheep and goats from Malaysia and Yemen. Eight morphological characters were investigated, namely the total body length, cervical papillae, right spicule, left spicule, right barb, left barb, gubernaculum and cuticular ridge (synlophe) pattern. Statistical analysis showed the presence of morphological variation between populations of H. contortus from Malaysia and Yemen, with minor variation in the synlophe pattern of these isolates. Isolates from each country were grouped together in the scatterplots with no host isolation. Body, cervical papillae and spicule lengths were the most important characters that distinguished between populations of the two countries. This variation between Malaysia and Yemen may be attributed to geographical isolation and the possible presence of a different isolate of this worm in each country.
Motility, viability and fertility of goldfish Carassius auratus (Pisces: Cyprinidae) post short-term cryopreservation

Nurlaili N, Eriani K, Salma I, Maulida S, Rahayu SR, Handayani LS, et al.

Cryo Letters, 2023;44(3):169-177.
PMID: 37883170

BACKGRUND: Goldfish Carassius auratus is a popular ornamental fish extensively cultured worldwide. Sperm cryopreservation is a common fish breeding method that ensures sperm availability around the year. Studies on cryopreservation of goldfish sperm, especially on the suitability of cryoprotectant types and pre-freezing time, are scarcely available.
OBJECTIVE: To determine the most suitable type of cryoprotectant and pre-freezing for the successful cryopreservation of goldfish sperm.
MATERIALS AND METHODS: A completely randomized design with two factors was utilized in this study. The first factor is the type of cryoprotectants, which included methanol, ethanol, ethylene glycol, glycerol, and DMSO. The second is pre-freezing times of 10, 20, 30, and 40 min at each of the pre-freezing temperatures of 4 degree C, -10 degree C, and -79 degree C, meaning that the total times for the ramping down of temperature were 30, 60, 90 and 120 min, respectively. The Ringer solution and 10% egg yolk were used as extender and extracellular cryoprotectant. The sperm was stored at -179 degree C for 7 days.
RESULTS: The ANOVA test showed that cryoprotectants and pre-freezing significantly affected the motility, viability, and fertility of goldfish sperm after freezing in liquid nitrogen for 7 days (P<0.05). Furthermore, 10% DMSO combined with 15% egg yolk with an pre-freezing time of 20 min can maintain sperm motility, viability, and fertility higher than other treatments, by 79%, 80%, and 33%, respectively. The agarose gel electrophoresis showed no DNA fragmentation in all samples, including fresh sperm.
CONCLUSION: We conclude that 10% DMSO combined with 15% egg yolk and 20 min pre-freezing is the best treatment for goldfish sperm cryopreservation. DOI: 10.54680/fr23310110412.