Related Haplotypes Research Articles

The role of gene-gene and gene-environmental interactions of polymorphic matrix metalloproteinases loci in the formation of the risk of stroke in men with hypertension

Analysis of the role of genetic polymorphisms of matrix metalloproteinases (MMPs), their gene-gene and gene-environment interactions in the formation of ischemic stroke in men with arterial hypertension (AI). The study included 523 men with arterial hypertension: 201 patients with ischemic stroke and 322 patients without stroke. The association of MMPs loci with stroke with hypertension was determined by logistic regression analysis in dominant, recessive, additive genetic models in PLINK v.2.050. For five SNPs co-located on chromosome 11 (314.3 kb), haplotypic analysis was performed, the relationship of haplotypes with stroke development was determined by the EM algorithm. Gene-gene and gene-environment interactions of MMPs with smoking and alcohol consumption during stroke development were evaluated by GMDR (Generalized Multifactor Dimensionality Reduction) using GMDR v.0.9 software. Polymorphic locus rs3025058 is associated with stroke in men in dominant and additive genetic models (OR=0.63-0.74, pperm=0.03). Four haplotypes of MMPs have a protective effect on the development of stroke with hypertension (OR=0.48-0.50, pperm=0.02-0.03). Four models of gene-gene interactions of polymorphic MMPs loci (OR=2.19-2.55, pperm<0.001) and three four-factor models of gene-environment interactions of MMPs with alcohol abuse (OR=2.82-3.11, pperm<0.001) are associated with a high risk of ischemic stroke in men with hypertension. rs3025058, rs1320632, rs11225395 and rs1799750 demonstrate the greatest contribution to gene-gene and gene-environment interactions in the formation of AI. Thus, the results of the study indicate that the interactions of MMPs genes with each other and with modifiable environmental factors play a significant role in the development of stroke with hypertension in men.

Genetic variants in SLC22A1 are related to serum lipid levels in Mexican women

Dyslipidemia is the main risk factor for coronary artery disease and is characterized by alterations in concentrations of lipids, including low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDL-c), and triacylglycerols. The participation of several genes in the development of dyslipidemia has been evidenced. Genetic variants in SLC22A1 have been associated with elevated cholesterol and LDL-c levels. The aim of this study was to evaluate the association between single-nucleotide polymorphisms (SNPs) in the SLC22A1 gene with atherogenic risk lipid levels in Mexican women. Anthropometric and biochemical measurements were performed, and four SNPs in SLC22A1 were genotyped by real-time polymerase chain reaction. The Hardy-Weinberg equilibrium was verified, and haplotype frequencies were calculated. We found significant differences between the allele frequencies of the SNPs analyzed with those reported in Mexico and in the world, which could be due to differences in the historical admixture of the women studied. Generalized linear models were evaluated to determine the association between genotypes and haplotypes with lipids levels. We identified a significant increase in total cholesterol and LDL-c levels in women who were carriers of the GA and AG genotypes of the polymorphisms rs628031 and rs594709, respectively, significant effect that is also shown in a dominant inheritance model. Interestingly, we identified an important relationship of the AGC-GAT haplotype with the elevation in LDL-c levels and AGA-GAT haplotype with the elevation in HDL-c levels. On the other hand, we found a strong linkage disequilibrium between the polymorphisms studied. Our results show that variants in the SLC22A1 gene influence serum levels of atherogenic risk lipids, suggesting that these variants probably affect the function of organic cation transporter-1 and therefore, on the regulation of lipid metabolism.

Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.).

Nitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll content, and leaf length) of the 225-rice-variety natural population from the Rice 3K Sequencing Project across normal nitrogen (NN) and low nitrogen (LN) environments. The LNGR phenotypic difference between NN and LN levels was used for gene analysis using a genome-wide association study (GWAS) combined with 111,205 single-nucleotide polymorphisms (SNPs) from the available sequenced data from the 3K project. We obtained a total of 56 significantly associated SNPs and 4 candidate genes for 4 LNGR traits. Some loci were located in the candidate regions, such as MYB61, OsOAT, and MOC2. To further study the role of candidate genes, we conducted haplotype analyses to identify the elite germplasms. Moreover, several other plausible candidate genes encoding LN-related or NUE proteins were worthy of mining. Our study provides novel insight into the genetic control of LNGR and further reveals some related novel haplotypes and potential genes with phenotypic variation in rice.

VNTR Typing of the Bacterial Rice Pathogen Burkholderia glumae Reveals the Coexistence of Several Diverging Lineages in a Single Field in Colombia.

Burkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. To estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. To detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or variable number tandem repeats (VNTRs), as well as part of the Toxoflavin toxA gene in all strains. Results show that the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan; data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, and that five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.

Precision medicine in diabetes: A non-invasive prenatal diagnostic test for the determination of fetal glucokinase mutations.

ABSTRACTHyperglycemia caused by mutations in the glucokinase gene, GCK, is the most common form of monogenic diabetes. Prenatal diagnosis is important, as it impacts on treatment. This study reports a monogenic non‐invasive prenatal diagnostic (NIPD‐M) test on cell‐free DNA in maternal plasma using the relative haplotype dosage. In three pregnancies of two families with known maternal GCK mutations, the fetal genotype was determined unambiguously already at 12 weeks of gestation. In summary, proof is provided of the feasibility for NIPD‐M in GCK diabetes.

Identification and phylogenetic analysis of voltage-gated sodium channel haplotypes in the malaria vector Anopheles sinensis using a high-throughput amplicon sequencing approach

BackgroundAnopheles sinensis is a dominant vector for malaria transmission in Asian countries. Voltage-gated sodium channel (VGSC) mutation-mediated knock-down resistance (kdr) has developed in many A. sinensis populations because of intensive and long-term use of pyrethroids. Our previous study showed that multiple mutations at position 1014 of the VGSC were heterogeneously distributed in A. sinensis populations across Sichuan, China.MethodsTo understand resistance genotypes at the haplotype level and reconstruct the phylogenetic relationship of VGSC haplotypes, a cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach was established to clarify haplotypes containing codon 1014 of the VGSC gene from a total of 446 adults collected in 12 locations of Sichuan, China.ResultsNineteen (19) haplotypes were identified, including 11 wild 1014L, 6 resistance 1014F, and 2 resistance 1014C haplotypes. We found that resistance haplotypes of A. sinensis VGSC were widely distributed at frequencies ranging from 3.67 to 92.61%. The frequencies of the 1014C haplotype in the southeast of Sichuan (Luzhou, Guangan, and Suining) were relatively higher than those in other sampling locations. Phylogenetic analyses support that kdr-type mutation at position 1014 is not singly originated and resistance 1014C haplotypes evolve from TTT-encoding 1014F.ConclusionsA cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach has been established in this study. The data revealed the patchy distribution of VGSC resistance haplotypes with overall high frequencies in Sichuan, China. Phylogenetic analyses support multiple origins and sequential evolution (1014L → 1014F → 1014C) for kdr-type mutations in A. sinensis.Graphical abstract

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

BackgroundHepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world.MethodsWe used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed.ResultsThe dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution).ConclusionsThe current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite.Graphical abstract

Molecular characterization of Trypanosoma vivax in tsetse flies confirms the presence of the virulent Tvv4 genotype in Kenya: Potential implications for the control of trypanosomiasis in Shimba Hills.

Trypanosoma vivax is a vector-borne protozoan parasite of livestock endemic to Africa and South America. To date, fifteen genotypes of the parasite have been described in vertebrate and insect hosts in East Africa. However, information regarding T. vivax diversity remains limited in many endemic countries in the sub-region, including Kenya. Such information could deepen insight into the local epidemiology of animal trypanosomiasis in Shimba Hills, a wildlife area in southeast Kenya where T. vivax is endemic and infects livestock. We employed two-gene conventional-PCR-sequencing and phylogenetic analysis to characterize T. vivax genotypes in tsetse flies collected between November 2018 and September 2019 in the wildlife-livestock interface of the Shimba Hills National Reserve. Phylogenetic analysis of Internal Transcribed Spacer-1 (ITS-1) sequences of T. vivax isolates confirmed the presence of two T. vivax genotypes in Shimba Hills of which >80% of T. vivax isolates from tsetse flies clustered within the virulent Tvv4-genotype clade. Tsetse infections with the Tvv4 genotype were also confirmed based on 18S rRNA gene sequencing. Expanded gene characterization identified three closely related haplotypes within the Tvv4-clade. The Tvv4-isolates were detected in male and female Glossina pallidipes tsetse flies, most of which were collected from grasslands and within two kilometres of the Shimba Hills National Reserve boundary. Considering that T. vivax is the most common trypanosome in the Shimba Hills area and causes severe clinical conditions in livestock, the Tvv4 genotype reported here for the first time in Kenya contributes to our understanding of these pathologies. The effectiveness of trypanocidal drugs in the management of Tvv4 is presently not clearly understood. Therefore, the parasite management in Shimba Hills should focus on vector control to reduce the density of G. pallidipes, especially in grasslands near the wildlife protectorate.

Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids

Numerous animal lineages have maternally inherited symbionts that are required for host reproduction and growth. Endosymbionts also pose a risk to their hosts because of the mutational decay of their genomes through genetic drift or to selfish mutations that favor symbiont fitness over host fitness. One model for heritable endosymbiosis is the association of aphids with their obligate bacterial symbiont, Buchnera We experimentally established heteroplasmic pea aphid matrilines containing pairs of closely related Buchnera haplotypes and used deep sequencing of diagnostic markers to measure haplotype frequencies in successive host generations. These frequencies were used to estimate the effective population size of Buchnera within hosts (i.e., the transmission bottleneck size) and the extent of within-host selection. The within-host effective population size was in the range of 10 to 20, indicating a strong potential for genetic drift and fixation of deleterious mutations. Remarkably, closely related haplotypes were subject to strong within-host selection, with selection coefficients as high as 0.5 per aphid generation. In one case, the direction of selection depended on the thermal environment and went in the same direction as between-host selection. In another, a new mutant haplotype had a strong within-host advantage under both environments but had no discernible effect on host-level fitness under laboratory conditions. Thus, within-host selection can be strong, resulting in a rapid fixation of mutations with little impact on host-level fitness. Together, these results show that within-host selection can drive evolution of an obligate symbiont, accelerating sequence evolution.

Determination of haplotype variation and relationship between desirable agronomic traits and microsatellite alleles on chromosomes 4B and 7D in bread wheat

Determination of haplotype variation and relationship between desirable agronomic traits and microsatellite alleles on chromosomes 4B and 7D in bread wheat

DNA barcode identification of Conopomorpha cramerella (Snellen, 1904) (Lepidoptera: Gracillariidae) and other moths affecting cacao in Papua New Guinea

AbstractEconomically important cacao (Theobroma cacao Linnaeus 1753) plantations in South East Asia and Papua New Guinea (PNG) are significantly affected by the cocoa pod borer (CPB) moth. Species identity of the pest is attributed to Conopomorpha cramerella (Snellen 1904), a gracillariid moth endemic to Australasian and Oriental tropic regions that has evolved a host preference for introduced cacao. Suspected presence of cryptic CPB biotypes is largely unsupported by earlier genetic work but remains a concern to organisations developing species‐specific lure and/or control tools for managing this pest. We report the use of DNA barcoding to investigate population and species genetic diversity of CPB infecting cacao plantations in PNG at the eastern periphery of the pest's distribution. DNA barcodes from 94.4% of 179 moths from three disjunct PNG provinces (East Sepik, Bougainville and East New Britain) matched to reported C. cramerella sequence accessions. Genetic diversity among C. cramerella in PNG was limited to four closely related haplotypes, two of which were common in PNG and have previously been reported in the Malay Archipelago at different frequencies. We found evidence of significant population genetic structure between mainland and eastern offshore PNG provinces marked by a reduction of genetic diversity at the offshore provinces. We suggest C. cramerella populations in these offshore island provinces likely arose recently from a genetically depauperate cohort of founders from western sources. Ten moths were genetically unmatched to C. cramerella. Of these, six incidentally captured and degraded adults had novel unmatched DNA barcodes. Four larvae infesting cacao pods were genetically matched to Thaumatotibia zophophanes (Turner 1946) (Lepidoptera: Tortricidae) and an undefined Conopomorpha species distantly related to C. cramerella. The extent to which these two additional moth species affect the cacao industry in PNG (and potentially elsewhere) remains unknown. However, their low representation here (&lt;2.3% of samples) indicates they may be of lesser prominence than the widespread C. cramerella. Nevertheless, organisations designing and/or implementing CPB controls tailored specifically for C. cramerella will need to ensure empirical evidence of control efficiency is monitored with respect to species identity of the captured pests.

Population genomic structure of killer whales (Orcinus orca) in Australian and New Zealand waters

AbstractPopulation genomic data sets have enhanced power to detect cryptic and complex population structure and generate valuable information for the conservation and management of wildlife species. Globally, killer whales (Orcinus orca) are considered to have a complex population structure due to their ability to specialize in a variety of ecological niches. In the Australasian region, they are found year round in New Zealand waters and are sighted in all Australian waters, with seasonal aggregations in the northwest (NWA) and southwest (SWA). Regionally, there is some knowledge regarding killer whale abundance, diet, acoustics, and social structure, but limited information about their population structure. Here, we present a population structure assessment of Australasian killer whales using 17,491 high quality genome‐wide single nucleotide polymorphisms (SNPs), combined with sequences of the mitochondrial DNA control region. The results indicate a minimum of three populations: New Zealand, NWA, and SWA. These populations present moderate levels of genomic diversity, negligible levels of inbreeding, small effective population sizes, and low contemporary migration rates among them. Mitochondrial DNA analysis elucidated five closely related haplotypes, suggestive of matrilineal societies, consistent with killer whales elsewhere. This information will assist conservation management of killer whales in the Australasian region.

Sequence analysis of Plasmodium vivax Duffy binding proteins reveals the presence of unique haplotypes and diversifying selection in Ethiopian isolates

BackgroundRed blood cell invasion by the Plasmodium vivax merozoite requires interaction between the Duffy antigen receptor for chemokines (DARC) and the P. vivax Duffy-binding protein II (PvDBPII). Given that the disruption of this interaction prevents P. vivax blood-stage infection, a PvDBP-based vaccine development has been well recognized. However, the polymorphic nature of PvDBPII prevents a strain transcending immune response and complicates attempts to design a vaccine.MethodsTwenty-three P. vivax clinical isolates collected from three areas of Ethiopia were sequenced at the pvdbpII locus. A total of 392 global pvdbpII sequences from seven P. vivax endemic countries were also retrieved from the NCBI archive for comparative analysis of genetic diversity, departure from neutrality, linkage disequilibrium, genetic differentiation, PvDBP polymorphisms, recombination and population structure of the parasite population. To establish a haplotype relationship a network was constructed using the median joining algorithm.ResultsA total of 110 variable sites were found, of which 44 were parsimony informative. For Ethiopian isolates there were 12 variable sites of which 10 were parsimony informative. These parsimony informative variants resulted in 10 nonsynonymous mutations. The overall haplotype diversity for global isolates was 0.9596; however, the haplotype diversity was 0.874 for Ethiopia. Fst values for genetic revealed Ethiopian isolates were closest to Indian isolates as well as to Sri Lankan and Sudanese isolates but further away from Mexican, Papua New Guinean and South Korean isolates. There was a total of 136 haplotypes from the 415 global isolates included for this study. Haplotype prevalence ranged from 36.76% to 0.7%, from this 74.2% were represented by single parasite isolates. None of the Ethiopian isolates grouped with the Sal I reference haplotype. From the total observed nonsynonymous mutations 13 mapped to experimentally verified epitope sequences. Including 10 non-synonymous mutations from Ethiopia. However, all the polymorphic regions in Ethiopian isolates were located away from DARC, responsible for junction formation.ConclusionThe results of this study are concurrent with the multivalent vaccine approach to design an effective treatment. However, the presence of novel haplotypes in Ethiopian isolates that were not shared by other global sequences warrant further investigation.

Mitochondrial DNA variation of Metapenaeus monoceros (Decapoda, Penaeidae) reveals high genetic variation within Bangladesh with distinct lineages in the Indian Ocean

AbstractThe speckled shrimp Metapenaeus monoceros is a commercially important penaeid shrimp in the Indo‐West Pacific region including Bangladesh. Phylogenetics of penaeid shrimps is still a debatable issue, and molecular variation within the species is large. This study focused on the phylogeography of M. monoceros, including an assessment of the phylogenetic relationships among seven other Metapenaeus species by assessing sequence variation in three mitochondrial markers, the cytochrome oxidase subunit 1 (CO1), control region (CR) and 16S rRNA (16S). In addition, the mitochondrial variation along the Bangladesh coastline was analysed. The mitochondrial variation has a clear geographical pattern with two distinct evolutionary lineages, one found in the western Indian Ocean and the Mediterranean Sea and the second in the eastern Indian Ocean. A phylogenetic analysis of Metapenaeus based on the three markers revealed polyphyletic relationships within the genus and that the taxonomy needs revision. The mtDNA variation in Metapenaeus monoceros in Bangladesh presents a single population (AMOVA, FST and ΦST p &gt; .05), which started to expand around 467 (CI: 186–753) kyr ago, and is characterized by a large number of closely related haplotypes. The study could be used to improve the management and conservation of the shrimp fishery in the region.

Niche differences in co-occurring cryptic coral species (Pocillopora spp.)

Cryptic species that are morphologically similar co-occur because either the rate of competitive exclusion is very slow, or because they are not, in fact, ecologically similar. The processes that maintain cryptic local diversity may, therefore, be particularly subtle and difficult to identify. Here, we uncover differences among several cryptic species in their relative abundance across a depth gradient within a dominant and ecologically important genus of hard coral, Pocillopora. From extensive sampling unbiased toward morphological characters, at multiple depths on the fore reef around the island of Mo’orea, French Polynesia, we genetically identified 673 colonies in the Pocillopora species complex. We identified 14 mitochondrial Open Reading Frame haplotypes (mtORFs, a well-studied and informative species marker used for pocilloporids), which included at least six nominal species, and uncovered differences among haplotypes in their relative abundance at 5, 10, and 20 m at four sites around the island. Differences in relative haplotype abundance across depths were greater than differences among sites separated by several kilometers. The four most abundant species are often visibly indistinguishable at the gross colony level, yet they exhibited stark differences in their associations with light irradiance and daily water temperature variance. The pattern of community composition was associated with frequent cooling in deeper versus shallower water more than warmer temperatures in shallow water. Our results indicate that these cryptic species are not all ecologically similar. The differential abundance of Pocillopora cryptic species across depth should promote their coexistence at the reef scale, as well as promote resilience through response diversity.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BackgroundThe Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets.ResultsPoached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico.ConclusionsPoached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

Sequencing Cell-free Fetal DNA in Pregnant Women With GCK-MODY.

Individuals with monogenic diabetes due to inactivating glucokinase (GCK) variants typically do not require treatment, except potentially during pregnancy. In pregnancy, fetal GCK genotype determines whether treatment is indicated, but noninvasive methods are not clinically available. This work aims to develop a method to determine fetal GCK genotype noninvasively using maternal cell-free fetal DNA. This was a proof-of-concept study involving 3 pregnant women with a causal GCK variant that used information from 1) massive parallel sequencing of maternal plasma cell-free DNA, 2) direct haplotype sequences of maternal genomic DNA, and 3) the paternal genotypes to estimate relative haplotype dosage of the pathogenic variant-linked haplotype. Statistical testing of variant inheritance was performed using a sequential probability ratio test (SPRT). In each of the 3 cases, plasma cell-free DNA was extracted once between gestational weeks 24 and 36. The fetal fraction of cell-free DNA ranged from 21.8% to 23.0%. Paternal homozygous alleles that were identical to the maternal GCK variant-linked allele were not overrepresented in the cell-free DNA. Paternal homozygous alleles that were identical to the maternal wild-type-linked allele were significantly overrepresented. Based on the SPRT, we predicted that all 3 cases did not inherit the GCK variant. Postnatal infant genotyping confirmed our prediction in each case. We have successfully implemented a noninvasive method to predict fetal GCK genotype using cell-free DNA in 3 pregnant women carrying an inactivating GCK variant. This method could guide tailoring of hyperglycemia treatment in pregnancies of women with GCK monogenic diabetes.

Genetic Profiling of CYP19 Gene Haplotype in Holstein Bulls

The CYP19 gene is a protein-coding gene that stimulates the transmutation of androgens to estrogens,aromatase activity is related to haplotypes of the CYP19 gene, therefore this study aimed to detect haplotypesof the CYP19 gene in the Holstein bulls. This study, conducted from October 2018 to June 2019. Forty-twoBulls, aged between 4-6 years old were used, which belonged to local farmers in Basra city, south of Iraq.The DNA was extracted from semen, PCR amplification was carried out to acquire the DNA sequence. Thesequences were analyzed by using some Bioinformatics tools. The results showed four haplotypes in theCYP19 gene as a result of silent and missense mutations in comparison with the same gene in GenBank, allthe haplotypes are recorded in GenBank, DDBJ and EMBL. These findings call for further studies to revealthe relationship of CYP19 gene haplotypes and semen characteristics to uncover bulls’ fertility

Noninvasive prenatal testing for \u03b2-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study

Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotypes. Recently, the nanopore sequencing technologies have become available and may be an ideal tool for direct construction of haplotypes. Here, we explored the feasibility of combining nanopore sequencing with the RHDO analysis in NIPT of β-thalassemia. Thirteen families at risk for β-thalassemia were recruited. Targeted region of parental genomic DNA was amplified by long-range PCR of 10 kb and 20 kb amplicons. Parental haplotypes were constructed using nanopore sequencing and next generation sequencing data. Fetal inheritance of parental haplotypes was classified by the RHDO analysis using data from maternal plasma DNA sequencing. Haplotype phasing was achieved in 12 families using data from 10 kb library. While data from the 20 kb library gave a better performance that haplotype phasing was achieved in all 13 families. Fetal status was correctly classified in 12 out of 13 families. Thus, targeted nanopore sequencing combined with the RHDO analysis is feasible to NIPT for β-thalassemia.

Phylogeography of Paris poliphylla var. yunnanensis based on chloroplast gene trnL-trnF sequences

Phylogeography is a research hotspot in the field of the genetic diversity and core germplasm construction of endangered rare plants. Paris polyphylla var. yunnanensis is a rare plant species mainly distributed in China. Wild individuals have been overexploited for the last few decades because of increasing demand for such medicines. Therefore, it is great significance to study the phylogeography of P. poliphylla var. yunnanensis based on chloroplast gene trnL-trnF sequences. In this study, chloroplast genes trnL-trnF were used in the phylogeography analysis of 15 wild and 17 cultivated populations of P. polyphylla var. yunnanensis. This study revealed that based on the results of neutrality tests and mismatch analysis, the rapid expansion of wild population has not been detected in P. polyphylla var. yunnanensis. After aligning and sorting the obtained cpDNA sequences, a total of 15 haplotypes were detected in all 32 populations. One haplotype was unique to the wild population, and 5 haplotypes were unique to the cultivated population. It can be seen that the haplotype richness of cultivated population was higher than that of wild population. The wild populations of P. polyphylla var. yunnanensis were divided into two groups according to evolutionary relationship of haplotypes and distribution map of haplotypes. The haplotype of branch Ⅰ was mainly distributed in Guizhou, and the haplotype of branch Ⅱ was located in Yunnan and Huidong, Sichuan. Therefore, it's speculated that Guizhou and the west Yunnan region may be glacial refuge in the evolutionary history of wild populations of P. polyphylla var. yunnanensis, and in order to protect the wild resources more effectively, wild populations of P. polyphylla var. yunnanensis in these two areas should be included in the protection zone.