Haplotype Diversity Research Articles

Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington’s disease

Many Mendelian disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, arise from expansions of CAG trinucleotide repeats. Despite the clear genetic causes, additional genetic factors may influence the rate of those monogenic disorders. Notably, genome-wide association studies discovered somewhat expected modifiers, particularly mismatch repair genes involved in the CAG repeat instability, impacting age at onset of HD. Strikingly, FAN1, previously unrelated to repeat instability, produced the strongest HD modification signals. Diverse FAN1 haplotypes independently modify HD, with rare genetic variants diminishing DNA binding or nuclease activity of the FAN1 protein, hastening HD onset. However, the mechanism behind the frequent and the most significant onset-delaying FAN1 haplotype lacking missense variations has remained elusive. Here, we illustrated that a microRNA acting on 3'-UTR (untranslated region) SNP rs3512, rather than transcriptional regulation, is responsible for the significant FAN1 expression quantitative trait loci signal and allelic imbalance in FAN1 messenger ribonucleic acid (mRNA), accounting for the most significant and frequent onset-delaying modifier haplotype in HD. Specifically, miR-124-3p selectively targets the reference allele at rs3512, diminishing the stability of FAN1 mRNA harboring that allele and consequently reducing its levels. Subsequent validation analyses, including the use of antagomir and 3'-UTR reporter vectors with swapped alleles, confirmed the specificity of miR-124-3p at rs3512. Together, these findings indicate that the alternative allele at rs3512 renders the FAN1 mRNA less susceptible to miR-124-3p-mediated posttranscriptional regulation, resulting in increased FAN1 levels and a subsequent delay in HD onset by mitigating CAG repeat instability.

Small proteins, great promises: Geographic bioprospecting of Bowman–Birk protease inhibitors and domestication side‐effects in African cowpea (Vigna unguiculata L.)

Societal Impact StatementThe legume crop cowpea is grown worldwide, but 90% of the world's total share is produced in Africa. It is a promising species due to its resilience properties, balance of macro and micronutrients and presence of health‐promoting bioactive compounds. In African countries, cowpea has a crucial role in guaranteeing food security as a subsistence crop for families and commercial income for small farmers. The discovery of compounds with high nutraceutical value and bioactive properties supports socio‐economic policies to improve health and nutrition, especially in low‐ and middle‐income countries. In turn, this encourages biodiversity protection and crop enhancement programmes.Summary Bowman–Birk protease inhibitors (BBIs) are a restricted group of small proteins in plants mainly involved in defence mechanisms against pests. BBIs are demonstrated to be active components capable of reducing the viabilities of different cancer cell lines. BBI bioactivity is directly linked to the inhibition capacity, but the variability and the efficiency against the physiological targets of different BBI isoforms remain still unexplored. We analysed the natural genetic diversity of two main genes encoding BBI trypsin‐trypsin (BBI‐TT) and trypsin‐chymotrypsin (BBI‐TC) in wild and domesticated cowpea samples mainly spread in Sub‐Saharan Africa. We analysed DNA sequences and respective amino acidic isoforms/isoproteins to explore signs of natural selection and haplotype relationships. Moreover, we calculated the binding energy between BBIs and their biological targets to identify which are the most efficient inhibitors and their geographical locations. We found a high level of haplotype diversity for both genes, almost exclusively in wild accessions and detected positive and negative selection signals in the amino acid sequences. Furthermore, in the wild diversity pool, some BBI‐TT and BBI‐TC mature proteins were potentially better interactors with the physiological targets. The long interaction between plant‐pathogen has selected new and useful isoforms in wild lineages that have allowed the chances of survival of the species to improve. On the other hand, the domestication process has produced an intense bottleneck leaving only poorly efficient BBI variants. In addition to providing information on the natural diversity and evolution of BBIs, our work discusses the potential applications in agriculture and human health.

Analysis of Genetic Structure and Genetic Diversity in Japanese Grey-Headed Lapwing Population Using mtDNA.

The grey-headed lapwing (Vanellus cinereus) is a wading species in East Asia. However, examples of regional population dynamics and genetic research are limited. To reconsider the natural history and current status of the grey-headed lapwing in Japan, we analyzed the genetic diversity of the Japanese grey-headed lapwing population. We collected 77 grey-headed lapwing samples from 12 locations across Japan during the breeding season and three individuals during the wintering season and extracted DNA; 496-bp sequences of the ND2, which form part of the mitochondrial DNA, were determined for genetic analysis of the population. Consequently, 10 haplotypes were detected in 80 individuals, and 67 individuals, 84% of the total, shared two haplotypes, namely Vc1 and Vc2. Furthermore, the results showed that the prevalence of Vc1 was higher mainly in northern Japan, while that of Vc2 was higher mainly in southern Japan. Genetic diversity analysis showed that the overall haplotype diversity in Japan was 0.617, which is not particularly low. The sequence of Vc1 was exactly the same as that of grey-headed lapwing in China. Our study revealed the genetic structure of the grey-headed lapwing, suggesting that as the grey-headed lapwing expanded its distribution area into southern Japan, many Vc2-positive individuals migrated southward, resulting in a higher detection rate of Vc2 in southern Japan.

Mitogenome-based genetic management of captive Great Hornbill in Thailand: Implications for reintroduction

The Great Hornbill (Buceros bicornis) is globally vulnerable due to high rates of deforestation and hunting and are therefore a target for restoration. Captive breeding programs in Thailand maintain many Great Hornbills, however active genetic management of captive hornbills was not incorporated into the species recovery plan. With Great Hornbill reintroductions planned for northern Thailand in the immediate future, lack of genetic profiles and phylogenetic relationships among potential founders might hamper population recovery efforts. We assessed the mitochondrial genome (mitogenome) diversity, genetic structure, and evolutionary history of 97 captive Great Hornbills across five zoos in Thailand. Among the 97 samples, we found 21 haplotypes with a haplotype and nucleotide diversity of h = 0.81336 ± 0.021 and pi = 0.00108 ± 0.00040, respectively. The maintenance of mitogenome diversity and no genetic differentiation between five captive populations (FST = 0.00000–0.09723, p > 0.05) might be a result of frequent founder exchange among facilities. Phylogenetic analysis revealed the existence of a southern clade BBITH13, indicating a genetically distinct southern population. To protect these genetic lineages and maintain adaptability of hornbills that have been reintroduced, breeding facilities that contain unique haplotypes should be given high priority in breeding plans. Our data support the evolutionary value of the captive hornbill population in Thailand and highlight the significance of incorporating active genetic management strategies into the species recovery plan for Great Hornbills.

Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842).

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.

Mitochondrial DNA diversity of sperm whales (Physeter macrocephalus) in the Gulf of California under a changing environment

The mitochondrial diversity of the sperm whale in the Gulf of California (GC) from 2004 to 2017 was analyzed using the control region from 95 samples and compared with two preceding studies. This study examined the relationship between the mitochondrial genetic diversity of sperm whales, and the abundance of jumbo squid (Dosidicus gigas) in the GC, as indicated by squid catches. Furthermore, the influence of climate regimes on this relationship was also assessed. Of the total 16 haplotypes registered for the GC, eight haplotypes, representing 50%, were identified in this study. One of these haplotypes was only recorded in the Atlantic Ocean, and another is newly documented. Haplotype diversity (h = 0.640 ± 0.051) and nucleotide diversity (π = 0.00158 ± 0.00019) showed lower values than those previously reported for the GC. The genetic differentiation index among three periods analyzed was significant (Fst = 0.27, p < 0.01), with a greater variability observed within periods (72.19%) compared to between periods (27.81%). This suggests either a differential influx of haplotypes or a preference of matrilines for specific areas within the GC. The sex ratio of 3.5:1 females to males was consistent with previously reported data for the GC and other regions. A temporal decrease in the number of haplotypes in the GC coincided with an increase in Sea Surface Temperature (SST), a decrease in chlorophyll values (Chl-a), and a reduction of giant squid catches. These trends suggest that shifts in the GC climate regime could exert selective pressure, favoring certain matrilineal lineages.

Haplotype diversity of 17 Y-STR in the Iranian population

The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.

Genetic diversity and population structure of Kawakawa Euthynnus affinis (Cantor, 1849) in Malaysia and its surrounding waters inferred by mitochondrial DNA cytochrome oxidase I and cytochrome b genes

Kawakawa (Euthynnus affinis) is a widely distributed epipelagic tuna, considered among the most economically significant species in the subtropical and tropical waters of the Indo-Pacific region. However, the lack of comprehensive information on the stock structure, management, and conservation of E. affinis populations in Malaysia raises concerns of potential overfishing and depletion of this marine fish. To ensure effective and successful species management, it is imperative to conduct a molecular- based assessment of the stock structure. In the present study, the genetic diversity and population structure of E. affinis in Malaysia and its surrounding waters were investigated using mitochondrial DNA cytochrome oxidase I (COI) and cytochrome b (Cyt b) genes. A total of 390 (COI) and 414 (Cyt b) individuals of E. affinis were sampled from 20 distinct locations situated within five geographic regions: the Straits of Malacca, South China Sea, Sulu Sea, Celebes Sea, and the Arabian Sea. The results revealed that the genetic divergence among 20 populations of E. affinis varied from low to high. The average haplotype diversity (Hd) and nucleotide diversity (π) for COI were calculated to be 0.5131 and 0.0043, respectively. On the other hand, the average haplotype diversity (Hd) and nucleotide diversity (π) for Cyt b were found to be 0.7450 and 0.0162, respectively. The analysis of haplotype distribution revealed that a total of 20 distinct haplotypes were identified for both the COI and Cyt b genes across 20 populations of E. affinis. The analysis of the Neighbor-Joining (NJ) tree and the Minimum Spanning Network (MSN) revealed the formation of three distinct clades among thesamples. AMOVA analysisshowed a significant genetic structure among the 20 populations of E. affinis, as indicated by the COI: FST = 0.5364 (P < 0.05) and Cyt b: FST = 0.9521 (P < 0.05). The neutrality test and mismatch distribution analysis indicated that the E. affinis specimens underwent a period of population expansion. This study marks a significant milestone as the first comprehensive documentation of genetic diversity and population structure of E. affinis across various locations in Malaysia, with an additional pioneering investigation conducted in the waters of Yemen.

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins.

Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Environmental DNA unveils deep phylogeographic structure of a freshwater fish.

Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.

The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P.maculata (Golden apple snails) across Taiwan.

The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.

Molecular phylogenetic analysis of Echinococcus granulosus sensu lato infecting sheep in Italy.

Cystic Echinococcosis (CE), caused by the larval form of Echinococcus granulosus sensu lato, is a neglected zoonosis still threatening public health worldwide. In Italy different epidemiological scenarios were reported depending on the geographical area and associated socio-economic activities. Although in northern Italy the occurrence of E. granulosus is considered sporadic, in the southern regions and, particularly in Sardinia, CE prevalence reaches high levels. We analysed CE cysts collected from infected sheep from various areas of mainland Italy and the Sardinia island, with the main objective to investigate intergenotypic and intragenotypic variations at national level. CE cysts were collected from slaughtered sheep following post mortem inspection at local abattoirs. Total genomic DNA was extracted and amplification and sequencing of the partial mitochondrial genes nad5 and cox1 were performed. A Bayesian phylogenetic tree was estimated on a nad5 dataset (n=260) composed of E. granulosus samples from this study (n=126) and all the nad5 haplotypes available in GenBank (n=134). In addition, haplotype network, diversity and neutrality analysis were performed on nad5 and cox1 sequences of Italian origin obtained in this study. E. granulosus sensu stricto (s.s.) was found to be the only Echinococcus species infecting sheep in Italy, mainly represented by G1 genotype (76%) and, to a lower extent, by G3 genotype (24%). Phylogenetic analyses revealed 40 nad5 and 33 cox 1 haplotypes, and the presence of two founder haplotypes, belonging to G1 and G3 genotype, showing 100% similarity with DNA sequences from different geographic regions. The lack of geographical segregation, high haplotype and low nucleotide diversity coupled with significant negative values of Tajima's D and Fu's Fs observed in this study indicated high genetic variation and demographic expansion of E. granulosus s.s. in Italy.

Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea.

The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.

Apis cerana Fabricius, 1793 in Sumatra: Haplotype Variations of Mitochondrial DNA and the Molecular Relationship with the Asian Honey Bees (Hymenoptera: Apidae)

Honey bee Apis cerana is widely distributed in Asia and the Indonesian archipelago, including Sumatra. We studied the molecular variations of A. cerana using cytochrome c oxidase subunits 1 and 2 genes (cox1 and cox2) and the cox1/cox2 intergenic spacers (igs) in several altitudes in the six provinces of Sumatra. We explored the haplotype distributions of those three mtDNA markers for A. cerana in the low-, mid-, and highlands of Sumatra. We also analyzed their relationship with A. cerana in Sundaland and Asia using those markers. Our study revealed 12 new haplotypes of A. cerana cox1 in Sumatra, while nine and eight new haplotypes for cox2 and igs, respectively. Apis cerana in North Sumatra, Lampung, and South Sumatra had the three highest haplotype variations. Most of the specific haplotypes of inter-colony A. cerana from Sumatra were found in the lowlands, while most were in the highlands for intra-colony variations. We found low gene flow among populations of A. cerana in Sumatra. One haplotype, Sumatra4 cox2 from North Sumatra, was the same as Java3 haplotype, presumably due to anthropogenic impact. The molecular phylogenetic tree of A. cerana in the Sundaland revealed that A. cerana from Sumatra has a close relationship to those of Borneo compared to Java.

Bitter taste sensitivity and frequency of bitter food intake in healthy Australian adults: a cross-sectional, mixed-methods study

Bitter taste perception plays a dual role in human nutrition and evolutionary biology; being identifiable in nutrient-dense foods such as cruciferous vegetables and historically signalled toxic compounds. The TAS2R38 gene, part of the taste 2 receptor family, is central to individual differences in bitter taste perception(1). While genetic variations are influential, dietary habits and food preparation also impact taste perception. However, research investigating the interplay between these factors and genetic variations in influencing bitter taste sensitivity and food intake is limited. This study aimed to elucidate the relationship between bitter taste sensitivity and TAS2R38 haplotype variations in the context of bitter food consumption among Australian adults. A cross-sectional, mixed-methods study was conducted. Healthy adults who had maintained a stable diet for at least three months were eligible. Data collection was via an online survey (REDCap), capturing self-reported demographics, dietary patterns specific to bitter foods including metrics of bitter food avoidance, frequency, liking and perceived healthfulness, alongside a Dietary Quality Index (DQI) derived from a food frequency questionnaire(2). Bitter taste sensitivity was assessed using self-reported intensity perceptions of 6-n-propylthiouracil (PROP) taste strips(3). Genotyping was conducted via TaqMan qPCR assays on DNA extracted from buccal swabs to ascertain TAS2R38 haplotypes. Data analysis utilised Analysis of Covariance (ANCOVA) and regression models, with all tests adjusted for confounding variables such as gender, age, and smoking status. A total of 222 participants (47.5 ± 17.7 years; 86% female; BMI 27.3 ± 7.1 kg/m2) completed the study. PROP sensitivity was strongly correlated with TAS2R38 haplotype, with supertasters predominantly having PAV/PAV, medium tasters with PAV/AVI, and non-tasters with AVI/AVI (p = 0.002). However, no relationship was observed between PROP sensitivity and either the frequency, liking, or avoidance of bitter foods (p&gt;0.05). DQI was significantly related to bitter food consumption; individuals in the lowest DQI quintile consumed bitter foods more frequently than those in the third (p = 0.007) and top quintiles (p = 0.001). The perceived healthfulness of bitter foods was significantly higher in those with AVI/AVI haplotypes (non-tasters) compared to those with PAV/AVI (medium tasters) (p = 0.001). Counterintuitively, participants who reported greater enjoyment of bitter tastes consumed bitter foods less frequently (p&lt;0.001). Our study confirms that TAS2R38 variants are predictive of PROP taste sensitivity, consistent with literature that identifies PAV/PAV individuals as supertasters. However, neither PROP sensitivity nor TAS2R38 haplotype influenced bitter food frequency or preference consumption patterns. Interestingly, those with lower Dietary Quality Index scores and less enjoyment of bitter taste consumed bitter foods more often. These observations highlight the need to investigate other factors influencing bitter food intake, such as additional sensory characteristics or psychological and behavioural aspects.

Genetic variants, haplotype determination, and function of novel alleles of CYP2B6 in a Han Chinese population

Amino acid variants in protein may result in deleterious effects on enzymatic activity. In this study we investigate the DNA variants on activity of CYP2B6 gene in a Chinese Han population for potential use in precision medicine. All exons in CYP2B6 gene from 1483 Chinese Han adults (Zhejiang province) were sequenced using Sanger sequencing. The effects of nonsynonymous variants on recombinant protein catalytic activity were investigated in vitro with Sf12 system. The haplotype of novel nonsynonymous variants with other single nucleotide variants in the same allele was determined using Nanopore sequencing. Of 38 alleles listed on the Pharmacogene Variation Consortium, we detected 7 previously reported alleles and 18 novel variants, of which 11 nonsynonymous variants showed lower catalytic activity (0.00–0.60) on bupropion compared to CYP2B6*1. Further, these 11 novel star-alleles (CYP2B6*39–49) were assigned by the Pharmacogene Variation Consortium, which may be valuable for pharmacogenetic research and personalized medicine.

Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences

Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.

Genetic diversity of mitochondrial DNA D-loop sequence in Bang Troi chicken breed

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima’s test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtD-loop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds.