DNA fingerprints of dogs and cats

Genetic Distances between Tailfin Anchovy (Coilia nasus) Populations Analyzed by PCR

The author established a PCR-based genetic platform to examine the hierarchical polar dendrogram of Euclidean genetic distances of one tailfin anchovy population, especially for Coilia nasus, which was further associated with other fish population, by connecting with specifically designed oligonucleotide primer sets. Five oligonucleotide primers were used to generate a total of 260 and 211 scorable fragments in Coilia populations I and II, respectively. The DNA fragments ranged from greater than (approximately) 100 to more than 2,000 bp. The average bandsharing values (BS) of individuals from the anchovy population I (0.693) displayed higher values than individuals from population II (0.675). The genetic distance between individuals established the existence of a close relationship in group II. Comparatively, individuals of one anchovy population were fairly related to other fish populations, as shown in the polar hierarchical dendrogram of Euclidean genetic distances. The noteworthy genetic distance determined between two Coilia nasus populations demonstrates that this PCR technique can be applied as one of the several devices for individuals and/or population biological DNA researches undertaken for safeguarding species and for production of anchovies in the littoral area of Korea.

Genetic Differences in Natural and Cultured River Pufferfish Populations by PCR Analysis

Genomic DNA (gDNA) extracted from two populations of natural and cultured river pufferfish (Takifugu obscurus) was amplified by polymerase chain reaction (PCR). The complexity of the fragments derived from the two locations varied dramatically. The genetic distances (GDs) between individuals numbered 15 and 12 in the cultured population was 0.053, which was the lowest acknowledged. The oligonucleotide primer OPC-11 identified 88 unique loci shared within each population reflecting the natural population. The OPC-05 primer identified 44 loci shared by the two populations. The average band-sharing (BS) values of individuals in the natural population (0.683±0.014) were lower than in those derived from the cultured population (0.759±0.009) (p<0.05). The shortest GD demonstrating a significant molecular difference was found between the cultured individuals # 15 and # 12 (GD=0.053). Individual # 02 of the natural population was most distantly related to cultured individual # 22 (GD=0.827). A cluster tree was built using the unweighted pair group method with arithmetic mean (UPGMA) Euclidean GD analysis based on a total of 578 various fragments derived from five primers in the two populations. Obvious markers identified in this study represent the genetic structure, species security, and proliferation of river pufferfish in the rivers of the Korean peninsula.

Genetic Distances of Rainbow Trout and Masu Salmon as Determined by PCR-Based Analysis

This study used a PCR-based genetic analysis platform to create a hierarchical polar dendrogram of Euclidean genetic distances for two salmonid species, Oncorhynchus mykiss (rainbow trout, RT) and Oncorhynchus masou (masu salmon, MS). The species were distantly related to other fish species based on PCR results from using the designed oligonucleotide primer series. Five oligonucleotide primers were used to generate 330 and 234 scorable fragments in the RT and MS populations, respectively. The DNA fragments ranged in size from approximately 50 bp to more than 2,000 bp. The bandsharing (BS) results showed that the RT population had a higher average BS value (0.852) than that for the MS population (0.704). The genetic distance between individuals supported the presence of adjacent affiliation in cluster I (RT 01–RT 11). The observation of a significant genetic distance between the two Oncorhynchus species verifies that this PCR-based technique can be a useful approach for individual- and population-based biological DNA investigations. The results of this type of investigation can be useful for species safekeeping and the maintenance of salmonid populations in the mountain streams of Korea.

Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

BACKGROUND

Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees.

RESULTS

Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards.

CONCLUSIONS

The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

Genetic Distances between Two Echiuran Populations Discriminated by PCR

Genomic DNA extracted from representatives of two populations, Gunsan and Chinese, of Urechis spp. was amplified using PCR with several primers. The band-sharing (BS) value between individuals no. 05 from the Gunsan population and no. 22 from the Chinese population was 0.206, which was the lowest recognized value. Oligonucleotides primer OPC-04 revealed 44 unique loci, which distinguished the Chinese population. Primer OPB-17 allowed the discovery of 22 loci shared by the two populations, which were present in all samples. Based on the average BS results, individuals from the Gunsan population demonstrated lower BS values (0.661±0.012) than did those from the Chinese population (0.788±0.014; p<0.05). The shortest genetic distance (GD) displaying a noteworthy molecular difference was between individuals CHINESE no. 12 and no. 13 (GD=0.027). Individual no. 06 from the Gunsan population was most distantly related to CHINESE no. 22 (GD=0.703). A group tree of the two populations was constructed by UPGMA Euclidean GD analysis based on a total of 543 fragments generated using six primers. The explicit markers recognized in this study will be used for genetic analysis, as well as to evaluate the species security and proliferation of echiuran individuals in intertidal regions of the Korean Peninsula.

A practical genome-enabled legitimacy assay for oil palm breeding and seed production

BACKGROUND

Legitimacy in breeding and commercial crop production depends on optimised protocols to ensure purity of crosses and correct field planting of material. In oil palm, the presence of three fruit forms permits these assumptions to be tested, although only after field planting. The presence of incorrect fruit forms in a cross is a clear sign of illegitimacy. Given that tenera forms produce 30% more oil for the same weight of fruit as dura, the presence of low levels of dura contamination can have major effect during the economic lifespan of an oil palm, which is around 25 years. We evaluated two methods for legitimacy test 1) The use of SHELL markers to the gene that determines the shell-thickness trait 2) The use of SNP markers, to determine the legitimacy of the cross.

RESULTS

Our results indicate that the SHELL markers can theoretically reduce the major losses due to dura contamination of tenera planting material. However, these markers cannot distinguish illegitimate tenera, which reduces the value of having bred elite tenera for commercial planting and in the breeding programme, where fruit form is of limited utility, and incorrect identity could lead to significant problems. We propose an optimised approach using SNPs for routine quality control.

CONCLUSIONS

Both dura and tenera contamination can be identified and removed at or before the nursery stage. An optimised legitimacy assay using SNP markers coupled with a suitable sampling scheme is now ready to be deployed as a standard control for seed production and breeding in oil palm. The same approach will also be an effective solution for other perennial crops, such as coconut and date palm.

Genetic Distances Within-Population and Between-Population of Tonguesole, Cynoglossus spp. Identified by PCR Technique

The higher fragment sizes (>2,100 bp) are not observed in the two C. spp. populations. The six oligonucleotides primers OPA-11, OPB-09, OPB-14, OPB-20, OPC-14, and OPC-18 were used to generate the unique shared loci to each tonguesole population and shared loci by the two tonguesole populations. The hierarchical polar dendrogram indicates two main clusters: Gunsan (GUNSAN 01-GUNSAN 11) and the Atlantic (ATLANTIC 12-ATLANTIC 22) from two geographic populations of tonguesoles. The shortest genetic distance displaying significant molecular difference was between individuals' GUNSAN no. 02-GUNSAN no. 01 (genetic distance=0.038). In the long run, individual no. 02 of the ATLANTIC tonguesole was most distantly related to GUNSAN no. 06 (genetic distance=0.958). These results demonstrate that the Gunsan tonguesole population is genetically different from the Atlantic tonguesole population. The potential of PCR analysis to identify diagnostic markers for the identification of two tonguesole populations has been demonstrated. As a rule, using various oligonucleotides primers, this PCR method has been applied to identify polymorphic/specific markers particular to species and geographical population, as well as genetic diversity/polymorphism in diverse species of organisms.

Genetic Distances between Two Cultured Penaeid Shrimp (Penaeus chinensis) Populations Determined by PCR Analysis

Genomic DNA samples were obtained from cultured penaeid shrimp (Penaeus chinensis) individuals such as fresh shrimp population (FSP) and deceased shrimp population (DSP) from Shinan regions in the Korean peninsula. In this study, 233 loci were identified in the FSP shrimp population and 162 in the DSP shrimp population: 33 specific loci (14.2%) in the FSP shrimp population and 42 (25.9%) in the DSP population. A total of 66 (an average of 9.4 per primer) were observed in DSP shrimp population, whereas 55 unique loci to each population (an average of 7.9 per primer) in the FSP shrimp population. The Hierarchical dendrogram extended by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (FRESH 01, 02, and DECEASED 12, 13, 15, 16, 17, 19, 20, 22) and cluster 2 (FRESH 03, 04, 05, 06, 07, 08, 09, 10, 11, and DECEASED 14, 18, 21). Among the twenty-two shrimp, the shortest genetic distance that exposed significant molecular differences was between individuals 20 and 16 from the DSP shrimp population (genetic distance=0.071), while the longest genetic distance among the twenty-two individuals that established significant molecular differences was between individuals FRESH no. 02 and FRESH no. 04 (genetic distance=0.477). In due course, PCR analysis has revealed the significant genetic distance among two penaeid shrimp populations.

Polymorphism analyses of 19 STRs in Labrador Retriever population from China and its heterozygosity comparisons with other retriever breeds

Pure breed dogs of Western origin are increasingly more popular in China as is a need to differentiate breeds and individual dogs for personal and forensic reasons. Research on genetic diversities of the canine population in China is rarely conducted. In this study, genetic distributions and forensic efficiencies of 19 canine STR loci in Labrador Retriever population from China were evaluated by using one available commercial canine kit in China. This panel was used to genetically define 214 Labrador Retrievers in China, as an example of one of the most important Western breeds and to compare them with Labrador Retrievers from America based on three overlapping STR loci. Moreover, genetic relationship analyses between Labrador Retriever population and two reference populations in America were performed. All 19 STR loci were polymorphic and conformed to Hardy-Weinberg equilibrium in the studied population. The STR panel was able to discern individual dogs with a high degree of accuracy. Breed-wide genetic heterozygosity comparisons based on present and published allele frequencies revealed that the studied population had the lower genetic heterozygosity than canine populations in America. Principal component analysis among Labrador Retriever population and other reference populations showed that the studied Labrador Retrievers were genetically close to the retriever breeds in America. Population genetic structure analyses among these canine breeds further revealed genetic differentiations between the studied Labrador Retriever population and other compared breeds. In conclusion, these STR loci had relatively high forensic values in Labrador Retriever population in China, which could be employed for individual identification and kinship testing.

Genetic Distances in Two Gracilaria Species (Gracilariaceae, Rhodophyta) Identified by PCR Technique

Genomic DNA was isolated from the Gracilaria vermiculophylla (GRV) and G. chorda (GRC) from Jangheung located in the southern sea of the Korean Peninsula, respectively and we performed clustering analyses, DNA polymorphisms and the genetic differences. The seven selected primers OPC-01, OPA-04, OPA-05, OPD-07, OPD-08, OPB-10, and OPD-16 generated average bandsharing (BS) value, the genetic distance and dendrogram. The size of DNA bands varies from 90 bp to 2,400 bp. The average BS value was 0.859±0.004 within GRV and 0.916±0.006 within GRC. The average BS value between two Gracilaria species was 0.340±0.003, ranged from 0.250 to 0.415. The dendrogram obtained by the seven primers, indicates two genetic clusters. The genetic distance between two Gracilaria species ranged from 0.059 to 0.513. The individual VERMICULOPHYLLA no. 07 of GRV was genetically closely related to VERMICULOPHYLLA no. 06 of GRV (genetic distance=0.059). Especially, two entities between the individual VERMICULOPHYLLA no. 10 of GRV and CHORDA no. 22 of GRC showed the longest genetic distance (0.513) in comparison with other individuals used. Accordingly, as mentioned above, PCR analysis showed that the GRV was a little more genetically diverse than the GRC species. We convinced that this DNA analysis revealed a significant genetic distance between two Gracilaria species pairs (p<0.01).

Genetic Distances of Paralichthys olivaceus Populations Investigated by PCR

The author carried out PCR-based genetic platform to investigate the hierarchical polar dendrogram of Euclidean genetic distances of one bastard halibut population, particularly for Paralichthys olivaceus, which was further connected with those of the other fish population, by involving with the precisely designed oligonucleotide primer sets. Eight oligonucleotides primers were used generating excessively alterating fragments, ranging in size of DNA bands from larger than approximately 100 bp to less than 2,000 bp. As regards average bandsharing value (BS) results, individuals from Hampyeong population (0.810) displayed lower bandsharing values than did individuals from Wando population (0.877). The genetic distance between individuals approved the existence of close relationship in the cluster II. Relatively, individuals of one bastard halibut population were fairly related to that of the other fish population, as shown in the polar hierarchical dendrogram of Euclidean genetic distances. The points of a noteworthy genetic distance between two P. olivaceus populations demonstrated this PCR procedure is one of the quite a few means for individuals and/or populations biological DNA investigates, for species security and proliferation of bastard halibut individuals in coastal region of the Korea.

Genetic Variations of Intra- and between-razor Clam Solen corneus Population Identified by PCR Analysis

The author undertook PCR-founded genetic platform to investigate the hierarchical dendrogram of Euclidean genetic distances of one razor clam population, particularly for Solen corneus, which was further associated with those of the other clam population, by engaging with the precisely designed oligonucleotide primer sets. Seven oligonucleotides primers were used producing a total of 639 counted bands in population A and 595 in population B, respectively, ranging in size of DNA fragments from larger than approximately 50 bp to less than 1,100 bp. Their primers generated 39 specific fragments (6.10%) in population A and 47 (7.90%) in population B, respectively Comparatively, individuals of one razor clam population were fairly related to that of the other clam population, as shown in the hierarchical dendrogram of Euclidean genetic distances. The analysis of genetic variation between razor clam populations could offer important statistics for fisheries and mariculture. Generally the results showed specific and/or conserved genetic loci between razor clam populations. Specific markers established by the author will be valuable for the genetic analysis, species protection and increase of razor clam individuals in coastal region of the Korean Peninsula.

Genetic Distances of Scallop (Chlamys farreri) Populations investigated by PCR Procedure

The author performed PCR-based genetic platform to measure the hierarchical dendrogram of Euclidean genetic distances of Korean scallop populations (KSP), particularly for Chlamys farreri, which was further compared with those of the Chinese scallop populations (CSP), by employing the with specifically designed oligonucleotide primer sets. The scallop is economically and ecologically very important bivalves in South Korea. Relatively, individuals of KSP population were fairly distantly related to that of CSP population, as shown in the hierarchical dendrogram of Euclidean genetic distances. Comparatively, individuals of KSP population were fairly distantly related to that of CSP population. Thus analysis of genetic difference between scallop populations could provide important statistics for fishery and aquaculture. Overall the results showed specific and/or conserved genetic loci between scallop populations. Information on the genetic distance of the bivalve would be helpful to understand scallop expansion or conservation in the coastal regions of South Korea. Specific markers developed by the author will be useful for the analysis of scallop population genetics and distribution in coastal region.

Euclidean Genetic Distances of Four Manila Clam (Ruditapes philippinarum) Populations analyzed by PCR Research

The PCR analysis was performed on DNA samples extracted from a total of 20 individuals using six oligonucleotides primers. The author accomplished clustering analyses to reveal the Euclidean genetic distances among four clam populations from Gochang, Seocheon, Taean and Anmyeon of the Korean peninsula. The oligonucleotides primer OPA-08 generated 5 unique loci to each population, approximately 550 bp and 600 bp, respectively, in the MCS population. Especially, the primer OPA-20 generated 15 unique loci to each population, which were identifying each population, approximately 400 bp, 750 bp and 800 bp, in the MCT population. Individuals from MCG clam population (0.637±0.227) exhibited higher bandsharing values than did individuals from MCG clam population (0.402±0.115) (P<0.05). The dendrogram obtained by the six oligonucleotides primers indicates four genetic clusters: cluster 1 (MCG 01, 02, 04 and 05), cluster 2 (MCS 06, 07, 08, 09 and 10), cluster 3 (MCT 11, 12, 13, 14 and 15) and cluster 4 (MCA 16, 17, 18, 19, 20 and MCG 03). Among the twenty clam individuals, the shortest genetic distance that displayed significant molecular differences was between individuals 14 and 15 from the MCT population (genetic distance = 0.094), while the longest genetic distance among the twenty individuals that displayed significant molecular differences was between individuals MCG no. 01 and MCG no. 02 (genetic distance = 0.687). Comparatively, individuals of MCS clam population were fairly closely related to that of MCT clam population, as shown in the hierarchical dendrogram of Euclidean genetic distances.

Genetic Distances of Crucian Carp Populations analyzed by PCR Approach

Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population (0.985±0.009) exhibited higher bandsharing values than did individuals from CAH population (0.779±0.049) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).

Geographical Variations and Genetic Distances of Three Saxidomus purpuratus Populations ascertained by PCR Analysis

Genomic DNA samples isolated from geographical purplish Washington clam (Saxidomus purpuratus) were obtained from three different regions in the Korean Peninsula: Geoje (Geoje population; GJP), Gunsan (Gunsan population; GSP) and a site of North Korea (North Korea population; NKP). The seven primers generated the total 369 loci that can be scored from the GSP clam population. 356 fragments were generated from the NKP clam population. The complexity of the banding patterns varies dramatically between the primers and three localities. In this study, 319 loci were identified in the purplish Washington clam from Geoje and 369 in the clam population from Gunsan: 221 specific loci (69.3%) in the GJP clam population and 300 (81.3%) in the GSP population. These results demonstrate that the primer detected a large quantity of specific fragments, suggesting that the genetic variation in the GSP is higher than in the GJP population. In particular, the BION-28 primer gave DNA profiles with more fragments than the other six primers in the NKP population. The oligonucleotides primer BION-75 produced 21 unique loci to each population, which were ascertaining each population, approximately 250 bp, 300 bp and 400 bp, in the GJP population. Outstandingly, the primer BION-50 detected 21 shared loci by the three populations, major and/or minor fragments of sizes 150 bp, which were matching in all samples. With regard to average bandsharing value (BS) results, individuals from GJP population (0.743) displayed higher bandsharing values than did individuals from GSP population (0.606). In the present study, the dendrogram gained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (GEOJE 01 ~ GEOJE 07), cluster 2 (GUNSAN 08 ~ GUNSAN 14), cluster 3 (N.KOREA 15 ~ N.KOREA 21). Among the twenty one clams, the shortest genetic distance that revealed significant molecular differences was between individuals 08 and 09 from the NKP population (genetic distance = 0.073), while the longest genetic distance among the twenty-one individuals that demonstrated significant molecular differences was between individuals GEOJE no. 03 and GUNSAN no. 09 (genetic distance = 0.669). Comparatively, individuals of GJP population were properly closely related to that of NKP population, as revealed in the hierarchical dendrogram of genetic distances. In due course, PCR analysis has revealed the significant genetic distance among three purplish Washington clam populations. PCR fragments discovered in this study could be valuable as a DNA marker of the three geographical clam populations to distinguish.

Recent development of allele frequencies and exclusion probabilities of microsatellites used for parentage control in the German Holstein Friesian cattle population

Background

Methods for parentage control in cattle have changed since their initial implementation in the late 1950’s from blood group typing to more current single nucleotide polymorphism determination. In the early 1990’s, 12 microsatellites were selected by the International Society for Animal Genetics based on their informativeness and robustness in a variety of different cattle breeds. Since then this panel is used as standard in cattle herd book breeding and its application is accompanied by recurrent international comparison tests ensuring permanent validity for the most common commercial dairy and beef cattle breeds for example Holstein Friesian, Simmental, Angus, and Hereford. Although, nearly every parentage can be resolved using these microsatellites, cases with very close relatives became an emerging resolution problem during recent years. This is mainly due to an increase of monomorphism and a trend to the fixation of alleles, although no direct selection against their variability was applied. Thus other effects must be presumed resulting in a loss of polymorphism information content, heterozygosity, and exclusion probabilities.

Results

To determine changes of allele frequencies and exclusion probabilities, we analyzed the development of these parameters for the 12 microsatellites from 2004 to 2014. One hundred sixty eight thousand recorded Holstein Friesian cattle genotypes were evaluated. During this period certain alleles of nine microsatellites increased significantly (t-values >5). When calculating the exclusion probabilities for 11 microsatellites, reduction was determined for the three situations, i.e. one parent is wrongly identified (p = 0.01), both parents are wrongly identified (p = 0.005), and the genotype of one parent is missing (p = 0.048). With the addition of BM1818 to the marker set in 2009, this development was corrected leading to significant increases in exclusion probabilities. Although, the exclusion probabilities for the three family situations using the 12 microsatellites are >99 %, the clarification of 142 relationships in 40,000 situations where one parent is missing will still be impossible.

Twenty-five sires were identified that are responsible for the most significant microsatellite allele increases in the population. The corresponding alleles are mainly associated with milk protein and fat yield, body weight at birth and weaning, as well as somatic cell score, milk fat percentage, and longissimus muscle area.

Conclusions

Our data show that most of the microsatellites used for parentage control in cattle show directional changes in allele frequencies consistent with the history of artificial selection in the German Holstein population.

Genetic Distances of Three White Clam (Meretrix lusoria) Populations Investigated by PCR Analysis

The twenty-one individuals of Meretrix lusoria were secured from Gunsan, Shinan and Yeonggwang on the coast of the Yellow Sea and the southern sea in the Korean Peninsula, respectively. Amplification of a single COI fragment (720 bp) was imagined, and no apparent size differences were observed in amplified fragments between Meretrix lusoria and M. petechialis individuals. The size of the DNA fragments also varied excitedly, from 200 to 1,600 bp. The oligonucleotides primer BION-08 produced the least loci (a total of 17), with an average of 2.43 in the Gunsan population, in comparison to the other primers used. Remarkably, the primer BION-13 detected 42 shared loci by the three populations, major and/or minor fragments of sizes 200 bp and 400 bp, respectively, which were identical in all samples. The dendrogram gained by the seven oligonucleotides primers highlight three genetic clusters: cluster 1 (GUNSAN 01 ~ GUNSAN 07), cluster 2 (SHINAN 08 ~ SHINAN 14) and cluster 3 (YEONGGWANG 15 ~ YEONGGWANG 21). The longest genetic distance among the twenty-one Meretrix lusoria individuals that displayed significant molecular differences was between individuals GUNSAN no. 01 and SHINAN no. 14 (genetic distance = 0.574). Comparatively, individuals of SHINAN population were fairly closely related to that of YEONGGWANG population. In this study, PCR analysis has discovered significant genetic distances between two white clam population pairs (P<0.05).

Genetic Differences of Three Pollicipes mitella Populations Identified by PCR Analysis

Genomic DNAs were extracted from the turtle leg (Pollicipes mitella, 1798) population of Tongyeong, Yeosu and Manjaedo located in the southern sea of Korea. The turtle leg population from Tongyeong (0.929) exhibited higher bandsharing values than did turtle leg from Manjaedo (0.852). The higher fragment sizes (>1,200 bp) are much more observed in the Yeosu population. The number of unique loci to each population and number of shared loci by the three populations, generated by PCR using 7 primers in the turtle leg (P. mitella) population of Tongyeong, Yeosu and Manjaedo. Genetic distances among different individuals of the Tongyeong population of the turtle leg (lane 1-07), Yeosu population of the turtle leg (lane 08-14) and Manjaedo population of the turtle leg (lane 15-21), respectively, were generated using the CLASSIFICATION option in Systat version 10 according to the bandsharing values and similarity matrix. The dendrogram, obtained by the seven decamer primers, indicated three genetic clusters: cluster 1 (TONGYEONG 01-TONGYEONG 07), cluster 2 (YEOSU 08-YEOSU 14), and cluster 3 (MANJEDO 15-MANJEDO 21). Tongyeong population could be evidently discriminated with the other two Yeosu and Manjaedo populations among three populations. The longest genetic distance (0.305) was found to exist between individuals’ no. 02 of the Tongyeong population and no. 13 of the Yeosu population. It seems to the authors that this is a result of a high degree of inbreeding in narrow region for a long while.

Genetic distances of three mollusk species investigated by PCR analysis

Three species of Nortamea concinua (NC) and Haliotis discus hannai (HDH) from Tongyeong and Sulculus diversicolor supertexta (SDS) are widely distributed on the coast of the Yellow Sea, southern sea and Jeju Island in the Korean Peninsula under the innate ecosystem. There is a need to understand the genetic traits and composition of three mollusk species in order to evaluate exactly the patent genetic effect. PCR analysis was performed on DNA samples extracted from a total of 21 individuals using seven decamer oligonucleotides primers. Seven primers were shown to generate the unique shared loci to each species and shared loci by the three species which could be clearly scored. A hierarchical clustering tree was constructed using similarity matrices to generate a dendrogram, which was facilitated by the Systat version 10. 236 specific loci, with an average of 56.3 per primer, were identified in the NC species. 142 specific loci, with an average of 44.7 per primer, were identified in the HDH species. Especially, 126 numbers of shared loci by the three species, with an average of 18 per primer, were observed among the three species. Especially, the decamer primer BION-75 generated 7 unique loci to each species, which were identifying each species, in 700 bp NC species. Interestingly, the primer BION-50detected 42 shared loci by the three species, major and/or minor fragments of sizes 100 bp and 150 bp, respectively, which were identical in all samples. As regards average bandsharing value (BS) results, individuals from HDH species (0.772) exhibited higher bandsharing values than did individuals from NC species (0.655). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (CONCINNA 01~CONCINNA 07), cluster 2 (HANNAI 08~HANNAI 14), cluster 3 (SUPERTEXTA 15~SUPERTEXTA 21). Comparatively, individuals of HDH species were fairly closely related to that of SDS species, as shown in the hierarchical dendrogram of genetic distances.

Genetic Distances and Variations of Three Clupeid Species Determined by PCR Technique

In this study, seven oligonucleotides primers were shown to generate the shared loci, specific loci, unique shared loci to each species and shared loci by the three species which could be obviously calculated. Euclidean genetic distances within- and between-species were also calculated by complete linkage method with the sustenance of the hierarchical dendrogram program Systat version 13. The genomic DNA isolated from herring (Clupea pallasii), Korean anchovy (Coilia nasus) and large-eyed herring (Harengula zunashi), respectively, in the Yellow Sea, were amplified several times by PCR reaction. The hierarchical dendrogram shows three chief branches: cluster 1 (PALLASII 01, 02, 03, 04, 06 and 07), cluster 2 (NASUS 08, 09, 10, 11, 12, 13 and 14), and cluster 3 (ZUNASHI 15, 16, 17, 18, 19, 20, 21 and PALLASII 05). In three clupeid species, the shortest genetic distance displaying significant molecular difference was between individual PALLASII no. 03 and PALLASII no. 02 (0.018). Individual no. 06 of PALLASII was most distantly related to NASUS no. 11 (genetic distance = 0.318). Individuals from herring (C. pallasii) species (0.920) exhibited higher bandsharing values than did individuals from Korean anchovy (C. nasus) species (0.872) (P<0.05). As a result, this PCR analysis generated on the genetic data displayed that the herring (C. pallasii) species was widely separated from Korean anchovy (C. nasus) species. Reversely, individuals of Korean anchovy (C. nasus) species were a little closely related to those of large-eyed herring (H. zunashi) species.

Genetic Distances and Variations of Three Geographic Hairtail Populations Identified by PCR Analysis

In the present study, muscle tissues were obtained separately from individuals from Atlantic hairtail population (AHP), Gunsan hairtail population (GHP) and Chinese hairtail population (CHP), respectively. The seven decamer primers were used to generate the shared loci, specific, unique shared loci to each population and shared loci by the three hairtail populations. Here, averagely, a decamer primer generated 64.7 amplified products per primer in the AHP population, 55.7 in GHP population and 56.4 in CHP population. The number of unique shared loci to each population and number of shared loci by the three populations generated by genetic analysis using 7 decamer primers in AHP, GHP and CHP population. 119 unique shared loci to each population, with an average of 17 per primer, were observed in the AHP population, and 28 loci, with an average of 4 per primer, were observed in the CHP population. The hierarchical dendrogram point out three main branches: cluster 1 (ATLANTIC 01 ~ ATLANTIC 07), cluster 2 (GUNSAN 08 ~ GUNSAN 14) and cluster 3 (CHINESE 15 ~ CHINESE 21). The shortest genetic distance displaying significant molecular difference was between individuals’ CHINESE no. 16 and CHINESE no. 18 (0.045). In the long run, individual no. 01 of the AHP population was most distantly related to CHINESE no. 19 (genetic distance = 0.430). Consequently, PCR analysis generated on the genetic data displayed that the geographic AHP population was widely separated from CHP population, while individuals of CHP population were fairly closely related to those of GHP population.

DNA fingerprinting in botany: past, present, future

Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".

Genetic Variations between Hairtail (Trichiurus lepturus) Populations from Korea and China

PCR analysis generated on the genetic data showed that the geographic hairtail (Trichiurus lepturus) population from Korea in the Yellow Sea was more or less separated from geographic hairtail population from China in the South Sea. The average bandsharing value (mean±SD) within hairtail population from Korea showed 0.859±0.031, whereas 0.752±0.039 within population from China. Also, bandsharing values between two hairtail populations ranged from 0.470 to 0.611, with an average of 0.542±0.059. As compared separately, the bandsharing values of individuals within hairtail population from Korea were comparatively higher than those of individuals within population from China. The hierarchical dendevrepogram resulted from reliable oligonucleotides primers, indicating two genetic clusters composed of cluster 1 (KOREANHAIR1~KOREANHAIR11) and cluster 2 (CHINESEHAI12~CHINESEHAI22). The genetic distances between two geographic populations ranged from 0.038 to 0.476. Individual No. 11 within hairtail population from Korea was genetically closely related with No. 10 (genetic distance=0.038). The longest genetic distance (0.476) displaying significant molecular difference was also between individual No. 01 within hairtail population from Korea and No. 22 from Chinese. In the present study, PCR analysis has revealed significant genetic distances between two hairtail population pairs (P<0.05).

Geographic Variations and Genetic Distance of Three Geographic Cyclina Clam (Cyclina sinensis Gmelin) Populations from the Yellow Sea

The gDNA isolated from Cyclina sinensis from Gochang (GOCHANG), Incheon (INCHEON) and a Chinese site (CHINESE), were amplified by PCR. Here, the seven oligonucleotide decamer primers (BION-66, BION-68, BION-72, BION-73, BION-74, BION-76, and BION-80) were used to generate the unique shared loci to each population and shared loci by the three cyclina clam populations. As regards multiple comparisons of average bandsharing value results, cyclina clam population from Chinese (0.763) exhibited higher bandsharing values than did clam from Incheon (0.681). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (GOCHANG 01~ GOCHANG 07), cluster 2 (INCHEON 08~INCHEON 14), cluster 3 (CHINESE 15~CHINESE 21). The shortest genetic distance that displayed significant molecular differences was between individuals 15 and 17 from the Chinese cyclina clam (0.049), while the longest genetic distance among the twenty-one cyclina clams that displayed significant molecular differences was between individuals GOCHANG no. 03 and INCHEON no. 12 (0.575). Individuals of Incheon cyclina clam population was somewhat closely related to that of Chinese cyclina clam population. In conclusion, our PCR analysis revealed a significant genetic distance among the three cyclina clam populations.

Study of p53 codon 72 polymorphism and codon 249 mutations in Southern India in relation to age, alcohol drinking and smoking habits

Germline polymorphisms of genes involved in different steps of tumorigenesis like p53, the tumor suppressor gene, are reported to determine the individual susceptibility to cancer. Lung cancer is one of the most common and lethal cancers and tobacco smoking remains its most important etiologic factors. The most frequently p53 mutated codons of lung cancer are 72 (exon 4) and 249 (exon 7). Since mutations in the p53 gene are present in ∼40% of all human lung cancers and are more common in smokers than in nonsmokers, we aimed to detect the status of p53 at codon 72 for Arg/Arg or Arg/Pro or Pro/Pro allele polymorphism and p53 codon 249 mutation in smokers and nonsmokers of South India. Allele frequencies in the nonsmokers were 0.16 for the Arg/Pro allele and 0.84 for the Pro/Pro allele in our study population. Among the smokers, the frequencies of the Arg/Pro, Arg/Arg, and Pro/Pro alleles were 0.88, 0.04, and 0.08, respectively. No mutation was detected in both smokers and nonsmokers in p53 codon 249. From the worldwide scenario, it can be speculated that the smokers, with Arg/Pro genotype are more prone for lung cancer or to other types of cancer.

DNA fingerprints of sheep using an M13 probe

The bacteriophage M13 DNA was used to detect hypervariable minisatellites in several families of Booroola sheep as well as Merino and Suffolk sheep. Digestion of sheep DNA gave rise to three to eight fragments with different restriction enzymes demonstrating considerable polymorphism between the different breeds. The length of informative DNA fragments varied in size from 6 to 20kb. The DNA fingerprints generated were individual specific and allowed for differentiation between closely related animals. The pattern obtained with sheep DNA was different from that observed with humans and other vertebrates in the proportion of high molecular weight DNA fragments present. Pedigree analysis of DNA patterns of dams and their offspring for several sets of twins and triplets showed a clear distinction between individuals and failed to reveal the presence of monozygosity.

DNA fingerprints of poultry

Human minisatellite probes cross-hybridize to DNA of several species of poultry (chicken, duck, turkey and goose), and detect high levels of polymorphism. The resulting DNA fingerprints are individual specific, and allow the discrimination even between closely related birds. The pattern of poultry DNA fingerprints is different from that of humans and other animals, having a higher average proportion of large DNA fragments. Pedigree analysis revealed a low number of allelic pairs of variable DNA fragments, indicating that most of the alleles are unresolved in the DNA fingerprint or too small to be detected. The total number of detectable loci in broilers, using probe 33.6, was estimated as 62, of which 13 loci are on average scoreable and available for use. Poultry DNA fingerprints can be used for individual identification, linkage studies and as an aid in breeding programmes.

Genetic analysis of fingerprints in Mérinos d'Arles x Booroola Merino crossbred sheep

The M13.13 minisatellite probe, consisting of a polymer of the M13 VNTR consensus sequence, cross-hybridized to ovine DNA and allowed detection of several polymorphic loci. Individual specific patterns were obtained in sheep using this probe. Pedigree analysis showed that individuals were heterozygous for most of the DNA fragments detected (88%). By studying the segregation of male's variable DNA fragments, a minimum of 10 loci were defined. The ovine DNA 'fingerprint' obtained with M13.13 is polymorphic enough to be used efficiently in animal identification, paternity testing, and possibly as a source of genetic markers for linkage analysis.

DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes

A multi-locus DNA probe, R18.1, derived from a bovine genomic library, detected DNA fingerprints of highly polymorphic loci in hybridization to genomic DNA from poultry and sheep, and of moderate polymorphic loci in cattle and human DNA. The average numbers of detected bands in chickens and sheep were 27.8 and 21.4, and the average band sharing levels were 0.25 and 0.33, respectively. In hybridization to cattle and human DNA, the results were less polymorphic; nevertheless, individual identification is feasible using probe R18.1. The results obtained by R18.1 were compared to results obtained by Jeffreys minisatellite probe 33.6 and two microsatellite oligonucleotides, (GT)12 and (GTG)5. The total number of detected loci using probes R18.1 and 33.6 were estimated in chickens through family analysis of broilers and the maximal number of detectable loci was calculated.

DNA fingerprinting in cattle using oligonucleotide probes

Oligonucleotide probes specific for simple tandem repeat sequences produce individual specific DNA fingerprints in man and all animal species tested so far. Here 11 different synthetic probes were hybridized to bovine genomic DNAs which had been digested with the restriction endonucleases HinfI, AluI and HaeIII. Two of these probes gave DNA fingerprint patterns which were analysed for three German breeds. Different parameters were calculated, such as the average number of bands per individual or the probability of finding identical fingerprints in two unrelated individuals. The number of polymorphic bands varies from 11 to 23 in the different breeds and the probability of finding the same banding pattern in two unrelated individuals ranges from 1.5 x 10(-7) to 2.4 x 10(-7). Hence this DNA fingerprinting procedure allows precise identification of individuals. It is also a useful additional method for paternity testing in cattle.

Restriction enzyme cleavage of fluorescently labeled DNA fragments--analysis of the method and its usage in examination of digestion completeness

Restriction enzymes have proven to be among the most valuable tools in molecular biology. In this work, we demonstrate that the cleavage of fluorescently labeled, PCR-amplified DNA can be used as a simple and highly sensitive technique for detection of sequences present in a percentage as low as 0.6% in a DNA pool. Due to the fact that fluorescent labeling of DNA fragments enables such sensitive detection and quantification of restriction enzyme cleavage, the method was further exploited in monitoring of the enzymatic digestion completeness and in determination of factors that influence restriction enzyme effectiveness. We analyzed the activity of six restriction endonucleases; the percentage of uncleaved DNA fragments predominantly ranged between 2.0 and 2.5 and the highest value was 8.00%. We conclude that, since the enzymatic digestion completeness may not always be assured, each assay based on restriction enzyme cleavage that is intended to be used in investigations of heterogeneity in a DNA pool should be constructed so that the presence of cleaved sequences is the indication of pool nonuniformity. When the presence of uncleaved sequences indicates pool heterogeneity, the results could be misleading due to possible incompleteness of enzymatic cleavage.