Greater Heterozygosity Research Articles

GENETIC VARIABILITY ASSESSMENT OF Sonneratia apetala (BUCH. -HAM.) IN THE SUNDARBANS OF BANGLADESH

Abstract Sundarbans is the single largest tract of natural mangrove forest in the world, which is situated in the south western coast of Bangladesh. This forest defends the south-western coastal region of the country from natural calamities, like cyclones, flood, tidal surges, tsunami etc. Sundarbans is the natural habitat for many mangrove plants. Sonneratia apetala exists in the low saline zone (LS), medium saline zone (MS) and in the high saline zone (HS) as a pioneer tree species of the Sundarbans. Genetic variability of S. apetala in these three saline zones were examined through the adoption of RAPD-PCR molecular marker. The expected heterozygosity of S. apetala in MS and HS (0.75±0.05 and 0.76±0.06, respectively) was greater than that of LS (0.60±0.13). Again, the average gene diversity over loci of this species in the MS and HS (0.59±0.37 and 0.62±0.38, respectively) was greater than that of LS (0.51±0.32). The greater heterozygosity and genetic diversity of S. apetala establishing in the MS and HS are the causes of its higher salt adaptability than that of growing in the LS in the Sundarbans. Due to higher genetic diversity and salt adaptability, S. apetala could persist in the increasing salinities in the Sundarbans. Moreover, S. apetala seedlings derived from the MS and HS zones of the Sundarbans can be planted in the high saline substrates in the coastal regions of Bangladesh, hence got added advantages for the coastal afforestation programs of Bangladesh.

Acceleration of the selection process in the population of Black and Spotted cattle by using genetic markers

Genetic researches of cattle breeds in the western region of Ukraine are ecologically necessary, and they also become the most actual in connection with the formation of breed associations. In addition, the research of the genetic characteristics of various breeds for use in agricultural production is an attempt to identify the most common genetically determined characteristics in the herd. The choice of such economically valuable characteristics is determined by modern methods of research in agriculture by selecting herds with such a gene pool in which this characteristic is the most typical. The genetic structure was evaluated by genetically determined polymorphism of blood groups and genetic-biochemical systems. Experiments were carried out on erythrocytes and blood plasma. Blood from the animals was taken from the jugular vein in a test tube with heparin. Polymorphism of proteins and enzymes was evaluated using the method of electrophoretic separation of proteins in 13 % starch gel in horizontal chambers followed with subsequent histochemical staining. Group erythrocyte antigens were determined according to the generally accepted methodology based on hemolytic tests using 48 reagents of 9 genetic systems. The genetic structure of this breed is characterized by the following features: the transferrin locus is characterized by the greatest heterozygosity – 0.729, but according to the Hardy-Weinberg law, this locus is in a balanced state (Р – 0.104). The dominant frequency of occurrence is the allele Tf A – 0.438, mainly as a result of AD1 and AD2 heterozygotes. The amylase locus (AM-l) is in an unbalanced state – there are not enough heterozygotes and too many homozygotes (Р – 0.013). The frequencies of occurrence of two alleles Am-l B and Am-l C are the same and amount to 0.500. Hemoglobin is monomorphic in all investigated animals (hemoglobin AA). For purine nucleoside phosphorylase (NP), there are no significant differences within the studied group of animals.The higher frequency of occurrence of the Np L allele is 0.872, but the Np H allele occurs less often, its frequency is 0.128, the heterozygosity of this locus is 0.225. As for blood groups, the vast majority of antigens detected with the help of 48 specific antisera are found in the antigenic spectrum of the investigated Black and Spotted dairy breed. However, the frequency of some antigens (less than 0.057) is extremely low (I1, Q, T1, T2, P1, P2, Y, R, U, I', B'', H''), others (J, B ', U') is slightly higher (0.082-0.099), and some (A2, G2, G3, B2, I2, O1, O2, Y2, D', G', E'2, O', Q', G'', C1, C2, E, W, X2, L, F, S, H'', Z) was sufficiently high (from 0.11 to 0.888). The Black and Spotted dairy breed has a unique genetic structure based on the investigated loci.

Chytrid fungus infection in alpine tree frogs is associated with individual heterozygosity and population isolation but not population-genetic diversity

Chytridiomycosis, a disease caused by the emerging fungus Batrachochytrium dendrobatidis (Bd), has been implicated in the decline of over 500 amphibian species. Population declines could have important genetic consequences, including reduced genetic diversity. We contrasted genetic diversity among both long-Bd-exposed and unexposed populations of the south-east Australian alpine tree frog (Litoria verreauxii alpina) across its range. At the population level, we found no significant differences in genetic diversity between Bd-exposed and unexposed populations. Encouragingly, even Bd-infected remnant populations that are now highly isolated maintain genetic diversity comparable to populations in which Bd is absent. Spatial genetic structure among populations followed an isolation-by-distance pattern, suggesting restricted movement among remnant populations. At the individual level, greater heterozygosity was associated with reduced probability of infection. Loss of genetic diversity in remnant populations that survived chytridiomycosis epidemics does not appear to be a threat to L. v. alpina. We suggest several factors underpinning maintenance of genetic diversity: (1) remnant populations have remained large enough to avoid losses of genetic diversity; (2) many individuals in the population are able to breed once before succumbing to disease; and (3) juveniles in the terrestrial environment have low exposure to Bd, providing an annual ‘reservoir’ of genetic diversity. The association between individual heterozygosity and infection status suggests that, while other work has shown all breeding adults are typically killed by Bd, males with greater heterozygosity may survive longer and obtain fitness benefits through extended breeding opportunities. Our results highlight the critical role of life history in mitigating the impacts of Bd infection for some amphibian species, but we infer that increased isolation as a result of disease-induced population extirpations will enhance population differentiation and thus biogeographic structure.

Reduced inbreeding depression in separate generations of onions

Abstract Mitigating reductions in vigor in onion seed production has been a great challenge to breeding programs. Therefore, we compared the effects of inbreeding depression among populations obtained from self-fertilization and crossbreeding with two and three plants. We evaluated eleven populations and three breeding methods (two and three-plant crossbreeding, and self-fertilization of one plant) and measured the characteristics related to seed yield (plant appearance, stem vigor, number of umbels, flowering uniformity, fruit setting, and resistance to Alternaria) from 2014 to 2015. Thirteen RAPD molecular markers were used to determine the genetic divergence among populations derived from different breeding methods. We found that inbreeding depression affects plant vigor in early generations that have greater heterozygosity. Three-plant crossbreeding results in greater seed yield in populations with low levels of inbreeding. The populations obtained from self-fertilization and two- and three-plant crossbreeding were genetically similar, demonstrating the efficiency of obtaining inbred lines without genetic divergence.

Sub-Genome Polyploidization Effects on Metabolomic Signatures in Triploid Hybrids of Populus

Allopolyploids are known to have superior advantages such as high growth speed. Triploids have even greater heterozygosity, explaining more phenotypic variance than 2n hybrid F1 and have therefore become new resources in breeding. To date, the metabolomic basis underlying polyploidization vigor remains unclear. Here, we identified and compared 235 metabolites in the shoot apical buds between multiple allo-triploid populations and parental 2n hybrid F1 in Populus via metabolome profiling using liquid chromatography–mass spectrometry (LC–MS) assays. Associations with growth vigor in three types of allo-triploid populations, namely first division restitution (FDR), second division restitution (SDR) and postmeiotic restitution (PMR) generated from doubled 2n female gametes and male gametes of 2n hybrid, were also investigated. Each allo-triploid population has different sub-genome duplicated. Major metabolomes were amino acids, secondary metabolism associated, and carbohydrates. We mapped 181 metabolites into known metabolism pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Ten compounds, i.e., fructose 1,6-diphosphate and xylulose, were more abundant in all allo-triploids than the 2n hybrid. Principal component analysis revealed the abundance of metabolites fell into distinct clusters corresponding to ploidy composition. Heterozygosity in triploids mainly effected the contents of carbohydrates and secondary metabolites rather than lipids. Comparisons between subgroups with different growth rates revealed some carbohydrates and secondary metabolites of flavonoids were positively associated with gene expression and the high growth vigor. The results provided an informative metabolomic basis for factors conferring growth vigor in polyploid Populus.

Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

BackgroundGenetic diversity is known to confer survival advantage in many species across the tree of life. Here, we hypothesize that such pattern applies to humans as well and could be a result of higher fitness in individuals with higher genomic heterozygosity.ResultsWe use healthy aging as a proxy for better health and fitness, and observe greater heterozygosity in healthy-aged individuals. Specifically, we find that only common genetic variants show significantly higher excess of heterozygosity in the healthy-aged cohort. Lack of difference in heterozygosity for low-frequency variants or disease-associated variants excludes the possibility of compensation for deleterious recessive alleles as a mechanism. In addition, coding SNPs with the highest excess of heterozygosity in the healthy-aged cohort are enriched in genes involved in extracellular matrix and glycoproteins, a group of genes known to be under long-term balancing selection. We also find that individual heterozygosity rate is a significant predictor of electronic health record (EHR)-based estimates of 10-year survival probability in men but not in women, accounting for several factors including age and ethnicity.ConclusionsOur results demonstrate that the genomic heterozygosity is associated with human healthspan, and that the relationship between higher heterozygosity and healthy aging could be explained by heterozygote advantage. Further characterization of this relationship will have important implications in aging-associated disease risk prediction.

Genetic Polymorphism of HPA 1-17 Alloantigen System in Heilongjiang Menggu Population

To explore the polymorphisms of the human platelet antigen (HPA) gene of Han and Menggu population of Heilongjiang province in China, to determine platelet antigen system with clinical significance by judging the rate of incompatibility of HPA, as well as to establish a database of donors HPA including the Han nationality and the minority nationality. The samples of unrelated healthy Menggu population (100 cases) people were selected from Heilongjiang province in China, and 123 cases in healthy Han population in Heilongjiang as control were collected. The technique of PCR-sequence specific primers (PCR-SSP) was used for genotyping of 34 alleles in HPA1-17 gene. The gene frequency and genotype frequency were separately calculated, and the allele frequency distribution in Menggu population was compared with the results from Han population. In the Han population, monomorphic HPA-4,HPA-7-14,HPA-16, 17 were found in the samples, none of HPA-b was found in these samples. For HPA-1, 2, 4, 5 and 6, aa homozygosity was predominant. In the Menggu population, monomorphic HPA 1, HPA 5, 6, HPA 7-14, HPA 16,17 were found in the samples, none of HPA-b was found in these samples. For HPA 2, 4 aa homozygosity was predominant. HPA-3, 15 had the greatest heterozygosity in 2 population. HPA-1a and HPA-3a frequency of Menggu population were significantly different from that of Han population in Heilongjiang. Distribution of the allele polymorphism of HPA 1-17 in Heilongjiang Han population is similar to that in Menggu population, and it shows its own characteristics. When the local HPA genotyped database of platelet donors in Heilongjiang is established, the count of Menggu donor should be increased.

Genetic divergence among interspecific Paspalum hybrids based on seed production traits

ABSTRACT The use of genetic divergence as a basis for identifying superior individuals, with greater heterozygosity, is important in view of the difficulty when selecting of dissimilar genotypes exhibiting high average for interest traits. The aim of this study was to evaluate the genetic divergence and the expression of seed production traits in seventeen apomictic Paspalum plicatulum × Paspalum guenoarum hybrids and two male parents (P. guenoarum). A randomized block design was used, with genotypes individually arranged into ten blocks. The following traits were assessed: total number of tillers/plant (TT), reproductive tiller/plant (RT), number of racemes per inflorescence (NRI), reproductive tiller height (RTH), inflorescence rachis length (IRL), number of seeds/inflorescence (NSI), weight of a thousand seeds (WTS) and seed production (SP). Genetic divergence among the genotypes was estimated using the Tocher method and UPGMA clustering, based on the generalized Mahalanobis distance (D2 ii’). The Tocher and UPGMA optimization methods showed high concordance. The traits that most contributed to genetic divergence were RTH (23.59%), IRL (21.63%), WTS (16.67%) and SP (14.23%). The presence of genetic diversity made it possible to identify divergent genotypes and those with high means for the traits studied, allowing the selection of genotypes with significant breeding potential. Repeated cross-breeding of female superior plants with the genotypes Azulão and H20 can result in a high heterosis effect on seed production characteristics.

Viability of Booby Offspring is Maximized by Having One Young Parent and One Old Parent.

It is widely expected that the quality of offspring will vary with the age of their parents and that this variation should influence animals’ choice of mates. However, theoretical predictions for age effects are contradictory and, to our knowledge, we do not know for any wild animal how the quality of offspring is affected by both parents’ ages across their lifespans, or whether mothers’ and fathers’ ages interact. We tackled this question using long-term data on a highly philopatric, insular population of the blue-footed booby (Sula nebouxii). In this species extra-pair paternity is most common in pairs of two young parents or two old parents, implying that these age combinations might prejudice offspring quality. Analysis of the viability of 3,361 offspring of parents up to 21 years old revealed that fledglings with two young parents or two old parents were least likely to become breeders, whereas fledglings with one young parent and one old parent were most likely to do so. For young parents of either sex, offspring viability increased with age of the other parent; for very old parents, it decreased. These effects could be mediated by parents flexibly modifying their investment in offspring in response to their own and their partners´ ages, but evidence for this was lacking. In 5,343 breeding attempts, although mothers’ and fathers’ ages independently affected four heavily care-dependent breeding traits at the clutch and nestling stages, their interaction did not affect any trait. The effects of parental age combinations on viability could also be mediated by genes: fledglings with one young parent and one old parent could benefit from greater heterozygosity or better genes.

Molecular analysis and validation of primitive races peach palm (Bactris gasipaes) by means of markers RAPD

Molecular markers were used to examine the genetic variability of eight landraces of peach palm (Bactris gasipaes var. gasipaes) and two wild populations (Bactris gasipaes var. chichagui), their relationships and genetic structures. Two hundred plants of these 8 races were used and 18 plants of the two wild populations, one from the Magdalena River, Colombia, and the other from the Xingu River, Para, Brazil. Eight primers were used to generate RAPD markers, of which 124 markers with 101 polymmorphic. The observed heterozygosity was 0.38, with 93% polymorphism, both slightly greater than in earlier studies. The gene flow medium was 1.12 among the races of peach palm, which is explained by the distance between most breeds analyzed. These values are significantly larger than those of [1], because it is a less accurate marker for this type of analysis. The Amazonian landraces had greater heterozygosity and % polymorphism than the Central American race. The structure of the dendrogram with the four previously studied landraces, essentially validating it and confirming two landrace groups - one Occidental and one Oriental. When the Jurua landrace was added to the analysis, it joined the other Occidental races, as expected by its geographic position. When the other landraces were added to the analysis, a consistency and some problems were observed. The consistency was that all the landraces joined the Occidental group, expected by their geographic positions. The problems were the grouping of the Vaupes landrace with the Jurua landrace, which are geographically distant and have different fruit sizes and shapes. The relationship between the Cauca landrace and the Inirida landrace was also problematic, since they are geographically separated. The two wild populations joined the landraces at a great distance, suggesting that they did not participate in the domestication of the cultivated landraces and indirectly reenforcing the hypothesis of a single origin in southwestern Amazonia.

Applications of platelet antigen gene typing and matching in the platelet transfusion

The aim of this study was to establishment of known HPA genotype platelet donor data base and carry out the platelet antigen gene typing and matching in the platelet transfusion so as to prevent the production of the antibody and to avoid the platelet transfusion refractoriness. HPA of the donors and the patients were genotyped by PCR-SSP. The platelet transfusion with the same ABO type and HPA genotypes as the patient was selected and infused if the solid-phase agglutination matching was consistent. The results showed that the distribution of HPA types in Chinese Mudanjiang area had its own characteristics. HPA-15 had the greatest heterozygosity, and then HPA-3. The effective rate was 94.4% if both the HPA types and the ABO types were coincident while the effective rate was 77.8% when only ABO types were coincident. It is concluded that the distribution of HPA types in Chinese Mudanjiang area presents genetic polymorphism. The platelet transfusion with genetic typing and matching of both HPA and ABO types is an effective way to avoid production of the antibody and platelet transfusion refractoriness.

Estrogen receptor 1 promoter polymorphism and digit ratio in men

The 2D:4D digit ratio, the relative lengths of the index and ring fingers in humans, is a widely used proxy measure for prenatal testosterone exposure. Varying distributions of androgen and estrogen receptors on the second and fourth digits, both of which regulate digit development, appears to be the basis for this effect. Polymorphism in a tandem repeat in the gene coding for the estrogen receptor α (ESR1) in zebra finches (Taeniopygia guttata) not only explains a significant amount of variation in digit ratio but also seems to explain the significant correlation between digit ratio and sexual behavior in these birds. Here, we investigate the effect of TA polymorphism in ESR1 on 2D:4D and aggressive behavior in men. We genotyped ESR1 polymorphism in samples collected for a previous study in which we had demonstrated an association between androgen receptor polymorphism and aggression, but not 2D:4D. We found a significant effect of ESR1 TA repeat number on left hand 2D:4D ratio. More TA repeats were associated with higher, more feminized, digit ratios. We found no effect on right hand 2D:4D. We also found an effect of ESR1 polymorphism on aggressive behavior. Greater heterozygosity in TA(n) was associated with lower physical aggression. Our results suggest that a significant amount of left hand 2D:4D variation and aggressive behavior is due to this variation in ESR1, and that some of the correlation between digit ratio and social behavior is due to pleiotropic effects of ESR1 variation on the two traits.

Genetic variability among Anopheles species belonging to the Nyssorhynchus and Anopheles subgenera in the Amazon region

Isoenzymatic analyses were performed involving species of the Nyssorhynchus and Anopheles subgenera in order to estimate the intra and interspecies genetic variability. Mosquitoes were caught at different localities in the Amazon region. The collection and rearing of mosquitoes in the laboratory followed specific protocols. For the genetic variability analyses, the technique of horizontal electrophoresis on starch and starch-agarose gel with appropriate buffer systems was used. The alloenzyme variation was estimated using the Biosys-1 software. Out of the 13 loci, eight were polymorphic. Anopheles nuneztovari presented the largest number of alleles per locus, while the smallest number was detected in Anopheles marajoara from Macapá. The largest number of polymorphic loci was found for Anopheles marajoara from Maruanum and the smallest for Anopheles benarrochi (Guayará Mirim). Anopheles darlingi (Macapá) presented the greatest heterozygosity (Ho = 0.167 +/- 0.071), while the lowest heterozygosity (Ho = 0.045 +/- 0.019) was observed in Anopheles intermedius (Pacoval) of the subgenus Anopheles. Wright's F coefficient revealed considerable genetic structuring between the populations of Anopheles darlingi (Fst = 0.110) and between the populations of Anopheles marajoara (Fst = 0.082). Considering all the species studied, the genetic distance ranged from 0.008 to 1.114. The greatest distance was between Anopheles mattogrossensis and Anopheles oswaldoi, while the smallest was between the Anopheles benarrochi populations.

Genetic variability and viral seroconversion in an outcrossing vertebrate population.

Inverse correlations between genetic variability and parasitism are important concerns for conservation biologists. We examined correlations between neutral genetic variability and the presence of antibodies to canine distemper virus (CDV) and feline parvovirus (FPV) in a free-ranging population of raccoons. Over 3 years there was a strong relationship between age and seroprevalence rates. Most young animals were seronegative to CDV and FPV, but the oldest age class was greater than 80 per cent seropositive to both viruses. CDV-seropositive animals had greater heterozygosity and lower measures of inbreeding compared with CDV-seronegative animals. This relationship was strongest among the youngest animals and did not occur during a 1 year CDV epidemic. In contrast, FPV-seropositive animals only had significantly lower measures of inbreeding in 1 year, perhaps because FPV-associated mortality is relatively low or primarily occurs among very young individuals that were under-represented in our sampling. These results suggest that even in large outcrossing populations, animals with lower heterozygosity and higher measures of inbreeding are less likely to successfully mount an immune response when challenged by highly pathogenic parasites.

Low allozyme variation in tigerfish Hydrocynus vittatus (Teleostei: Alestidae) from the Okavango panhandle, with notes on the selection of candidates for artificial breeding

To ensure the utilisation of optimal tigerfish gene pools for artificial propagation, the hypothesis that tigerfish from the Okavango system should have greater heterozygosity than those from smaller river systems was tested. This electrophoretic analysis provides the first report of the quantity and pattern of genetic variation for tigerfish of the Okavango Delta to be considered for artificial propagation and as candidates for an evolutionary significant unit. Mean heterozygosity was 1% in the Okavango, as compared to 1.9% in the Upper Zambezi and 5.6% in the Olifants River systems. Possible reasons for this anomaly, in terms of the Hardy-Weinberg principle, include the founder effect caused when the Okavango and Zambezi rivers became separated, and/or that the Okavango is a more stable system and therefore that a large variation might not be required in its individuals for survival. Significant differences of genotypes were found among all populations previously studied. The selection of potential candidates for artificial breeding is discussed.

Genetic Structure of Tree and Shrubby Species Among Anthropogenic Edges, Natural Edges, and Interior of an Atlantic Forest Fragment

Two species, Psychotria tenuinervis (shrub, Rubiaceae) and Guarea guidonia (tree, Meliaceae), were used as models to compare the genetic structure of tree and shrubby species among natural edges, anthropogenic edges, and a fragment interior. There were significant differences between two genetic markers. For isozymes, P. tenuinervis presented greater heterozygosity (expected and observed) and a higher percentage of polymorphic loci and median number of alleles than G. guidonia. For microsatellites, there was no difference in genetic variability between the species. Only P. tenuinervis, for isozymes, showed differences in genetic variability among the three habitats. There was no genetic structure (F (ST) < 0.05) among habitats in both plant species for both genetic markers. Isozymes showed great endogamy for both plant species, but not microsatellites. The forest fragmentation may have negative effects on both spatial (among edges and interior) and temporal genetic variability.

Concordance between life history traits, invasion history, and allozyme diversity of the Everglades invader Melaleuca quinquenervia

During the century following its initial introduction in 1886, the Australian tree Melaleuca quinquenervia (Myrtaceae) dispersed from a few introduction points to occupy over 200,000 ha, primarily in historic Everglades wetlands of southern Florida. Cellulose acetate gel electrophoresis (CAGE) was used to investigate the allozyme diversity and population genetic structure of 208 individuals in a dozen populations resulting from this invasion. The analyses showed that these populations have a high (82%) rate of polymorphic loci and an average of 2 alleles/locus. There was substantial heterozygosity (mean H e = 0.356), which concords well with recent studies reporting a greater number of introduction events and sources than generally recognized. The introduction history and distributional patterns within Florida have led to geographic structuring ( G ST = 0.419) in which the Gulf Coast metapopulation has a greater effective number of alleles and greater heterozygosity than the Atlantic Coast metapopulation. The gene diversity in M. quinquenervia was comparable to other tropical woody species. Its strong population divergence was reminiscent of pioneer species and consistent with its status as a plant invader in Florida.

The Reliability of Haplotyping Inference in Nuclear Families: Misassignment Rates for SNPs and Microsatellites

Single nucleotide polymorphisms (SNPs) are widely used when investigators try to map complex disease genes. Although biallelic SNP markers are less informative than microsatellite markers, one can increase their information content by using haplotypes. However, assigning haplotypes (i.e., assigning phase) correctly can be problematic in the presence of SNP heterozygosity. For example, a doubly heterozygous individual, with genotype 12, 12, could have haplotypes 1-1/2-2 or 1-2/2-1 with equal probability; in the absence of additional information, there is no way to determine which haplotype is correct. Thus an algorithm that assigns haplotypes to such an individual will assign the wrong one 50% of the time. We have studied the frequency of haplotype misassignments, i.e., haplotypes that are misassigned solely because of inherent marker ambiguity (not because of errors in genotyping or calculation). We examined both SNPs and microsatellite markers. We used the computer programs GENEHUNTER and SIMWALK to assign the haplotypes. We simulated (a) families with 1–5 children, (b) haplotypes involving different numbers of marker loci (3, 5, 7 and 10 loci, all in linkage equilibrium), and (c) different allele frequencies. Misassignment rates are highest (a) in small families, (b) with many SNP loci, and (c) for loci with the greatest heterozygosity (i.e., where both alleles have frequency 0.5). For example, for triads (i.e., one-child families with both parents genotyped), misassignment rates for SNPs can reach almost 50%. Family sizes of 4–5 children are required in order to ensure a misassignment frequency of ≤5% for ten-SNP haplotypes with allele frequencies of 0.25–0.5. For microsatellites, a family size of at least 2–3 children is necessary to keep haplotyping misassignments ≤5%. Finally, we point out that it is misleading for a computer program to yield haplotype assignments without indicating that they may have been misassigned, and we discuss the implications of these misassignments for association and linkage analysis.

Status of Austro-Asiatic groups in the peopling of India: An exploratory study based on the available prehistoric, linguistic and biological evidences.

Among the most contentious currently debated issues is about the people who had settled first in the Indian subcontinent. It has been suggested that the communities affiliated to the Austro-Asiatic linguistic family are perhaps the first to settle in India and the palaeoanthropological evidences suggest the earliest settlement probably around 60,000 years BP. Recent speculations, based on both traditional genetic markers and DNA markers, seem to corroborate the aforesaid view. However, these studies are inadequate both in terms of the representation of the constituent groups within this broad linguistic category as well as the number of samples that represent each of them. We strongly feel that, before making any formidable conclusions on the peopling of India and/or the history of settlement, it is necessary to ascertain that the Austro-Asiatic speakers, represented by over 30 different tribal groups, either genetically constitute a homogenous single entity or are a heterogeneous conglomeration, derived from different sources. As a first step towards this we tried to collate and analyse the existing information geographic, ethno-historic, cultural and biological. The results of the analyses of anthropometric and genetic marker data indicate that the Austro-Asiatic groups, particularly the Mundari speakers, with certain exceptions, show greater homogeneity among them when compared to the other linguistic groups, although certain groups show as outliers. However, traditional genetic markers show lower within population heterozygosity compared to Dravidian and other Indian populations. This is contrary to what has been claimed in case of certain DNA markers. Given that relatively greater heterozygosity among the Austro-Asiatic populations has been taken as one of the important evidences supporting greater antiquity of these populations one should await results of detailed DNA studies being currently undertaken by us, involving a number of Austro-Asiatic and other ethnic populations of India to resolve the issue unequivocally.

PCR with sequence-specific primer-based simultaneous genotyping of human platelet antigen-1 to -13w.

Accurate human platelet antigen (HPA) typing is important for patients with diagnosis of alloimmune thrombocytopenic syndromes and provision of HPA-matched blood components for these patients. Thirteen sequence-specific primers (SSPs) designed on the basis of known published polymorphisms for HPA-1 to HPA-13w, respectively, were employed for simultaneous HPA genotyping. All PCR amplifications were carried out with identical cycling conditions in 96-well plates containing primer mixtures. A total of 300 blood samples from unrelated volunteer donors in Taiwan were included in the study. All primers had specific amplification products. The typing results were available within 4 hours each time for up to four blood samples tested. Among the 13 HPAs, HPA-3 had the greatest heterozygosity with a gene frequency of 0.3267, 0.4967, and 0.1767 for HPA-3a/HPA-3a, HPA-3a/HPA-3b, and HPA-3b/HPA3-b, respectively. For the remaining 12 HPAs, the predominance of a/a homozygosity was noted for HPA-1, -2, -4, -5, and -6, with a frequency ranging from 0.9200 to 0.9967. The frequency of a/a homozygosity was 1.0000 for HPA-7w to -13w, except for HPA-10w, for which one case was observed to be HPA-10aw/HPA-10bw heterozygous. Excluding HPA-3, b/b homozygosity was noted in only one case (HPA-6b/HPA-6b). The prevalence rates of HPA-1 to -13w in this study were consistent with previous reports using different methods. An extended, streamlined PCR-SSP protocol for simultaneous genotyping of HPA-1 to HPA-13w was established. This allows fast and reliable diagnosis of alloimmune thrombocytopenia, and is readily applicable to large-scale genetic population studies.