Genetic analysis of three US population groups using an X-chromosomal STR decaplex

Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

BACKGROUND

Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.

RESULTS

Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average F_ST = 0.001-0.107; p <  0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.

CONCLUSION

This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.

Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization

Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis.

New sequence variants detected at DXS10148, DXS10074 and DXS10134 loci

A great amount of population and forensic genetic data are available for X-STRs supporting the need for having a common and accurate nomenclature among laboratories allowing for better communication, data exchange, and data comparison. DXS10148, DXS10074 and DXS10134 are commonly used X-STRs particularly due to their inclusion in the commercial kit Investigator Argus X-12 (Qiagen). Samples from West Africa and Iraq were sequenced for all three X-STRs allowing the detection of new DNA sequence variants. At DXS10148, variation was detected at four bases downstream from the flanking region from the repeat motif. The sequence AAGG-AAAG has been detected for the first time as a varying (AAGG-AAAG)1-3 motif, in the present work. One additional string when compared to the common one (AAGG-AAAG)2 adds eight bases to the fragment size of the tetranucleotide STR. This means that 2 repeats are added in these cases to the fragment size of the allele, while the presence of only one copy will reduce the expected allele size by 2 repeats. At DXS10074 two varying stretches consisting of AC and AG dinucleotide repeats were observed in the upstream flanking region, six bases from the main repeat core that also influence the expected allele size. DXS10134 revealed a simpler nomenclature in the Guinea-Bissau sample set when compared to the previously described allele nomenclature. This detected new hidden variation also has impact on the actual allele nomenclature at this locus as it contributes to a new class of short alleles so far undetected in other studies.

Population genetic data for 15 X chromosomal short tandem repeat markers in three U.S. populations

314 African American, 434 U.S. Caucasian, and 398 U.S. Hispanic individuals were typed at X STR markers DXS6795, DXS9902, DXS8378, DXS7132, DXS6803, DXS6789, DXS7424, DXS101, GATA172D05, DXS7130, GATA165B12, HPRTB, GATA31E08, DXS10147, DXS7423. High forensic efficiency parameter values confirm the potential usefulness of these markers in certain specific kinship situations involving female offspring as well as identity testing. Alleles previously unobserved in U.S. populations were noted in this study at 8 different markers. Additionally, null alleles and a triallelic pattern were observed and described. Pairwise comparisons indicated consistency with similar published populations at overlapping markers. These data represent a substantial increase in the quantity of U.S. X chromosomal short tandem repeat data available to the community.

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.

Capillary electrophoresis of an X-chromosome STR decaplex for kinship deficiency cases

During the two last decades, STR markers located on the autosomes have been gaining relevance and have nearly replaced the use of other type of markers in most cases of genetic identification, paternity testing, as well as in other situations of kinship analysis. Nevertheless, in some complex cases, independently of the number of polymorphisms being typed, autosomal markers convey very little information. Depending on the parentage constellation available for analysis, as well as the gender of the subjects, this problem can sometimes be solved by using markers that have different modes of transmission. Therefore, most forensic laboratories are nowadays prepared to analyse lineage markers (Y chromosome and mtDNA) and many have recently set up methods for the analysis of X-STRs. In the present chapter, a method is described for the typing of ten X chromosome-specific markers in a single PCR amplification reaction, followed by capillary electrophoresis separation and fluorescent detection in an ABI Genetic Analyser apparatus. This typing strategy was developed and optimized for the simultaneous amplification of ten X-linked specific STRs well distributed along the chromosome: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423.

Development of multiplex assay with 16 SNPs on X chromosome for degraded samples

We selected 16 new X chromosomal SNPs (rs4827155, rs471205, rs7884160, rs16982419, rs985251, rs3813932, rs6630351, rs4132871, rs5966270, rs7471388, rs6641116, rs6521038, rs5990560, rs5959408, rs414960, and rs3006142) and developed the two X chromosomal SNPs Octaplex systems using multiplex single base extension reactions. To make the systems more useful for analyzing degraded DNA samples, we designed primers to render amplicons of 100 bp or shorter (shorter PCR products). Statistical analyses of the 16 SNPs indicated a high usefulness for the Japanese forensic practice. In addition, results of tests on degraded DNA confirm the usefulness of this technique in such samples.

Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample

We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni's correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PD(F)) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F (ST) between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.

A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers.

Development and characterization of two mini-X chromosomal short tandem repeat multiplexes

This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.

Genetic profile characterization of 10 X-STRs in four populations of the southeastern region of Brazil

Ten X-chromosomal short tandem repeats (DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423) were analyzed in four populations of the southeastern region of Brazil (São Paulo, Rio de Janeiro, Vitória and Belo Horizonte). No deviations from the Hardy-Weinberg equilibrium were observed for any of the analyzed loci in the four populations. The average diversity per locus varied between 68% for DXS8378, DXS7133, and DXS7423 and 83%, for DXS6809, with Rio de Janeiro being the most diverse population. Overall power of discrimination values in females varied between 0.99999999990 and 0.99999999997 and between 0.9999991 and 0.9999995 in males. These high values show the potential of this system for forensic application and relationships' testing in the studied groups. Genetic comparisons (exact tests of population differentiation and pairwise genetic distances) revealed significant differences between Brazilian and other populations from Europe, Latin America and Africa, as well as among different Brazilian populations.

Sixteen X-chromosomal STRs in two octaplex PCRs in Japanese population and development of 15-locus multiplex PCR system

X-chromosome short tandem repeat (STR) polymorphisms are a useful tool in the fields of human population genetics and personal identification and are indispensable in investigating complex kinship or deficiency cases in circumstances where information on mtDNA or Y-chromosome polymorphisms is unavailable. The purpose of this study was to construct a multiplex polymerase chain reaction (PCR) system capable of analyzing a large number of X-STR loci and establish a 16-X-STR database in the Japanese population We developed two octaplex X-STR systems, one including the DXS7424, GATA172D05, HPRTB, DXS8377, GATA31E08, DXS9895, DXS7423, and DXS981 loci and the other the DXS6803, DXS6789, DXS6800, DXS6809, DXS7133, DXS7132, DXS101, and DXS6807 loci, and conducted a population study in 512 Japanese individuals comprising 339 men and 173 women. A 16-locus multiplex system produced unwanted PCR products due to mixture of the DXS9895 primer with the primers of two other loci. However, a 15-locus multiplex system exclusive of the DXS9895 locus did not. The 15-locus multiplex system amplified the largest number of loci among the X-STR multiplex systems used and afforded a power of discrimination of 0.99999999999997 in women and 0.999999997 in men.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.

An INDEL polymorphism at the X-STR GATA172D05 flanking region

A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Belém). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Belém.

Variants of the melanocortin 1 receptor gene (MC1R) and P gene as indicators of the population origin of an individual

The population origin of an individual is often requested to be determined from specimens left at a crime scene for identifying a suspect and individual identity. The melanocortin 1 receptor gene (MC1R) and P gene are associated with human pigmentation. Although several studies have reported that these genes are highly polymorphic in human populations, it is unclear if the allele variants can be used to determine the population origin of an individual. We aimed to determine the ethnic origin of an individual by using single nucleotide polymorphisms (SNPs). Eighteen SNPs in the MC1R gene and P genes were genotyped in 52 individuals by the direct sequencing method, and 4 SNPs (MC1R gene: R163Q and P gene: IVS5 + 1001, IVS13 + 113, and H615R) were selected on the basis of differences in frequencies. Subsequently, we genotyped these four SNPs in 422 volunteers from six ethnically defined populations using a polymerase chain reaction-based assay. The results revealed that the allele variants were present with high frequencies in Asian populations but were low in European and African populations. On the basis of these results, we defined a specific combination of a genotype (R163Q) and a diplotype group (IVS5 + 1001, IVS13 + 113, and H615R). This study indicates that the specific combination of a genotype and a diplotype group would be effective in estimating the population origin of an individual from a list of population groups.

Populationsgenetik des humanen X-Chromosoms

Die mitochondriale DNA und das Y-Chromosom (ChrY) weisen einen sehr hohen Informationsgehalt hinsichtlich der Entwicklungsgeschichte des Menschen und der verwandtschaftlichen Nähe humaner Populationen auf. Das liegt daran, dass mit Ausnahme der pseudoautosomalen Regionen des ChrY beide genomischen Kompartimente nicht rekombinieren und dass die Typisierung haploider Marker automatisch die Identifizierung von Haplotypen erlaubt. Das X-Chromosom (ChrX) nimmt hinsichtlich seines Rekombinationsverhaltens eine intermediäre Stellung zwischen den Autosomen und dem ChrY ein. Auch seine populationsgenetische Bedeutung beruht z. T. auf der leichteren Identifizierbarkeit von Haplotypen. Während ChrY und mtDNA aber jeweils nur einen einzigen Locus mit einheitlicher Entwicklungsgeschichte repräsentieren, setzt sich das ChrX aus mehreren Abschnitten zusammen, die jeweils eine eigene Historie reflektieren können. Daher erscheinen ChrX-Studien immer dann besonders sinnvoll, wenn Subpopulationen voneinander unterschieden oder regionale ethnische Strukturen erforscht werden sollen. Aus populationsgenetischer Sicht spielt die Analyse von Kopplungsungleichgewichten zwischen ChrX-Markern eine besondere Rolle, da mit ihrer Hilfe genetische Isolate und die Abstammung einzelner Gruppierungen von kleinen Gründerpopulationen nachgewiesen werden können. Populationen mit häufigen und hohen Kopplungsungleichgewichten haben eine besondere Bedeutung für die Identifizierung der Gene, deren Variation zur Ätiologie multifaktorieller Erkrankungen beiträgt.

Allele frequency distribution of 13 X-chromosomal STR loci in Pakistani population

Short tandem repeat (STR) markers are extensively being used for human identification as well as paternity and forensic case work. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. Many X-linked microsatellites have been evaluated but further studies are required to determine population specific statistics. Here, we report allele frequencies of 13 X-linked microsatellites (DXS8378, DXS9902, DXS6810, DXS7132, DXS981, DXS6793, DXS6801, DXS6789, GATA172D05, HPRTB, GATA31E08, DXS8377, and DXS7423) in the Pakistani population. Blood samples were collected from individuals representing all major ethnic groups of the Pakistan population. A total of 5-18 alleles were observed for each locus and altogether 109 alleles for all 13 X-STR loci. Heterozygosity in females ranged from 0.524 to 0.884. No significant deviation was observed from Hardy-Weinberg equilibrium for all 13 microsatellites. In addition, there was no evidence of linkage disequilibrium in any pairs of these markers. These results strongly suggest that the X-linked microsatellites described here can potentially serve as an extension to autosomal systems currently used in parentage analysis and forensic case work.

Genetic data of 10 X-STRs in a Spanish population sample

In this work, we present population genetic data of 10 X-chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) obtained from sample of 145 unrelated female individuals belonging to Valencia (Spain), a region located in the east of the Iberian Peninsula. All the markers studied present high genetic diversities, similar to those previously reported in other European population samples. No deviations from Hardy-Weinberg equilibrium were observed, with the exception of DXS101 locus. Allele frequencies and parameters of forensic interest for each X-STR were calculated. High mean exclusion chance and power of discrimination values were obtained by combining these 10 X-linked markers. Population comparisons (exact test of population differentiation; pairwise genetic distances) were carried out and low genetic distances were found between our sample and those from other Spanish or European regions.

Analysis of 10 X-STRs in three African populations

Three African populations were genetically studied through a decaplex X chromosome short tandem repeat (STR) system, which includes the following loci: DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789. A total of 237 unrelated male individuals from Angola, Mozambique and Uganda were typed. DXS8377 revealed to be the most polymorphic marker and in contrast, locus DXS7423 was the least informative in Angola and Mozambique and DXS8378 in Uganda. No significant associations between alleles of any pair of loci were found in these three population groups. The overall mean exclusion chances for the 10-plex in parentage testing, when both mother and daughter are investigated are above 1 in 4.2 million being the highest in Mozambique (1 in 5.3 million); in duos these values are approximately 1 in 60 thousand. Concerning the overall power of discrimination, this decaplex can discriminate 1 in nearly 41 million Ugandan men and 1 in around 30 million Angolan and Mozambican men; raising an order of magnitude of over 13 digits in all population groups for women. All these parameters demonstrate the potential of this decaplex for parentage testing as well as for identification purposes.

Genetic diversity of 10 X chromosome STRs in northern Portugal

Genetic data of 10 X chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) were obtained in a sample of unrelated males born in the five northern Portuguese districts. In a global sample of 347 individuals, no shared haplotypes were found for this set of markers and single locus gene diversities were high, varying between 0.678 for DXS7423 and 0.921 for DXS8377. Linkage disequilibrium analysis did not reveal consistent evidence of association between the X-STRs used. Population comparisons of northern Portuguese districts (exact test of population differentiation; pairwise genetic distances) and analysis of molecular variance supported genetic homogeneity of this region and therefore a common genetic database was considered. In comparisons with other European data, the only population samples showing statistically significant differences to northern Portugal were Germany and Latvia. The present work demonstrates that these genetic markers are highly discriminating and therefore useful for human identification purposes and anthropological research.