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Knowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection. [ABSTRACT FROM AUTHOR]

Abstract: Leptospirosis outbreaks occur regularly in Argentina and other South American countries, but little is known about their epidemiological relationships. Application of new molecular tools, such as the Multiple-Locus Variable-number tandem repeat Analysis (MLVA) is limited by scant available data on regional strains. We have analyzed the genetic diversity of a collection of 31 strains of Leptospira interrogans isolated in Argentina during the past five decades from humans and animals, including a strain from an environmental source and another isolated from an opossum. Genotyping was performed by MLVA using the loci VNTR4, VNTR7, VNTR9, VNTR10, VNTR19, VNTR23 and VNTR31, as described by Majed et al. [Identification of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J Clin Microbiol 2005;43:539–45 ]. Clustering analysis revealed eight distinct MLVA genotypes, with a dominant one, genotype A. Strains with this genotype were consistently isolated since 1960, representing 55% of the total strains and spanning an extensive geographical distribution. Other seven genotypes were less frequent, and only genotypes A and Hond Utrecht IV were isolated during the last decade. Different kinds of repeat blocks for each VNTR locus were identified by sequence analysis. VNTR copy number differences among genotypes always involved only one of these blocks. MLVA patterns obtained reveal the genetic diversity and relationships between strains, and constitute the framework for the genotyping of leptospires in the region. [Copyright &y& Elsevier]

Abstract: The present work tries to investigate the population structure and variation of the Amerindian indigenous populations living in Argentina. A total of 134 individuals from three ethnic groups (Kolla, Mapuche and Diaguitas) living in four different regions were collected and analysed for 26 Y-SNPs and 11 Y-STRs. Intra-population variability was analysed, looking for population substructure and neighbour populations were considered for genetic comparative analysis, in order to estimate the contribution of the Amerindian and the European pool, to the current population. We observe a high frequency of R1b1 and Q1a3a* Y-chromosome haplogroups, in the ethnic groups Mapuche, Diaguita and Kolla, characteristic of European and Native American populations, respectively. When we compare our native Argentinean population with other from the South America we also observe that frequency values for Amerindian lineages are relatively lower in our population. These results show a clear Amerindian genetic component but we observe a predominant European influence too, suggesting that typically European male lineages have given rise to the displacement of genuinely Amerindian male lineages in our South American population. [Copyright &y& Elsevier]

Abstract: Although serotype O157:H7 has been implicated in most cases of haemolytic-uraemic syndrome (HUS), there is growing concern about non-O157 serotypes of verocytotoxigenic Escherichia coli (VTEC). Multiple-locus variable-number tandem repeat analysis (MLVA) has been focused on the specific typing of O157:H7 isolates, but recently, a generic MLVA assay for E. coli and Shigella has been developed. We performed a study of the polymorphism in 7 generic VNTR loci both in VTEC O157:H7 and non-O157 isolates from Argentina, in order to asses the ability of the method to type this group of isolates and to get insight into their genetic diversity. Sixty-four isolates from cattle, patients with diarrhoea, and contaminated food belonging to 8 different serotypes were studied. All of them could be typed by this method and revealed 41 different MLVA genotypes. The MLVA dendrogram showed 2 main clusters which corresponded to O157:H7 and non-O157, respectively. Our results confirm the suitability of this MLVA method for analyzing VTEC isolates belonging to several serotypes, both O157:H7 as well as non-O157, highlight the genetic variability of the O157:H7 serotype and the need of additonal research in order to find more VNTR loci that could allow a higher discrimination among non-O157 VTEC. [Copyright &y& Elsevier]

Abstract: During the military governments in Argentina in the 1970s, the bodies of people who had been detained and later killed were deposited in individual graves as well as common graves. The identity of the majority of the bodies was not provided. During 2008, the Argentine Forensic Anthropology Team (EAAF) processed nine bone fragments from bodies found in a group of graves in the Province of Buenos Aires. Nuclear DNA (nDNA) profiles were obtained by amplifying autosomal STRs (using the Identifiler®, Profiler® and COfiler® kits), Y-STR (Y-Filer®) and mini-STR using kits developed “in-house”. The mitochondrial DNA (mtDNA) HV1 and HV2 regions were also sequenced on the same bone samples. Blood samples were analyzed from 21 individuals who reported to the EAAF that they had a family member missing from the aforementioned time period. This study presents the results of the comparison made between the bone sample genetic profiles and those of the family members, based on the genetic marker used (STR, Y-STR and/or mtDNA) and on the proposed kinships for each hypothesis. From the 9 bone samples analyzed, a total of 8 individual skeletons were observed. Of those 8 individuals, 4 were identified through kinship analysis. [Copyright &y& Elsevier]

Abstract: The development of the molecular biology techniques has made possible the study of the genetic background of American populations where a substantial contribution of the aboriginal component exists, but its individuals had lost the ethnic identity because of dramatic historical, cultural and social changes. The aim of the present work was to investigate the origin of the paternal lineages present in La Esperanza (Jujuy, Argentina), a population originated at the end of XVIII century as a consequence of the installation of a sugar plantation. DNA of 37 non-related males was purified from buccal swabs and subjected to STR PCR amplification of 11 Y chromosome loci using a commercial kit. In addition, 4 binary markers commonly used in diagnosis of ethnic origin (DYS199, M89, M207, and M173) were characterized by RFLP-PCR. From the 37 individuals analyzed, 34 different STRs based haplotypes were observed, 31 of them being unique, which shows the high heterogeneity of the genetic composition of the population. A search in the Y-Haplotype Chromosome Reference Database allowed to identify 11 Amerindian, 14 European, 2 Arabs and 2 Africans haplotypes. The 8 remaining haplotypes were not possible to assign unequivocally. On the other hand, the analysis of binary markers permits to include all the individuals analyzed (29) into a known haplogroup: 17 individuals carry the haplogroup Q1a3a (Amerindian), 9 the R1 (European), 1 the R (European) and 2 F (Eurasian). We conclude that the STRs and binary markers should be used jointly to get more accurate information about the ethnic origin and genetic diversity of human populations. [Copyright &y& Elsevier]

Abstract: We present genetic data for ten X-STRs (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902 y DXS6789) in two Native American populations from the North and Northwest regions of Argentina, namely Toba and Colla. The present study results support the usefulness of these markers in kinship investigation and also in population genetics studies. [Copyright &y& Elsevier]

Abstract: We present the haplotype analysis of 9 Y-STRs in 93 males from Buenos Aires province, sampled for paternity testing in our laboratory. We found a high haplotype diversity, 0.985, and only 6 haplotypes out of 76, were present in more than one male. About 25% of the haplotypes found do not appear in the YHRD Haplotype Reference database, while more than a half of them are not present in the SHDG database. Among the 76 haplotypes, 30% and 20% of them are described in the database as present in Italy and Spain respectively. These values are in accordance to the migration history of the country, since European immigrants mainly came from Spain and Italy. On the other hand, it is relevant to find and describe haplotypes which are not currently included in the databases. [Copyright &y& Elsevier]

Abstract: The population of Mendoza, like the entire population of Argentina, has a heterogeneous genetic constitution. It is the result of two major contributors; Native Americans and Europeans and, in a lesser degree, Western Africans, brought to the territory as slaves during colonial times. In order to investigate the proportion of genetic contributions of the parental populations to nowadays population of Mendoza, a set of 13 autosomal and 9 Y-STRs routinely used in forensic typing were selected. Although these markers are not the best suited for tracing ancestry, they might provide clues about the genetic structure of a population. A total of 242 male unrelated donors inhabiting Mendoza province were analyzed and compared with Argentinean Amerindian, Caucasian and African-American, reference samples. Genetic distance, based on R st values, and STRUCTURE analysis were performed for both polymorphic systems. Our results demonstrate a tri-parental genetic contribution whose proportions differs between autosomal or Y-STRs markers. Autosomal STRs denoted 46.8% European, 31.6% Native American and 21.5% African contributions. Instead, Y-STRs showed 67% European, 21% Amerindian, and 12% African ancestral lineages. These results are consistent with the history of submission undergone by the native populations during the conquest of the Americas and underscore the impact of the European male genetic contribution to extant population of Argentina. Probably our results underestimate the Caucasian and overestimate the Native American and African contributions since the polymorphisms employed are not as sensitive as the ancestry informative markers (AIMs). [Copyright &y& Elsevier]

Abstract: Allele frequency data of genetic markers employed in paternity testing and forensic casework is essential for the statistical analysis of the results obtained by these molecular markers. In 2004, our group developed and launched a free on-line reference database including autosomal STRs allele and Y-STR haplotype frequencies for 10 Argentinean provinces (http://www.ffyb.uba.ar/marcadores/antecedentes.asp). The dataset included 2710 individuals typed by means of 13 autosomal STRs and 239 individuals with the minimal Y-STRs haplotype (YHRD). In order to further improve the available information on-line, the database was increased for both autosomal and Y-STR markers. A total of 6501 genotypes from unrelated donors were added to the previous database. These samples were obtained from Buenos Aires, Chubut, Rio Negro, Santa Fe, Mendoza, Misiones, Corrientes, Chaco, Formosa and Salta, and typed at least with 13 autosomal STRs and 1336 unrelated males were also typed for Y-STRs. In parallel, protocols for DNA analysis and reference bibliography were updated. The present update attained a total of 9211 genotypes and 1575 Y-chromosome haplotypes from the Argentinean population. This contribution offers on-line statistical information about highly standardized genetic markers to the forensic and molecular anthropology research communities. [Copyright &y& Elsevier]

Abstract: The use of miniSTR markers is a valuable tool in the forensic laboratory since it allows high-quality genetic profiles to be obtained on low copy number (LCN) or degraded DNA taken from different samples, such as cadaveric material, paraffin-embedded tissue, chewing gum, traces of saliva, pieces of cloth, cigarette butts, bone samples, etc. In addition, it is useful to have additional STR loci to solve paternity cases with one or more inconsistencies or to increase the amount of genetic information for incomplete family studies, where the genetic profile of the alleged father has to be reconstructed. Genetic frequencies and forensic parameters were calculated for 12 non-CODIS miniSTR loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, D17S1290, D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) from a total of 506 unrelated individuals from various provinces in the central region of Argentina (Cordoba, Buenos Aires, Salta, Entre Rios and Santa Fe). The application of these miniSTR markers allowed LR>1000 values to be obtained in kinship cases with incomplete families whose results had not been significant when using commercial kits. In conclusion, a database with Argentine population frequencies from these 12 miniSTR markers may be very useful in adding supplementary information for the forensic genetic laboratory. [Copyright &y& Elsevier]

Abstract: It is well known that the use of STR (Short Tandem Repeats) for forensic purposes requires the existence of databases that reflect the allele distribution in the population they will be applied. During the last years we have received a greater affluence of samples from different regions of Argentina, instead of receiving almost only from Buenos Aires city, as we did six years ago. Because of this change in the population we are working with, our aim is to study the distribution of allele frequencies for 15 STR loci and calculate the statistical parameters of forensic interest, in a sample provenient from different regions of Argentina. A total of 375 unrelated individuals from different provinces in Argentina, were included for the analysis. DNA was obtained from blood samples with salting out Miller''s method, and AmpFlSTR® Identifiler was applied. Capillary electrophoresis of the amplification products were performed on an ABI PRISM® 3100 Genetic Analyzer (Applied Biosystems). The 3100 Data Collection Software–v1.0.1 (Applied Biosystems) and GeneScan–v3.7 (Applied Biosystems) and Genotyper Software-v3.7 (Applied Biosystems) were used. Statistical analysis for allele frequencies, power of discrimination and power of exclusion were calculated using PowerStats software. Deviation from Hardy–Weinberg equilibrium, observed and expected heterozygosity was calculated with Arlequin V3.1 software. All the loci studied were in Hardy–Weinberg equilibrium, and statistical parameters calculated were consistent with the bibliography. This database is a useful tool for routine forensic applications in our population. [Copyright &y& Elsevier]

Abstract: Short tandem repeat (STR) loci are the most informative DNA genetic markers for attempting to individualize biological material for application at paternity and forensic cases. Before a new marker system can be introduced into forensic casework, a database for the relevant population must be established for statistical evaluation of the evidence. Therefore, this report presents allele frequency data and parameters of biological or legal interest, such as heterozygosity value and power of exclusion in Buenos Aires Province (Argentina) population sample for the loci D19S433 and D2S1338. Blood samples (N =473) were collected form individuals unrelated throughout Buenos Aires Province on FTA cards. Following DNA extractions, multiplex PCR amplifications were carried out using AmpFlSTR Identifiler PCR Amplification kit (Applied Biosystems) and amplified products analyzed on an Applied Biosystems DNA sequencer (Model 3130). Heterozygosity value is estimated as 0.81184 for D19S433, and 0.85201 for D2S1338. Both STR loci are in Hardy–Weinberg equilibrium. For D19S433, power of exclusion and power of discrimination are estimated as 0.621 and 0.937, respectively. For D2S1338 the same parameters are 0.699 and 0.968. The allele frequency data can be used for deriving estimates of multiple locus profile frequencies for identity testing purposes. [Copyright &y& Elsevier]

Abstract: As a collaborative effort in solving sexual assault cases where there is no suspect, the DNA profiles associated with 273 cases were analyzed. Such cases were submitted from different Criminal Investigation Units belonging to eight judicial departments of Buenos Aires Province. A single NN male profile was recovered from the evidences by differential lysis with DNA IQ System (Promega) and typing with IdentiFiler kit. Comparative analysis of the compiled DNA profiles showed that in 45% of the cases the evidence DNA profile matched in at least two unrelated cases. Associations between groups of unsolved cases provided a valuable tool in aiding law enforcement investigations. [Copyright &y& Elsevier]

Abstract: Forensic laboratories must add as much genetic information as possible in order to solve the broadened variety of post-mortem paternity and kinship cases now routinely presented. Often, use of STR autosomal markers alone is not enough to reach a high discrimination power, especially when dealing with degraded post-mortem material or complex family pedigrees. In order to expand the set of genetic markers used to solve challenging cases, and since reference databases are required in forensic application, allele frequencies and forensic parameters for 38 InDel and 50 SNP binary markers were calculated from a sample of thirty (for SNPs) and fifty (for InDels) unrelated individuals from the two most populous cities of Argentina: Córdoba and Buenos Aires. DNA was extracted with a modified salting out procedure and amplification products were detected on an ABI 3130 Genetic Analyzer (Applied Biosystems). No significant deviations from Hardy–Weinberg expectations were found. In the analyzed sample, no pairwise linkage disequilibrium between InDels and SNPs was found neither among the 88 binary markers nor the 17 STR markers from commercial kits. Comparisons were also made with previously studied populations. The present database will be useful for forensic and paternity purposes for the above mentioned cities of Argentina. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples. [Copyright &y& Elsevier]

Abstract: The allele frequencies for 17autosomal short tandem repeats were determined in a sample of 1933 unrelated individuals from Mendoza, Argentina. The calculated parameters: polymorphism information content (PIC); discrimination power (DP); matching probability (MP); typical paternity index (TPI) and power of exclusion (PE), showed Penta E as the most valuable marker from the studied sample set. All loci met Hardy–Weinberg expectations using the Bonferroni correction for the number of loci analyzed. The mutation rate for these markers was analyzed by studying a total of 596 trio mother/son/father. We found a total of 14 mutations in different markers; all of them were single-step. [Copyright &y& Elsevier]

Abstract: Allele frequencies for 15 short tandem repeat (STR) loci present in AmpFℓSTR® Identifiler® PCR Amplification Kit (Applied Biosystems) were obtained from a sample of 839 unrelated individuals undergoing paternity testing. This sample includes individuals from all regions in Entre Rios province of Argentina. The most polymorphic loci were FGA, D18S51 and D2S1338. All the analyzed loci meet Hardy–Weinberg equilibrium after Bonferroni correction. Total non-discrimination probability and combined power of exclusion for the 15 tested STR loci were 1.91×10−18 and 0.9999995, respectively. [Copyright &y& Elsevier]

Abstract: A sample of 566 unrelated males from Mendoza province was typed for 12 Y-STRs loci, 237 of these males were typed for 17 Y-STRs. When analyzing only the minimal haplotype of 9 Y-STRs we found a total of 398 different haplotypes, of which 317 were unique, and the haplotype diversity was 0.9931. If we analyzed the 12 Y-STRs, which make up the extended haplotype, we observed that 87% of the total of 470 different haplotypes are unique, and the haplotype diversity was 0.9989. In the 237 males typed with 17 Y-STRs included in the AmpFISTR YFiler Amplification Kit (AB Applied Biosystems), we found 226 different haplotypes of which 96% are unique, and the most frequent haplotype appears only 3 times in the study population. On the other hand, in a total of 173 father/son pairs, mutations were observed in DYS389I/II, DYS385a/b, DYS439 and DYS458 markers. In addition, there were duplications on DYS19 and DYS437 markers. However, the mutation rates are similar to those already described. The comparison between our data and previous one from Mendoza, other Argentinean provinces and different world populations, reflected a similar haplotype distribution to that depicted by European populations. The most frequent haplotype is the modal for the European haplogroup R1b, this supports its European origin. [Copyright &y& Elsevier]

Abstract: The 12 Y-chromosome STRs included in the “minimal haplotype” plus “SWGDAM core set” (DYS438 and DYS439) and DYS437, were typed in 224 unrelated males from Mendoza province, Argentina. The amplifications were performed using PowerPlex®Y Systems (Promega Corp.) and AmpFISTR YFiler Amplification Kit (AB Applied Biosystems). A total of 203 different haplotypes were identified, of which 186 were unique and 17 were found in two or more individuals. Allele frequency and haplotype diversity (HD) were calculated. [Copyright &y& Elsevier]

Abstract: Allele frequencies and forensic parameters for twelve miniSTR autosomal loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677, D20S480, D6S2439, D6S1056, D9S1118, D4S2639 and D17S1290) were calculated from a sample of 506 unrelated individuals from the Central-East Region of Argentina. No significant deviations from Hardy–Weinberg expectations were found. Furthermore, comparisons with other previously studied populations were made. These twelve miniSTR markers may help forensic laboratories in solving parentage testing as well as in typing degraded DNA samples. [Copyright &y& Elsevier]