Individualization and estimation of relatedness in crocodilians by DNA fingerprinting with a Bkm-derived probe

Major histocompatibility complex class I polymorphism in Asiatic lions

Asiatic lions (Panthera leo persica), whose only natural habitat in the world is the Gir forest sanctuary of Gujarat State in India, are highly endangered and are considered to be highly inbred with narrow genetic diversity. An objective assessment of genetic diversity in their immune loci will help in assessing their survivability and may provide vital clues in designing strategies for their scientific management and conservation. We analyzed the comparative sequence polymorphism at exon 2 and exon 3 of major histocompatibility complex (MHC) class I in three groups of lions, i.e. wild Asiatic (from Gir forest), captive-bred Asiatic (from zoological parks in India), and Afro-Asiatic hybrid groups (from zoological parks in India) through polymorphism chain reaction-assisted sequence-based typing. The two exons were amplified, cloned, sequenced, and analyzed for polymorphism at nucleotide and putative translated product level. The analysis revealed extensive sequence polymorphism not only between clones derived from different lions but also the clones derived from a single lion. Furthermore, the wild Asiatic lions of Gir forest exhibited abundant sequence polymorphism at MHC class I comparable with that of Afro-Asiatic hybrid lions and significantly higher than that of captive-bred Asiatic lions. We hypothesize that Asiatic lions of Gir forest are not highly inbred as thought earlier and they possess abundant sequence polymorphism at MHC class I loci. During this study, 52 new sequences of the multigene MHC class I family were also identified among Asiatic lions.

Microgeographic variation in Caiman latirostris

In theory, geographic scale is related to genetic variation at the population level, whereas microgeographic scale may reveal intra-population structure such as social groups and families. In the present work, both levels of genetic variation in the broad-snouted caiman (Caiman latirostris) were evaluated in small wetlands associated with the Piracicaba River and some of its tributaries in the state of São Paulo, Brazil. Genetic variation was determined using microsatellite DNA markers originally developed for the American alligator (Alligator mississipiensis) and previously tested in pedigreed captive broad-snouted caimans. Using these markers, we were able to detect variability among individuals from different sites, even those within a small geographic distance. Genetic results suggest that the groups sampled at each site are composed predominantly of related individuals. A possible combination of high mortality and low natality rates results in a low number of successfully dispersed individuals per generation. Future studies using a recently constructed Caiman latirostris microsatellite library (Zucoloto et al., 2002) might help us to understand metapopulation processes that may be occurring within this species.

Assessing probability of ancestry using simple sequence repeat profiles: applications to maize hybrids and inbreds

Determination of parentage is fundamental to the study of biology and to applications such as the identification of pedigrees. Limitations to studies of parentage have stemmed from the use of an insufficient number of hypervariable loci and mismatches of alleles that can be caused by mutation or by laboratory error and that can generate false exclusions. Furthermore, most studies of parentage have been limited to comparisons of small numbers of specific parent-progeny triplets thereby precluding large-scale surveys of candidates where there may be no prior knowledge of parentage. We present an algorithm that can determine probability of parentage in circumstances where there is no prior knowledge of pedigree and that is robust in the face of missing data or mistyped data. We present data from 54 maize hybrids and 586 maize inbreds that were profiled using 195 SSR loci including simulations of additional levels of missing and mistyped data to demonstrate the utility and flexibility of this algorithm.

Genetic variation in Asiatic lions and Indian tigers

Previous reports have suggested that Asiatic lions and tigers are highly inbred and exhibit very low levels of genetic variation. Our analyses on these species have shown much higher degrees of polymorphism than reported. Randomly amplified polymorphic DNA (RAPD) analysis of 38 Asiatic lions, which exist as a single population in the Gir Forest Sanctuary in India, shows an average heterozygosity of 25.82% with four primers. Sperm motility studies by our colleagues corroborate this data. In Indian tigers, microsatellite analysis of five CA repeat loci and multilocus fingerprinting using Bkm 2(8) probe on a population of 22 individuals revealed a heterozygosity of 22.65%. Microsatellite analysis of loci Fca 77 and Fca 126 revealed polymorphism amongst the Asiatic x African lion hybrids, which has enabled us to use these as markers to discriminate the pure Asiatic lions from the hybrids. A similar analysis was used to identify hybrids of Indian and Siberian tigers through polymerase chain reaction (PCR) amplification of hair samples. To ascertain the variation which existed before the population bottleneck at the turn of the present century, microsatellite analysis was performed on 50- to 125-year-old skin samples from museum specimens. Our results show similar levels of genetic variability as in the present population (21.01%). This suggests that low genetic variability may be the characteristic feature of these species and not the result of intensive inbreeding. DNA fingerprinting studies of Asiatic lions and tigers have helped in identifying individuals with high genetic variability which can be used for conservation breeding programs.

Assessment of genetic diversity by DNA profiling and its significance in silkworm, Bombyx mori

Silkworm genetic resources that are being maintained in different countries are yet to be adequately tapped to develop elite varieties that are suited to different agro-eco-climatic conditions of countries like India. This is mostly due to unavailability of efficient protocols that could uncover usable genetic variability in silkworms. Molecular markers are known to provide unambiguous estimates of genetic variability of populations since they are independent of confounding effects of environment. The DNA fingerprinting assays, based on random amplified polymorphic DNA (RAPD) and banded krait minor satellite DNA (Bkm) 2(8) multilocus probes, which successfully characterise the diverse silkworm genotypes at their DNA level, are described. The use of these two DNA fingerprinting assays in estimation of within- and between-population genetic diversity is discussed.

DNA fingerprinting in silkworm Bombyx mori using banded krait minor satellite DNA-derived probe

The genomic DNA from thirteen different ecotypes and inbred lines of silkworm, Bombyx mori, were analyzed by digesting with BstNI and HinfI restriction enzymes followed by hybridization with banded krait minor satellite DNA (Bkm)-2(8) minisatellite probe. The DNA fingerprinting revealed 9-31 discrete intense bands, some of which were ecotype/inbred line-specific. Individual specific DNA fingerprints in two representative genotypes and their F1 hybrid offspring were also obtained. Individuals of a given parental line showed very similar profiles and the hybrid offspring showed the combined profile of both parents. The presence of bands specific to diapausing and nondiapausing strains and to particular genotypes indicate their potential use for marker-assisted breeding and varietal identification.

Biological significance of minisatellites

Minisatellites are tandemly repeated, highly variable DNA sequences found in most higher eukaryotes. These contain a core sequence resembling the chi sequence of Escherichia coli, which is a binding site for recombination proteins. Based on this, a generalized function of minisatellites to provide binding sites for recombination proteins in eukaryotes has also been suggested. However, recent discoveries of trinucleotide repeat expansion mutations associated with at least four human genetic diseases, several short repeats acting as motifs for binding of various transcription factors, and several minisatellite-binding nuclear proteins, which are expressed in specific tissues and bind to specific sequences, strongly suggest that different families of minisatellites may have different functions. A banded krait minor (Bkm) satellite DNA, consisting of highly conserved GATA repeats, which is arranged in a sex-specific manner, is hypervariable. We have found a sex- and tissue-specific factor designated as Bkm-binding protein (BBP), which specifically binds to Bkm (GATA), in the germ cells of the heterogametic sex [ovary, in the case of female heterogamety (in snakes); and testis, in the case of male heterogamety (in mice, rats and humans)]. It is in these tissues that decondensation of the W and Y chromosomes occurs. We suggest that GATA repeats of Bkm bring about a coordinated decondensation of the W and Y sex chromosomes in the germ cells in response to BBP, which may serve as a "switch" for the activation of the genes present on the W and Y sex chromosomes. Since the number of GATA repeats, in tandem, necessary for the binding of BBP is flexible, there is no selection pressure on the maintenance of the exact length of the repeats, unless it is reduced below a threshold at which the binding is completely abolished.

DNA fingerprinting in captive population of the endangered Siberian crane (Grus leucogeranus)

DNA fingerprinting was used to estimate genetic diversity within the endangered Siberian crane (Grus leucogeranus) captive population consisting of several dozens of founders originating from the two wild populations of eastern and western Siberia. Similarity and difference among captive individuals were demonstrated by the unweighted pair-group (UPGMA) clustering procedure. Quantitative characteristics of the eastern and western captive population groups such as average percentage differences (APD) and heterozygosity showed a high extent of genetic variability of 77.9-79.3% and heterozygosity of 0.85-0.72 within each group. Genetic heterogeneity of the captive population structure observed here provides guidelines for management of the species gene pool in captivity. These data also indicate that monitoring of genetic diversity through DNA fingerprinting can facilitate the efforts of Siberian crane management and restoration.

Generic affinities among crocodilians as revealed by DNA fingerprinting with a Bkm-derived probe

Genetic fingerprint profiles have been successfully used for establishing biological relationships, in linkage analysis, and in studies of population structure but have not so far been used for ascertaining phylogenetic relationships among related groups of species and genera. This is largely because these profiles are thought to evolve too rapidly to be informative over large time intervals. However, we show here that among the Crocodilia, whose phylogeny is a debated issue, these profiles can provide phylogenetically useful information. By using the probe Bkm-2(8), DNA fingerprints with distinct bands distributed in the size range 0.5-23.0 kb were obtained for individuals of 18 species belonging to seven of the eight genera of crocodilians. These genetic profiles showed individual-, species-, and restriction enzyme-specific patterns. In addition, striking differences were observed in the copy number of Bkm-related sequences in genomes of different crocodilian species. The qualitative data from DNA fingerprint profiles, and quantitative data on copy number variation in Bkm-related sequences, suggest that these genera belong to two distinct groups, one of which includes Alligator, Paleosuchus, and Caiman; the other includes Crocodylus, Osteolaemus, Tomistoma, and Gavialis. A close relationship between Tomistoma and Gavialis is also suggested by these results.

DNA analysis in forensics, disease and animal/plant identification

During 1993, significant advances have been achieved in applications of DNA analysis to forensic science, disease assessment, and animal/plant identification. These advances include the development of simple and high sample-throughput techniques for highly informative personal identification, rapid screening for pathogens and the development of polymorphic genetic markers in plants and animals.