Genetic characterisation of Malaysian edible nest swiftlet (Aerodramus fuciphagus Thunberg, 1812) using microsatellite and molecular sexing markers

The White-nest swiftlet (Aerodramus fuciphagus) is a swiftlet species which produce edible bird nest (EBN) from pure saliva, that is considered of high value in the international market. Due to increased demand and high value of the nests, over-harvesting had occurred in many locations, believed to be their natural habitats including in Malaysia. However, the introduction of swiftlet ranching or farming has increased the overall population of this species, leading to exclusion of this swiftlet species from the list of protected animals under the legislation Wildlife Conservation Act 2010 (Act 716), Malaysia. Exploitation and rapid population expansion of this species will trigger unpredictable changes in its genetic structure and reproduction over time. It is with these in mind that the present study was conducted. The main objectives of the study were to determine the genetic structure and correctly differentiate the sex of A. fuciphagus in Peninsular Malaysia. These main objectives were accomplished using microsatellite and molecular sexing markers. In the study analysing the genetic structure of A. fuciphagus, 90 A. fuciphagus samples (blood, embryos, feathers and muscle tissues) were randomly collected from three different populations (N = 30 per population): i) Northern Region (NR), that was Perak, ii) Eastern Region (ER), that comprised of Kelantan and Terengganu, and iii) Southern Region (SR) which was Johor. DNA was extracted from the samples and were assessed for 12 species-specific and cross-species microsatellite loci. PCRs were accomplished by using touchdown programmes, and the PCR products were separated using Polyacrylamide Gel Electrophoresis (PAGE). The results showed that eight microsatellite loci were polymorphic (11 to 15 alleles per locus). Observed heterozygosity values for all populations were low to moderate, ranging from 0.28 (SR) to 0.44 (ER) and lower than the expected heterozygosity values. All loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) (p<0.05). The mean of inbreeding coefficients (FIS) ranged from 0.465 (ER) to 0.636 (SR), indicating that inbreeding was present in the sampled populations. The genetic distance between populations showed that SR and NR tended to be the most distantly related. The mean FST value was 0.059. Analysis of molecular variation (AMOVA) indicated that a greater proportion of the genetic diversity was within the populations (92.9%) than among populations (7.06%). The structure analysis showed that the populations could be grouped into two clusters; SR was in a cluster of its own, while ER and NR were clustered together. In the molecular sexing study, seven primer sets for sexing birds were screened in A. fuciphagus using a total of 13 feather samples that were randomly selected from Perak. From the screening analysis, only one primer set (P8/WZ/W) was successfully differentiated the sex of A. fuciphagus. PCR amplification produced a single 255 bp DNA fragment for males which was derived from CHD-Z (CHD gene region in the sex chromosome Z), while for the females it produced two fragments (144 and 255 bp). The 144 bp fragment was from CHD-W. Results from sequencing showed that there were no variations in the base sequences of the CHD-W and CHD-Z amplified fragments within the same sexes, except for one male sample (A23) where at position 166, a base substitution occurred (from G to A). Phylogenetic analysis of CHD-W showed that four (Apodiformes, Pelecaniformes, Gruiformes and Accipitriformes) out of the five orders investigated had 100% similarity among birds from the same order. Whilst phylogenetic analysis of CHD-Z did not show 100% similarity among birds from the same order. The results suggest that for the CHD gene, evolution occurred at a higher rate in males compared to females. In conclusion, this study suggests that there was sufficient genetic variation among the EBN swiftlets in Malaysia. However, the risk of inbreeding should be a concern. Therefore, it is important to ensure a healthy population size for the industry to grow as this will significantly decrease the effects of genetic drifts in the founder populations, as well as maintain the genetic diversity and adaptive ability of the A. fuciphagus populations. In addition, the accomplishment to correctly identify the sex of A. fuciphagus using molecular sexing marker is beneficial for further studies on sex ratio and breeding management in A. fuciphagus.

Text FP 2019 79 - Full Text.pdf Available under License Creative Commons Attribution Non-commercial No Derivatives. Download (3MB) Text FP 2019 79.pdf Restricted to Repository staff only Available under License Creative Commons Attribution Non-commercial No Derivatives. Download (3MB)

Actions (login required)

View Item