Development of Microsatellite Markers for Siamese Crocodile (Crocodylus siamensis) (original) (raw)
Related papers
Kasetsart Journal. Natural Sciences, 2008
Marfan syndrome (MFS) is an autosomal dominant disorder of connective tissue with marked interfamilial and intrafamilial variation in phenotype. The primary defect in affected patients resides in the gene for ®brillin-1 (FBN1) on 15q21. Linkage analysis has shown no locus heterogeneity in the classic phenotype, although substantial allelic heterogeneity exists. Recently it has been shown that the size of the gene is approximately 200 kb. These and other factors have precluded routine mutation screening for presymptomatic and prenatal diagnosis. Previously we described four intragenic microsatellite polymorphisms that can be used for haplotype segregation analysis. The utility of this approach is limited because the markers do not fully span the gene and show incomplete informativeness, with 16% homozygosity for the most common haplotype. We have now identi®ed and localized highly polymorphic microsatellite markers that fall within 1 Mb of FBN1. Complete haplotype heterozygosity was observed in a population of 50 unrelated control individuals when thē anking markers and existing intragenic polymorphisms were used in combination. We demonstrate the utility of haplotype segregation analysis in the presymptomatic diagnosis and counseling of families showing atypical or equivocal manifestations of MFS.
Analysis of Microsatellites and Parentage Testing in Saltwater Crocodiles
Journal of Heredity, 2004
Fifteen microsatellite loci were evaluated in farmed saltwater crocodiles for use in parentage testing. One marker (C391) could not be amplied. For the remaining 14, the number of alleles per locus ranged from two to 16, and the observed heterozygosities ranged from 0.219 to 0.875. The cumulative exclusion probability for all 14 loci was .9988. The 11 loci that showed the greatest level of polymorphism were used for parentage testing, with an exclusion probability of .9980. With these 11 markers on 107 juveniles from 16 knownbreeding pairs, a 5.6% pedigree error rate was detected. This level of pedigree error, if consistent, could have an impact on the accuracy of genetic parameter and breeding value estimation. The usefulness of these markers was also evaluated for assigning parentage in situations where maternity, paternity, or both may not be known. In these situations, a 2% error in parentage assignment was predicted. It is therefore recommended that more microsatellite markers be used in these situations. The use of these microsatellite markers will broaden the scope of a breeding program, allowing progeny to be tested from adults maintained in large breeding lagoons for selection as future breeding animals.
Genetics and Molecular Research, 2014
We tested microsatellites that were developed for the saltwater crocodile (Crocodylus porosus) for cross-species amplification and to provide an estimate of inter-and intraspecific variation among four species of Neotropical crocodiles (C. rhombifer, C. intermedius, C. acutus, and C. moreletii). Our results indicated that with the exception of 2 loci in C. intermedius, all 10 microsatellite loci were successfully amplified in the 4 species, producing a set of variably sized alleles that ranged in number between 2 and 14 alleles per locus. Similarly, private alleles (i.e., unique alleles) also were reported in all 4 species for at least 3 loci. The mean observed and expected heterozygosities (averaged across species for all 10 loci combined) ranged from 0.39 to 0.77 and from 0.44 to 0.78, respectively. In addition to this, we evaluated these microsatellites in 2 populations of C. acutus and C. moreletii to assess their utility in estimating intraspecific levels of polymorphisms. These ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (3): 5492-5502 (2014) Assessment of microsatellites in Neotropical crocodiles microsatellites also showed considerable allelic variation in population level analysis. The set of 10 microsatellite loci in our study had the potential to be used as a tool in population and conservation genetic studies of Neotropical crocodiles.
2015
Tomistoma schlegelii, also referred to as the “false gharial”, is one of the most exclusive and least known of the world’s fresh water crocodilians, limited to Indonesia and Malaysia. The species has been recognized for over a century from a museum specimen, and its distribution has been a mystery for a long time. Its lack of economic value and local cultural significance (the skin is not traded locally) has also contributed to the lack of studies on the false gharial. Tomistoma schlegelii within the Southeast Asia region has been found to suffer from population reduction. This species has to live in small environments, because of the current habitat destruction, hence leading to a steady reduction of species number and, this can be as a reason for an increase in the rate of inbreeding. Nevertheless, lack of information on the genetic variability and structure of the species in Malaysia remains a matter of concern. Hence, the objectives of this study were to determine the current ge...
The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation
Conservation Genetics Resources, 2020
Microsatellite DNA is among the several molecular tools used for determining genetic variability and inbreeding depression in threatened populations. It has been used extensively for population genetics studies in conservation of crocodilians. Even though single nucleotide polymorphisms have higher precision compared to microsatellite DNA markers, microsatellites offer a cost advantage which is particularly important to researchers in the global south. Here, we review the role of microsatellite DNA as a conservation tool in crocodilians. Employing appropriate keywords in three online databases, we studied 78 publications, where microsatellite DNA had been used to study crocodilian species. We found that 504 species-specific markers were designed for 13, out of a total of 24 crocodilian taxa. Genus Crocodylus had the highest number of speciesspecific markers and was the most studied taxa using microsatellites. Moreover, microsatellite markers developed for C. porosus were successful in cross amplification of microsatellite markers in 19 other crocodilian species. Microsatellite based studies had highest focus on analyses of multiple populations of a single species. Based on our review of microsatellite based studies on populations of crocodilian species, we recommend that microsatellite DNA markers are an effective conservation tool that can provide critical information on population structures of threatened crocodilian species.
Conservation Genetics Resources, 2014
Crocodylus palustris (Indian mugger) is an endangered species with declining populations due to illegal hunting and habitat destruction. The situation warrants conservation efforts for which understanding the genetic structure of the extant populations becomes important. Here, we describe 14 new mugger-specific microsateillte markers (Simple Sequence Repeats, SSRs), developed from SSR-enriched partial genomic DNA library and ESTs. All markers were validated using 48 population samples. In general, markers were highly polymorphic; amplified 2-12 alleles/marker with H e and H o ranging from 0.23-0.91 and 0.25-1.0, respectively. Notably, all markers except CpSSR10, also exhibited near 100 % cross-species transferability when tested on *30 samples belonging to ten related crocodilians. These microsatellite markers are thus expected to be highly useful for the population genetics and other conservation studies on Indian mugger and other crocodilians.
PLOS ONE, 2017
The Siamese crocodile (Crocodylus siamensis) and Saltwater crocodile (C. porosus) are two of the most endangered animals in Thailand. Their numbers have been reduced severely by hunting and habitat fragmentation. A reintroduction plan involving captive-bred populations that are used commercially is important and necessary as a conservation strategy to aid in the recovery of wild populations. Here, the genetic diversity and population structure of 69 individual crocodiles, mostly members of captive populations, were analyzed using both mitochondrial D-loop DNA and microsatellite markers. The overall haplotype diversity was 0.924-0.971 and the mean expected heterozygosity across 22 microsatellite loci was 0.578-0.701 for the two species. This agreed with the star-like shaped topology of the haplotype network, which suggests a high level of genetic diversity. The mean ratio of the number of alleles to the allelic range (M ratio) for the populations of both species was considerably lower than the threshold of 0.68, which was interpreted as indicative of a historical genetic bottleneck. Microsatellite markers provided evidence of introgression for three individual crocodiles, which suggest that hybridization might have occurred between C. siamensis and C. porosus. D-loop sequence analysis detected bi-directional hybridization between male and female individuals of the parent species. Therefore, identification of genetically non-hybrid and hybrid individuals is important for long-term conservation management. Relatedness values were low within the captive populations, which supported
Conservation Genetics Resources, 2012
The Chinese alligator (Alligator sinensis) is one of the most endangered crocodilians in the world. In this study, 14 novel microsatellite loci were developed for this rare species via 454 high-throughput sequencing. These polymorphic microsatellites yielded an average of 2.93 alleles per locus among 40 individuals scored. The observed and expected heterozygosities (H O and H E) ranged from 0.025 to 0.975 and from 0.025 to 0.651, with averages of 0.439 and 0.426, respectively. These microsatellite markers will be useful for individual identification, mate choice for captive breeding and other relevant genetic investigations of Chinese alligator.