Heterozygosity Research Articles

Impact of silvicultural practices on the genetic variations between sugar maple (Acer saccharum Marsh.) stands in the Northern Forest, U.S.A

Tree harvesting practices that enhance genetic diversity are essential for the long-term sustainability of our forests. Using eSSRs, which are markers within expressed genes and thus, potentially subjected to natural selection and reveal adaptive potential, this study examines the effects of selection (SE) and shelterwood (SW) management systems using unmanaged (UM) stands as reference on the genetic diversity of sugar maples in the Northern Forest, USA. Comparison between management types shows no difference between SE and SW, but compared to UM, both have lower allelic richness (AR) while only SE has lower expected heterozygosity (HE). Size class comparison shows that seedlings have higher AR and HE than poles and mature trees. Two-way interactions between management types, size classes, and study stands from each of the four states that comprise the Northern Forest region (Maine, New Hampshire, Vermont and New York) were also examined. Results show that seedlings in UM and SW have higher AR compared to all size classes in SE and poles and mature trees in SW, while only seedlings from SW have higher HE compared to poles and mature trees in SE and SW. Only in Maine was there a difference in AR between SW and SE stands per state. Seedlings in New Hampshire and Maine have higher HE, as well as seedlings and mature trees in New York compared to the poles in New Hampshire and mature trees in Maine. Overall, the results indicate genetic erosion in sugar maple stands in the Northern Forest region. This genetic impact may be due to several factors including the intensity of cutting associated with SE and SW systems and size of the canopy gaps created. Higher seedling genetic diversity in SW compared to SE may be due to their more open stand structure that facilitates gene flow and seedling recruitment. When using SE, longer cutting cycle paired with lower level of residual basal area is recommended. This approach allows for a more open stand structure that could facilitate pollen and seed exchanges from the stands, improving their genetic diversity. In both SE and SW systems, leaving high-quality growing stocks will enhance their genetic diversity and ensure their sustainability. This study increases our awareness of the potential genetic impacts of forest harvesting practices and guides the development of recommendations to alleviate genetic erosion in sugar maple stands.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

BackgroundThe Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.ResultsHO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).ConclusionsEvaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Comparison of population genetic structure of Pinus mugo Turra forest stands in the Giant Mountains by analysis of nSSR molecular marker data

Abstract Pinus mugo (dwarf mountain pine) communities in the protected area of Krkonoše National Park are extremely valuable. After extensive deforestation during the sixteenth to nineteenth centuries, P. mugo recovered naturally in some parts of the Giant Mountains, and in some places imported seeds were likely used for reforestation. To distinguish between native and possibly introduced local P. mugo populations, genetic variations between 12 populations from the Czech Sudeten part of the Giant Mountains and between the two populations from the Tatra Mountains were analysed using 12 nuclear microsatellite markers (nuclear simple sequence repeats). Based on the simple sequence repeat data, 146 alleles were found, and Shannon’s information index, number of private alleles, and expected heterozygosity (HE) of populations averaged 1.12, 0.16, and 0.53, respectively. Analysis of molecular variance indicated that most of the variation was detected within populations. Low levels of genetic differentiation were also observed (average FST = 0.023). The population structure was examined by Bayesian clustering. The results of STRUCTURE analysis confirmed that the introduced populations were different from the autochthonous populations. Some of the introduced Czech Sudeten populations had similar genetic structure as the more distant native populations from the Tatra Mountains. Our results provide important genetic information for the reconstruction of natural communities in the Giant Mountains.

Genetic diversity and population structure of four Anatolian sheep revealed by genome-wide ddRADseq data

This is the first wide-scale study to reveal next-generation sequencing-based and comprehensive study to reveal genetic diversity, population structure, and phylogenetic relationships of some of Türkiye's indigenous fat-tailed sheep breeds. A total of 80 animals belonging to Akkaraman (AKR), Güney Karaman (GKR), Morkaraman (MKR), and Karakaş (KRK) sheep breeds were genotyped with genome-wide of 296.097 single nucleotide polymorphisms (SNPs) data recovered from double digest restriction site-associated DNA sequencing (ddRADseq) libraries processed by Illumina HiSeq X Ten instrument. Minor allele frequency (MAF) ranged from 0.311 (MKR) to 0.316 (AKR and GKR). Observed heterozygosity (HO) values were higher than expected values (HE) across all populations with a mean of 0.307. Negative inbreeding coefficient (FIS) values were observed in four sheep populations varying between −0.034 (AKR) to −0.060 (MKR). Cross-entropy criterion-based ADMIXTURE analysis demonstrated that four Anatolian sheep breeds were represented by two ancestral populations in which GKR and AKR were distinct, while KRK and MKR were mixed populations. Genetic distance-based tree, discriminant analysis of principal components (DAPC), and ADMIXTURE analyses confirmed that GKR, which is believed to be derived from the AKR breed, has become genetically different from other sheep populations. Moreover, no migration from and into the GKR breed was detected, while a migration edge was drawn from the KRK and MKR clade into the AKR breed by the TreeMix algorithm. This study confirmed that high-density SNP data obtained from advanced next-generation sequencing (NGS) platforms are efficient in genetically distinguishing animal breeds, even varieties. It is recommended that further NGS-based studies could be carried out to better characterize different indigenous livestock populations raised in Türkiye.

Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data.

Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.

Genetic diversity and inbreeding in an endangered island-dwelling parrot population following repeated population bottlenecks

Genetic diversity and population structure can have important implications for the management of threatened species. This is particularly true for small, isolated populations that have experienced significant declines or population bottlenecks. The Norfolk Island green parrot Cyanoramphus cookii is an endangered species at risk of inbreeding and loss of genetic diversity due to its restricted range and the population bottlenecks experienced in recent decades. To assess the severity of inbreeding and loss of genetic diversity in the population we analyzed single nucleotide polymorphisms (SNPs) for 157 unique genetic samples collected from nestlings and randomly captured adult birds between 2015 and 2022. We also assessed the population for genetic structure, calculated sex ratios, and looked for evidence of past population bottlenecks. Our analysis revealed that 17.83% of individuals sampled were highly inbred (F > 0.125), although expected heterozygosity (HE) did not significantly differ from observed heterozygosity (HO) and the average inbreeding coefficient was low. The estimated effective population size (Ne) was 43.8 and we found no evidence of genetic structure. Demographic simulations provided support for scenarios including multiple population bottlenecks, when compared to those with a single population bottleneck or no past bottlenecks. We discuss the implications of our findings for the future management of the species including any potential attempt to establish an insurance population via translocation. Our study highlights the importance of considering population genetics when determining appropriate management actions for threatened species and the need to assess non-model species on an individual basis.

Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs.

Tunchang pigs are an indigenous pig population in China known for their high tolerance to roughage, delicious meat, and fecundity. However, the number of Tunchang pigs has been declining due to the influence of commercial breeds and African swine fever, which could potentially lead to inbreeding. To assess the inbreeding level and the genetic basis of important traits in Tunchang pigs, our research investigated the patterns in "runs of homozygosity" (ROHs) using whole genome resequencing data from 32 Tunchang pigs. The study aimed to determine the length, number, coverage, and distribution model of ROHs in Tunchang pigs, as well as genomic regions with high ROH frequencies. The results of the study revealed that a total of 20,499,374 single-nucleotide polymorphisms (SNPs) and 1953 ROH fragments were recognized in 32 individuals. The ROH fragments in Tunchang pigs were predominantly short, ranging from 0.5 to 1 megabases (Mb) in length. Furthermore, the coverage of ROHs varied across chromosomes, with chromosome 3 having the highest coverage and chromosome 11 having the lowest coverage. The genetic diversity of Tunchang pigs was found to be relatively high based on the values of HE (expected heterozygosity), HO (observed heterozygosity), pi (nucleotide diversity), Ne (effective population size), and MAF (minor allele frequency). The average inbreeding coefficients of Tunchang pigs, as determined by three different methods (FHOM, FGRM, and FROH), were 0.019, 0.0138, and 0.0304, respectively. These values indicate that the level of inbreeding in Tunchang pigs is currently low. Additionally, the study identified a total of 13 ROH islands on all chromosomes, which in total contained 38,913 SNPs and 120 genes. These ROH islands included genes associated with economically important traits, including meat quality (GYS1, PHLPP1, SLC27A5, and CRTC1), growth and development (ANKS1A, TAF11, SPDEF, LHB, and PACSIN1), and environmental adaptation (SLC26A7). The findings of this research offer valuable perspectives on the present status of Tunchang pig resources and offer a reference for breeding conservation plans and the efficient utilization of Tunchang pigs in the future. By understanding the inbreeding level and genetic basis of important traits in Tunchang pigs, conservation efforts can be targeted towards maintaining genetic diversity and promoting the sustainable development of this indigenous pig population.

SSR Marker Acquisition and Application from Transcriptome of Captive Chinese Forest Musk Deer (Moschus berezovskii).

Forest musk deer (Moschus berezovskii) is one of the most endangered medicinally important wild animals in the world. Forest musk deer farming is the main way of production of musk. However, the single provenance and lack of genetic information lead to reduced genetic diversity of forest musk deer. Therefore, more SSR markers need to be developed to identify forest musk deer germplasm. In this study, bone marrow derived mesenchymal cells were used to construct cDNA library for transcriptome sequencing. The datasets were de novo assembled and annotated. 9 polymorphic simple sequence repeat (SSR) markers were finally identified and used to detect population genetic diversity. 6.07Gb clean data were generated using Illumina sequencing technology, and de novo assembled into 138,591 transcripts and 81,553 unigenes. 5,777 simple sequence repeats (SSRs) were identified, in which there were 578 repeating motif types, with mono-nucleotide and tri-nucleotides comprising 55.88% and 25.60%, respectively. 100 primer pairs were designed to validate amplification and polymorphism using DNA from fecal samples. 9 polymorphic SSRs were developed and used to detect population genetic diversity of 122 forest musk deer in 2 farms. The average number of alleles per locus varied from 4 to 15 (average = 8.3). The observed heterozygosity (HO) per locus ranged from 0.102 to 0.941, while the expected heterozygosity (HE) per locus was from 0.111 to 0.651. All loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.001). The polymorphism information content (PIC) of these loci varied from 0.108 to 0.619. 9 polymorphic SSR markers were developed in this research. These sites can be used for breeding planning and conservation of germplasm resources.

Genetic diversity in creole pigs in south central Peru.

The creole pigs represent 67% of the national population in Peru. They are a source of economic income in rural communities, and due to their rusticity, they are not much labor demanding. However, knowledge about its genetic diversity remains scarce. The objective of this study was to determine the population structure and genetic diversity of creole pigs from rural communities in south central Peru. Thirteen microsatellites were used to characterize 120 creole pigs from the departments of Ayacucho (57) and Apurimac (63). The samples were taken from hair follicles and ear tissue. Nine microsatellites were highly polymorphic and informative (PIC > 0.5) for both departments. The Ayacucho population had a mean number of alleles (MNA) and expected heterozygosity (HE) of 8.8 and 0.68, respectively, while in the Apurimac population, these were 8.9 and 0.71, respectively. Both populations showed in less than 50% of their loci a deviation from Hardy-Weinberg equilibrium. There was a moderate genetic structure according to the analysis of molecular variance and the FST statistics (0.06), which was corroborated by Bayesian methods. In conclusion, the genetic diversity was mostly due to the intrapopulation variance (91%). Some individuals from Ayacucho shared similar alleles with those from Apurimac. This latter result may be due to their geographic proximity and the introduction of the same new exotic breeds. This is the first research on the genetic diversity of creole pigs in south central Peru. In fact, this study could serve as a basis for conservation strategies and actions in this region.

Assessing the genetic vulnerability of Macaúba palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] through the mating system and genetic diversity of open‐pollinated progenies

AbstractAt present, intelligent and sustainable agriculture presupposes a compromise between maximising crop yield and minimising its risk of genetic vulnerability. Breeding programmes should implement strategies that allow the development of superior genotypes and preserve genetic diversity, especially in perennial plants. The Macaúba palm (Acrocomia aculeata) is a species with the potential to produce oil at a level comparable to that of the oil palm, even in water‐deficient areas, which motivates its commercial interest and drives an increase in demand for seedlings from natural populations for commercial plantations. Therefore, to evaluate the impact of this selection procedure on the reduction of genetic diversity and, consequently, the genetic vulnerability of commercial planting, in the present study we analysed the population mating system and the genetic diversity of Open‐Pollinated Progenies (OPPs) from selected seed‐trees in relation to the genetic diversity of respective native populations (NPs). To achieve this, we evaluated the mating system and genetic diversity employing 14 microsatellite markers (SSR). The mating system indices estimated for A. aculeata palm indicated that the species present a mixed mating system () with a predominance of outcrossing. However, at the population level, the outcrossing rate ranged from . The biparental inbreeding rate was considered moderate (), with some variation between populations (from 0.0005 to 0.275). The multilocus correlated paternity was , ranging from 0 to 0.112 at population level, indicating that a significant portion of the progeny consisted of half‐sibs. The results demonstrate that there was no significant loss of genetic diversity of OPPs derived from artificial selection within NPs. In the OPPs the number of alleles (Na = 2.55) was similar to that of NP (Na = 2.56). Furthermore, the mean values of observed heterozygosity (HO) between NP and OPPs were similar, with a mean of 0.366 and 0.356, respectively. In conclusion, the procedure adopted to produce commercial seedlings in the present study should not represent a high risk of genetic vulnerability. In addition, our results will provide a guidance to breeders regarding selection intensity in both natural and improved populations, aiming to optimise the advancement of generations, thereby maximising future genetic gains while preserving genetic diversity. However, we recommend verifying the outcrossing rate and genetic diversity at the population level, as these factors could have significant effects on the vulnerability of the species and the macaúba crop.

Development of polymorphic simple sequence repeat markers in Agastache rugosa and their application in genetic evaluation and cross-taxon transferability of Agastache species

Agastache is a genus of perennial herbaceous plants belonging to the mint family, Lamiaceae. Several Agastache species are commercially cultivated and used as medicinal, culinary, and ornamental plants. However, information on the genetic diversity and population structure of the species remains unclear. In the present study, genetic diversity within Agastache species was analyzed using simple sequence repeat (SSR) markers. In this study, 249,746 SSRs were identified in the A. rugosa genome and primer pairs were designed for 56,675 SSRs. The majority of SSR repeat types were dinucleotides (60.65%), followed by trinucleotides (12.38%), and pentanucleotides (12.10%). PCR conditions were established for 250 primer pairs, 111 of which were found to be polymorphic in A. rugosa germplasm. The number of alleles (NA) ranged from 2 to 19, major allele frequency (MAF) ranged from 0.11 to 0.95, observed heterozygosity (HO) ranged from 0 to 0.89, and polymorphic information content (PIC) ranged from 0.09 to 0.92. Cross-species amplification of SSRs markers in other Agastache species showed amplification rates of 82.6% for A. foeniculum and 78.1% in A. urticifolia, with an average of 80.37%. Cluster analysis of the 19 A. rugosa accessions using SSRs markers revealed four major clusters, and population STRUCTURE analysis using 79 SSRs markers revealed three groups and three subgroups among the A. rugosa populations. The SSRs markers developed can contribute to applications such as varietal identification, genetic diversity analysis, and population structure analysis of A. rugosa germplasm.

Traditional Management of Maize in the Sierra Sur, Oaxaca, Maintains Moderate Levels of Genetic Diversity and Low Population Differentiation Among Landraces

Oaxaca is one of the areas of early maize diversification, with 28 to 35 recognized agronomic races. Campesinos (farmers) cultivate at least ten different races in the Los Loxicha region. There is evidence of introgression between them; however, some traditional practices have promoted further differentiation evidenced by the presence of different landraces, clearly recognized by various morphological and phenological characteristics. Therefore, moderate levels of genetic diversity and low levels of population differentiation are expected. Seven communities belonging to two municipalities were selected in 2005. In total, 140 semistructured interviews were administered, inquiring about cultural practices, which included questions about maize seed, ear, and cob management and selection and maize cultivation. Based on interviews and permissions, 30 maize plants from each of 28 fields (milpas) with maize crop belonging to five landraces (Conejo, Hueso, Tablita, Tepecente, and Pinto) were sampled. From the 82 ISSR loci amplified, Hueso and Conejo exhibited the highest and lowest number of loci (70 and 56 loci, respectively); 72% of loci analyzed in the five populations were polymorphic. The Hueso landrace presented the highest percentage of polymorphism (73%) and Conejo the lowest (54%). The expected heterozygosity (HeT) for the five landraces was 0.225 ± 0.032, and the genetic diversity of Nei (HST) was 0.225 ± 0.034. The population differentiation values obtained with GST indicated that Tablita and Hueso were the least differentiated, while the most differentiated were Pinto and Tepecente. STRUCTURE analysis identified two genetically differentiated groups (k = 2), consistent with the length of their agricultural cycle (number of days until flowering). UPGMA analysis showed that milpas belonging to the same landrace and with a specific agricultural cycle length were grouped, regardless of their geographic distribution. These results indicate that traditional management of maize in the Los Loxicha region, particularly as it relates to the selection of ears and seeds and control of the agricultural cycle, maintains a balance between morphological differentiation, moderate levels of genetic diversity and gene flow, and low levels of population differentiation. This has contributed to the high richness and low evenness of agronomic races reported for the mountainous regions of the Sierra Madre del Sur and for Oaxaca.

Long-term effects of restoration on the links between above-and belowground biodiversity in degraded Horqin sandy grassland, Northern China

Long-term ecological restoration plays an important role in the sustainable development of degraded grassland ecosystem. In this study, the levels of species diversity, genetic diversity and soil microbial diversity in restored grassland were measured by vegetation survey, DNA barcoding and soil microbial high-throughput sequencing technology, so as to explore the relationship between above- and belowground biodiversity and its driving factors in Horqin sandy grassland. In this study, the results found that herb are dominated in restoration grassland types. Plant species richness (SR) from post-non-grazing restoration plot (NGR) communities was significantly higher than other restoration communities (10 ± 1.1, p = 0.004). Genetic diversity indices of dominant plant species in chloroplast DNA (cpDNA), were remarkable greater than nuclear DNA (nrDNA) in each recovering sandy grassland plots (amplitude of difference was 44.8%–70.5% in allelic richness (AR), 81.9%–128.1% in expected heterozygosity (HE)). The soil bacterial and fungal richness from natural mobile dune grassland (NM) communities was notably lower than that from recovering grassland types (1641.9 ± 100.4, p &amp;lt; 0.001; 533 ± 16.6, p &amp;lt; 0.001). In this study, heterogeneous levels of genetic variability among different recovering sandy grassland types were detected. Correlation analyses revealed that there were positive correlations between species diversity and genetic diversity (SR &amp;amp; AR: r = 0.56, R2 = 0.31, p &amp;lt; 0.001; SR &amp;amp; HE: r = 0.33, R2 = 0.11, p = 0.045) and a negative correlation between soil microbial diversity and genetic diversity (r = -0.44, R2 = 0.19, p = 0.005). The final structural equation model explained 38% of the variance in SR, 57% in AR, 52% in soil microbial diversity (SD), 49% in aboveground biomass (AGB), 87% in soil organic carbon (SOC), 47% in soil alkali-hydrolyzable nitrogen (SAN) and 69% in soil available phosphorus (SOP). Long-term ecological restoration had significant direct positive effects on AGB, SOC, SAN, SOP, AR, SR and SD. There was a negative correlation between above- and belowground biodiversity and biological and abiotic factors. The results of this study have clarified the above- and underground biodiversity levels of sandy grassland and the relationship with driving factors under long-term ecological restoration measures, and will provide effective support for the management and sustainable development of sandy grassland.

Macrogenetics reveals multifaceted influences of environmental variation on vertebrate population genetic diversity across the Americas.

The broad scale distribution of population-specific genetic diversity (GDP ) across taxa remains understudied relative to species diversity gradients, despite its relevance for systematic conservation planning. We used nuclear DNA data collected from 3678 vertebrate populations across the Americas to assess the role of environmental and spatial variables in structuring the distribution of GDP , a key component of adaptive potential in the face of environmental change. We specifically assessed non-linear trends for a metric of GDP, expected heterozygosity (HE ), and found more evidence for spatial hotspots and cold spots in HE rather than a strict pattern with latitude. We also detected inconsistent relationships between HE and environmental variables, where only 11 of 30 environmental comparisons among taxa groups were statistically significant at the .05 level, and the shape of significant trends differed substantially across vertebrate groups. Only one of six taxonomic groups, freshwater fishes, consistently showed significant relationships between HE and most (four of five) environmental variables. The remaining groups had statistically significant relationships for either two (amphibians, reptiles), one (birds, mammals), or no variables (anadromous fishes). Our study highlights gaps in the theoretical foundation upon which macrogenetic predictions have been made thus far in the literature, as well as the nuances for assessing broad patterns in GDP among vertebrate groups. Overall, our results suggest a disconnect between patterns of species and genetic diversity, and underscores that large-scale factors affecting genetic diversity may not be the same factors as those shaping taxonomic diversity. Thus, careful spatial and taxonomic-specific considerations are needed for applying macrogenetics to conservation planning.

Serum 21-Deoxycortisol for Diagnosis of Nonclassic Congenital Adrenal Hyperplasia in Women With Androgen Excess.

Nonclassic congenital adrenal hyperplasia (NCCAH) requires exclusion before diagnosing polycystic ovary syndrome (PCOS). Increasing use of liquid chromatography and tandem mass spectrometry (LC-MS/MS) necessitates revision of immunoassay-based criteria for NCCAH. Measurement of 21-deoxycortisol (21DF) may simplify the diagnosis of heterozygosity (HTZ), the presence of 1 affected CYP21A2 allele, which currently relies on complex molecular studies. We aimed to determine LC-MS/MS-specific criteria for NCCAH and HTZ and compare the diagnostic accuracy of 21DF and 17-hydroxyprogesterone (17OHP). A cross-sectional study involving 99 hyperandrogenic females was performed. We identified females who had undergone both a synacthen stimulation test (SST) and CYP21A2 genotyping from 2010 to 2017, and prospectively recruited females referred for an SST to investigate hyperandrogenic symptoms from 2017 to 2021. Steroids were compared between genetically confirmed NCCAH, HTZ, and PCOS. Optimal 17OHP and 21DF thresholds for HTZ and NCCAH were determined by receiver operating characteristic analysis. Basal 17OHP, stimulated 17OHP, and 21DF were measured in 99, 85, and 42 participants, respectively. Optimal thresholds for NCCAH were 3.0 nmol/L and 20.7 nmol/L for basal and stimulated 17OHP, respectively. Basal and stimulated 21DF thresholds of 0.31 nmol/L and 13.3 nmol/L provided 100% sensitivity with specificities of 96.8% and 100% for NCCAH, respectively. Diagnostic thresholds for HTZ of 8.0 nmol/L, 1.0 nmol/L, and 13.6 for stimulated 17OHP, 21DF, and the ratio (21DF + 17OHP)/cortisol each provided 100% sensitivity with specificities of 80.4%, 90.5%, and 85.0%, respectively. LC-MS/MS-specific 17OHP thresholds for NCCAH are lower than those based on immunoassay. LC-MS/MS-quantified 17OHP and 21DF accurately discriminate HTZ and NCCAH from PCOS.

Documentation of Genetic Diversity by Insulin-Like Growth Factor1 Receptor (Exon2) Gene for Fallow Deer (Dama dama) in Iraq.

Insulin-Like Growth Factor1 Receptor (Exon2) (IGF1R) gene plays a vital role in physiological impacts, such as growth, development, reproduction, and metabolism. A significant difference was noted between the IGR1R (exon 2) gene and the body weight of Dama dama. In addition, the heterozygosity pattern (AB) was significantly higher than the other pattern (AA). There are three single nucleotide polymorphisms (SNPs; 144G>C, 147A>G, and 210A>C) within the IGF-1R (exon 2) locus. The statistical analyses indicated the presence of three different haplotypes (GAA, CAA, and GGC). The analysis of relative frequencies indicated that the most frequent haplotype in the studied Dama dama population was Hap3 (GGC) (43.4782%) out of the three observed haplotypes. The results of SSCP-PCR revealed the variability of the target gene between the genotype frequencies in Fallow deer (Dama dama) with a high level of significance (P≤0.01) with two patterns (AA and AB) and an absence of BB pattern. The allele frequency of AA record a high level (71.74%) than the other genotype (AB) (28.26%), with a high-frequency level of the A allele (0.86) than the B allele (0.14). In current findings, SSCP genotyped in the Dama dama DNA observed an estimated 72% monomorphic loci and 28% polymorphic loci approximately. Hardy Weinberg equilibrium test (HW) was applied to the SSCP-PCR data matrix, and the statistical test was based on a chi-square (χ2) test. Chi-square was (55.928%) with a highly significant level (P≤0.01) recorded in the present study. As related to AA and AB genotypes mean, a significant difference (P≤0.05) was noted between IGF1R (exon 2) gene with a body weight of Dama dama, as well as the heterozygosity pattern (AB), was significantly (P≤0.05) higher than the other pattern (AA) (30.34±3.01kg versus 24.85±1.94kg), respectively. A significant impact (P≤0.05) between IGF1R (exon2) polymorphism and heart girth was founded to be related to the AB pattern (heterozygous) (76.92 ± 3.20 cm), whereas the lower value was related to the AA pattern (71.33 ± 2.49 cm). No significant differences in effects were shown in relation to body length and height at the shoulder. The present study is also interested in genetic characterization by calculating (Ne) as a tool for genetic diversity. Therefore, the number of alleles detected (Na) indicates that two alleles only were unique in the population of the study, with (1.3204) being the number of efficient alleles (Ne). Moreover, Shannon's Information index was recorded at 0.4073. The observed homozygosity (O.Hom.) and heterozygosity (HO) were (0.7174 and 0.2826), respectively. The values of expected homozygosity (E.Hom.) and heterozygosity (HE) were 0.7547 and 0.2453, respectively. The genetic diversity of Nei was 0.2427. The results showed an unexpected influx of IGF1R diversity measured by Fis and recorded the value (- 0.1646). In this sense, the results of the current study may be considered an approximation to the total genetic diversity of the population of Dama dama in Iraq, but the information obtained is relevant to proposing the strategies of conservation for the genetic diversity observed.

Development and characterization of 165 SNP markers in Mimosa bimucronata (Candolle) O. Kuntze

Mimosa bimucronata (Candolle) O. Kuntze, native to the American tropics, is the worst invasive tree species in China, where it is distributed in the southern coastal areas of Guangdong and Fujian provinces. It is characterized by rapid growth and waterlogging resistance, and was introduced in China for slope and bank protection. However, there is still a lack of effective molecular markers for its invasion management. In this study, we used a qubit dsDNA HS assay kit to extract DNA, and DNBSEQ-500 whole genome re-sequencing technology to obtain single nucleotide polymorphism (SNP) markers. In total, we developed and characterized 165 SNP markers. Observed (HO) and expected heterozygosity (HE) ranged from 0.0667 to 0.1000 and 0.1800 to 0.5000, respectively. The polymorphic information content (PIC) ranged from 0.1638 to 0.3750. These SNP markers will help to analyze the population genetic structure and manage M. bimucronata.

Microsatellite DNA markers for the commercially important fish Hypophthalmus donascimientoi (Pisces: Siluriformes: Pimelodidae) in the Amazon basin: isolation, characterization and amplification in congeneric species.

The genus Hypophthalmus comprises six species (H. edentatus, H. marginatus, H. fimbriatus, and H. oremaculatus), and the recently described: H. donascimientoi and H. celiae. The popular name for Hypophthalmus spp. in Brazil is mapará, this name refers to the six species. This group of fish has commercial importance for the states of Amazonas and Pará and, for this reason, requires studies to identify fish stocks. One approach is to use molecular markers, which have been very useful in studies with identification and population analysis of fish. Microsatellite molecular markers (SSRs) are one of the most informative markers for this purpose. There is little populations study of Hypophthalmus using SSRs, and there are less than six loci for the species Hypophthalmus marginatus available in the literature. With the construction of a genomic library of H. donascimientoi, we aimed to isolate and characterize SSRS markers and evaluate the extent of interspecific amplification. A genomic library was constructed with regions enriched of microsatellite for Hypophthalmus donascimientoi. A total of 126 contigs with 42 SSRs were used to design flanking primers for 39 microsatellites. Fifteen loci were characterized in three locations of the Solimões/Amazonas Rivers. The number of alleles ranged from one to 17 with a total of 126 alleles. The mean observed heterozygosity (HO) and expected heterozygosity (HE) were 0.721-0.692, respectively (S.d. HO 0.061 and HE 0.060). Two loci showed significant deviation in the HWE. The PIC ranged from 0.375 to 0.908. Such identified, 12 highly informative loci, and two moderately informative loci. Among the fifteen loci characterized, seven were successfully amplified in four other species of the genus. The microsatellite showed promise for estimating the genetic variability of H. donascimientoi and can be used as an efficient tool in population analyses of this species and in congeneric species analyzed.

Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding

In the 1940s, the Agronomic Institute of Campinas (IAC) started a grapevine breeding program to develop new cultivars adapted to the tropical and subtropical regions of Brazil. More than 2,000 crosses were carried out over 50 years, using 850 varieties as parents. However, among the thousands of hybrids developed by the program, only 130 are still maintained in the IAC grapevine germplasm collection. Little is known about their genetic makeup and usefulness for current breeding programs. In this study, we genotyped 130 Brazilian grape hybrids at 21 polymorphic microsatellite markers to evaluate the genetic diversity and population structure of the hybrids and verified their disclosed pedigrees. The results showed that the hybrid collection is highly diverse, with an expected heterozygosity (HE) of 0.80 and an observed heterozygosity (Ho) of 0.78. Strong structure in three subgroups based mainly on the usage and combination of parental groups was revealed by STRUCTURE software and confirmed by discriminant analysis of principal components (DAPC). Through molecular profiling analysis, fourteen synonyms, one homonym and one duplicate were identified. Parentage analysis confirmed 24 full parentages, as well as 33 half-kinships. In addition, 18 pedigrees were invalidated, and seven mislabeling events were identified. No compatible parent was identified for 33% of the IAC hybrids, highlighting severe genetic erosion in the IAC germplasm. The molecular characterization of the breeding hybrid bank collection contributes to our understanding of the genetic basis of the varieties, guiding the efficient utilization of available genetic diversity. Together, our results could be applied to other breeding programs and assist in the selection of parents, management of the breeding collection, and conservation of grapevine genetic resources.

Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study

Each year, 92 million pregnant women are at risk of contracting malaria during pregnancy, with the underestimation of the mortality and morbidity burden associated with Plasmodium vivax. During pregnancy, P.vivax infection is associated with low birth weight, maternal anaemia, premature delivery, and stillbirth. In the State of Acre (Brazil), high transmission leaves pregnant women at greater risk of contracting malaria and having a greater number of recurrences. The study of genetic diversity and the association of haplotypes with adverse pregnancy effects is of great importance for the control of the disease. Here we investigate the genetic diversity of P.vivax parasites infecting pregnant women across their pregnancies. P.vivax DNA was extracted from 330 samples from 177 women followed during pregnancy, collected in the State of Acre, Brazil. All samples were negative for Plasmodium falciparum DNA. Sequence data for the Pvmsp1 gene was analysed alongside data from six microsatellite (MS) markers. Allelic frequencies, haplotype frequencies, expected heterozygosity (HE) were calculated. Whole genome sequencing (WGS) was conducted on four samples from pregnant women and phylogenetic analysis performed with other samples from South American regions. Initially, the pregnant women were stratified into two groups-1 recurrence and 2 or more recurrences-in which no differences were observed in clinical gestational outcomes or in placental histological changes between the two groups. Then we evaluated the parasites genetically. An average of 18.5 distinct alleles were found at each of the MS loci, and the HE calculated for each marker indicates a high genetic diversity occurring within the population. There was a high percentage of polyclonal infections (61.7%, 108/175), and one haplotype (H1) occurred frequently (20%), with only 9 of the haplotypes appearing in more than one patient. Most pregnant women had polyclonal infections that could be the result of relapses and/or re-infections. The high percentage of H1 parasites, along with the low frequency of many other haplotypes are suggestive of a clonal expansion. Phylogenetic analysis shows that P.vivax population within pregnant women clustered with other Brazilian samples in the region. FAPESP and CNPq - Brazil.