Index Fst Research Articles

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam.

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.

Gene Frequency Shift in Relict Abies pinsapo Forests Associated with Drought-Induced Mortality: Preliminary Evidence of Local-Scale Divergent Selection

Current climate change constitutes a challenge for the survival of several drought-sensitive forests. The study of the genetic basis of adaptation offers a suitable way to understand how tree species may respond to future climatic conditions, as well as to design suitable conservation and management strategies. Here, we focus on selected genetic signatures of the drought-sensitive relict fir, Abies pinsapo Boiss. Field sampling of 156 individuals was performed in two elevation ecotones, characterized by widespread A. pinsapo decline and mortality. The DNA from dead trees was investigated and compared to living individuals, accounting for different ages and elevations. We studied the genes gated outwardly-rectifying K+ (GORK) channel and Plasma membrane Intrinsic Protein (PIP1) aquaporin, previously related to drought response in plant model species, to test whether drought was the main abiotic factor driving the decline of A. pinsapo forests. A combination of linear regression and factor models were used to test these selection signatures, as well as a fixation index (Fst), used here to analyze the genetic structure. The results were consistent among these approaches, supporting a statistically significant association of the GORK gene with survival in one of the A. pinsapo populations. These results provide preliminary evidence for the potential role of the GORK gene in the resilience to drought of A. pinsapo.

Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing

BackgroundDomestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation.MethodsIn this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks.ResultsUsing fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions.ConclusionsA wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.

When does habitat fragmentation lead to changes in populations gene pool of pedunculate oak (Quercus robur L.)?

Development of agriculture in the forest and forest-steppe zones of the vast East European plain over the past millennium has resulted to a significant decrease of broad-leaved forests habitat. It is expected that the disintegration of the forest tree species distribution ranges will lead to the erosion of the population genetic diversity of due to limited gene flow, impacts on gene pools of genetic drift and inbreeding. To investigate this threat, we analyzed the genetic diversity and differentiation among 20 populations of pedunculate oak (Quercus robur L.) from the Ural Mountains (Russia) and neighboring lowlands and foothills. A set of 412 nuclear SNPs loci was used for our study. A positive correlation (r = 0.168, p < 0.05) was observed between genetic and geographical distances. The most genetic variation was distributed within populations (fixation index FST = 0.054). It was found that the values of genetic diversity are similar in large continuous mountain stands (effective number of alleles ne = 1.340, observed heterozygosity HO = 0.213, expected heterozygosity HE = 0.200), in spatially highly fragmented forests of the Cis-Urals (ne = 1.340, HO = 0.210, HE = 0.200) and geographically isolated marginal habitats with populations of hundreds individuals (ne = 1.338, HO = 0.206, HE = 0.198). Only in populations with few dozen individuals, we revealed a statistically significant decrease in the genetic diversity (ne = 1.312, HO = 0.211, HE = 0.184) and increase of numbers of full sibs and level of kinship (the kinship-coefficient Kin = 0.078–0.128 vs Kin = -0.002–0.035 in other populations). Overall, our study demonstrates that the current gene pool of Q. robur populations in the study area remains stable under conditions of significant forest decline and habitat fragmentation. The historically short period of these processes in the region and the genetically successful gene flow between populations over long distances might be reasons for this phenomenon.

Genetic and Flower Volatile Diversity in Natural Populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria: Toward the Development of a Core Collection.

We studied the genetic and flower volatile diversity in natural populations of Origanum vulgare subsp. hirtum (Link) Ietsw. in Bulgaria using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers and gas chromatography/mass spectrometry (GC/MS) analysis of flower volatiles from individual plants. Two regions, including the Kresna Gorge and Eastern Rhodopes, typical for the species comprising eight populations and 239 individual plants were included in this study. An analysis with 11 SSR markers and eight SRAP primer combinations showed that SRAP markers were substantially more informative than the SSR markers and were further used for genetic diversity analysis. The results showed low-range to mid-range genetic differentiation between the populations with pairwise fixation index (Fst) values ranging between 0.0047 and 0.11. A total of 10 genetic clusters were identified. An analysis of the flower volatile diversity identified a total of 63 compounds with the vast majority of plants belonging to the carvacrol chemotype and just a single plant to the thymol chemotype. Large deviations were observed for individual compounds within each region as well as within the populations. Hierarchical clustering showed a clear sample grouping based on the two different regions. In addition, an in-depth analysis identified six major and 23 minor metabolite clusters. The overall data set and cluster analysis were further used for the development and testing of a simple and straightforward strategy for the selection of individual plants for the development of a core collection representing the sampled natural populations for this species in Bulgaria. The proposed strategy involves precise genetic clustering of the tested plants followed by the selection of a minimal set from each genetic cluster representing the different metabolite clusters. The selected core set was further compared with a core set extracted by the PowerCore software. A comparison of the genetic and metabolic affiliation of the members of both sets showed that the reported approach selected representatives from each genetic cluster and minor metabolic cluster, whereas some metabolic clusters were unrepresented in the PowerCore set. The feasibility and efficiency of applying the pointed strategy for the development of a core collection representing both the genetic and metabolite diversity of natural populations in aromatic and medicinal plants toward subsequent steps of selection and breeding are discussed.

Genetic Variability of Nile Tilapia Strains as Determined by Microsatellite DNA Markers

AbstractThe main purpose of the present study was to investigate the genetic variability of Nile Tilapia Oreochromis niloticus strains by using microsatellite DNA markers and to compare these data with those previously obtained with single‐nucleotide polymorphisms (SNPs). Five mixed‐sex strains and four YY‐male strains were analyzed. All nine microsatellite loci were polymorphic; the number of unique alleles per locus varied from 6 at UNH216 to 33 at UNH880. Strong correspondence was observed between the level of expected heterozygosity (He) or observed heterozygosity and the number of alleles per locus (A) or the number of private alleles. Strains with high levels of heterozygosity typically had higher values of A and the presence of private alleles. In general, mixed‐sex strains had higher genetic variability than YY‐male strains. Four mixed‐sex strains (GIFT, Ismailia Canal, LSA hybrid, and Miami) had the highest level of genetic variability, with mean He ranging from 0.630 to 0.798 and mean A ranging from 5.11 to 9.78. Three YY‐male strains (Fishgen YY Dark–Group 2, Fishgen YY Red, and Til‐Aqua YY) had low genetic variability, with mean He ranging from 0.282 to 0.367 and mean A ranging from 1.89 to 3.56. All investigated strains demonstrated low values of the inbreeding coefficient FIS (from –0.266 to 0.014), suggesting that mating of closely related individuals is being avoided during maintenance of these strains. Pairwise genetic differentiation index FST values had a broad range (from 0.0915 to 0.6063), indicating different levels of genetic differentiation between strains. A dendrogram constructed according to shared allele distance showed the existence of two distinct clusters among strains. The present data on genetic variability of Nile Tilapia strains demonstrated substantial similarity with data from a previous study of SNPs in the same populations.

Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin.

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

Comparison of morphology and genetic diversity between broodstock and hybrid offspring of oriental river prawn, Macrobrachium nipponense based on morphological analysis and SNP markers.

Hybridization is an effective method for the genetic improvement of farmed species. In this study, three broodstock populations (Changjiang, CJ, Dongting, DT, and Dianshan, DS) of oriental river prawn, Macrobrachium nipponense were used, and DS was used as the female broodstock. Through three-line hybridization, two hybrid populations were finally obtained. The F3 generation of the broodstock population and the F1 generation of the hybrid population were cultured indoors for 3 months. Through morphological analysis (cluster analysis, discriminant analysis and path analysis) it was found that the hybrid population and the broodstock had some differences, but not enough to reach the subspecies level, and the dominant traits exhibited differentiation and reorganization. This study identified SNP genetic markers, carried out systematic evolution analysis and genetic diversity analysis and found that the nucleotide diversity π and heterozygosity Het of the hybrid population were higher than those of the broodstock. Among broodstocks, the differentiation index (Fst ) of SCD and SDC was smallest (0.055). This research provides some valuable reference for genetic breeding.

Population genetic data for 12 X-STR loci in the Central Saudi region using investigator Argus X-12 amplification kit

Background X-chromosome short tandem repeat (X-STR) markers are important in forensic identity investigations and kinship analysis. Subject and methods In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of Saudi Arabia in order to develop an allelic frequency database for the markers included in the kit. Results DXS10146 locus was the most informative with 21 alleles, while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci, either as individual markers or as linkage groups, provide genetic information with high discrimination that is appropriate for forensic purposes with polymorphism information content (PIC), power of exclusion (PE), and paternity index (PI) varying from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically closer to the Egyptian and Emirati populations and distant to the Turkish population. Conclusion The current study revealed that Investigator® Argus 12 X-STR kit would support the forensic application, kinship testing involving female offspring, and human identification in the Saudi population.

Identification of Main Oyster Species and Comparison of Their Genetic Diversity in Zhejiang Coast, South of Yangtze River Estuary

Oysters are an important aquaculture species distributed worldwide, including in Zhejiang Province, located on the east coast of China. Because of the high diversity and complicated introduction history of oysters and their seedlings, there has been much disagreement regarding the origin of each species, and the dominant and indigenous species remain unclear. We sampled 16 batches of oysters from seven sites in three aquaculture bays and found two main oyster species, Crassostrea sikamea and Crassostrea angulata. The former occupied the higher intertidal zone and comprised more than 70% of the cultured oysters. Based on the cytochrome oxidase C subunit I (COI) and mitochondrial noncoding region (MNR), C. sikamea showed higher genetic diversity than C. angulata. The analysis of molecular variance among COI sequences of these species from the Xiangshan Bay populations were comparable to those of other populations and showed that most of the molecular variance was within groups, which was consistent with the low pairwise fixation index FST values. The neutrality test revealed that C. sikamea experienced population expansion events, whereas for C. angulata, the significant Fu’s Fs and non-significant Tajima’s D test results may indicate a possible population expansion event, implying that C. sikamea is likely an indigenous species. The method established based on internal transcribed spacer 1 digestion by the HindIII restriction enzyme is useful for identifying C. sikamea and C. angulata in the local region. The specific primers on the MNR sequence show potential for distinguishing C. sikamea from four other important Crassostrea oysters. These results highlight the abundance of C. sikamea on the Zhejiang coast and lay the foundation for protecting and utilizing the local oyster germplasm resources and for the sustainable development of the oyster industry.

Genetic differentiation over a small spatial scale in the smooth newt (Lissotriton vulgaris)

Understanding the distribution of genetic variation is central for both population biology and conservation genetics. Genetic population structure can be primarily affected by the species’ dispersal ability, which is assumed to be limited in many amphibians. In this study, we estimated allelic differentiation metrics and FST indices to investigate genetic variation among natural breeding ponds of smooth newts (Lissotriton vulgaris) over a small spatial scale. Based on six microsatellite loci, we found a small, but significant allelic differentiation among clusters of natural breeding ponds (i.e. ‘local regions’), which result was in line with the calculation of corresponding hierarchical FST values. Analysis of molecular variance also indicated significant between-region variation in the study area. Pairwise estimations showed that only the furthermost regions differed from each other in both differentiation measures, but this difference was not attributable to geographic distances between ponds. Our results provide evidence that hierarchical genetic structure can be characteristic to breeding ponds of smooth newts on a small spatial scale in their natural breeding habitat, but dispersal distance may be less limited than previously thought in these philopatric caudates.

Population Genetic Structure and Breeding Pattern of Higher Group Termite Globitermes sulphureus (Haviland) (Blattodea:Termitidae)

The subterranean termite Globitermes sulphureus (Blattodea: Termitidae) can be found in tropical regions. We chose seven novel species-specific microsatellite markers to infer the breeding pattern of G. sulphureus based on its colony and population genetic structure in eight selected populations (natural-n = 4 and metropolitan-n = 4) in Kedah and Penang, Malaysia. A strong correlation with their geographical location is shown by the acquired genetic gap for all studied populations from this study. The breeding pattern of family structure and comparisons of estimated F-statistics among G. sulphureus workers suggests 60% of all colonies are mixed families, whereas the remaining are simple families. Average relatedness values within simple and mixed family colonies are similar (r = 0.121). Positive fixation index FST values (FST = 0.086) indicate all eight populations (&gt;500 m apart) have a significantly moderate genetic differentiation and low levels of inbreeding based on the low overall inbreeding coefficient FIT value of 0.391. Furthermore, four populations; Palapes USM (PU), Tmn Astana (TA), Kg Teluk (KT), and Penang National Park (NP), deviate from Hardy–Weinberg equilibrium (HWE, all p = 0.000) and five studied polymorphic loci (GS1, GS10, GS15, GS27 and GS29) are possibly under selection. The findings also reveal signs of a bottleneck effect in two populations: Tikam Batu (TB) and Penang National Park (NP), indicating genetic drift.

Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho.

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58–49.61 Mbp). These results were confirmed using FST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.

Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA

Abstract. Astarini IA, Ningsih EY, Simanungkalit D, Ardiana SA, Al Malik MD, Yusmalinda NLA, Sembiring A, Pertiwi NPD, Cahyani NKD, Collins A. 2021. Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA. Biodiversitas 22: 1644-1651. Longtail tuna (Thunnus tonggol, Family: Scombridae) is an economically valuable neritic species found in tropical and subtropical waters in the Indo-Pacific region. High catch numbers, which have been decreasing, could negatively impact this tuna’s population level. Little research has been conducted on the longtail tuna population in Indonesia. This study aims to determine the genetic diversity and potential population structure of longtail tuna landed in four fish markets in Indonesia (representing three sampling locations because two markets are relatively close to each other) based on sequences of a region of mitochondrial control region (d-loop). A total of 101 samples, out of 110, were identified and confirmed as T. tonggol species by amplifying and sequencing a fragment of d-loop (amplicons ranging from 482 - 523 bp). Neighbor-joining analysis resulted in a topology with all samples grouped into one clade with an average genetic distance of 0.020. Meanwhile, haplotype diversity (Hd) and nucleotide diversity (?) values of the longtail tuna samples were 0.9939 and 0.0192, respectively. The fixation index (Fst) value was -0.00507, with p&gt; 0.05, which indicates that there is no significant population structure among the longtail tuna collected from four fish markets representing three sampling locations. The results of this analysis can be used as basic data in planning sustainable fisheries management efforts.

Population Genetic Structure of Pacific Herring Clupea pallasii in the Northwestern Pacific Ocean Based on Microsatellite Analysis

The population genetic structure of Pacific herring Clupea pallasii in the northwestern Pacific Ocean is studied based on the polymorphism analysis of 11 microsatellite loci. Significant genetic differences are found between lacustrine and marine forms of herring (FST 0.0197−0.0521). The herring of lakes Ainskoe and Vilyui are separate populations. Based on the genetic differentiation index FST (0.0086−0.0218), the samples of marine forms are divided into two geographical groups: the Sea of Okhotsk and the Sea of Japan group, and the Bering Sea group. Within these groups, five population groups are differentiated: (1) Peter the Great Gulf, (2) northwestern Sea of Okhotsk (Okhotsk), (3) Shelikhov Gulf Shelikhova (Gizhiginsk), (4) Karaginsky Gulf, and (5) northern Bering Sea. During a period of high abundance, herring lacks clear ecological boundaries; its population structure can change over several generations on a significant part of the distribution range. The modern population structure of the marine forms was formed by a depression of the Bering Sea population and a population explosion in the Sea of Okhotsk.

Identification of Target Chicken Populations by Machine Learning Models Using the Minimum Number of SNPs.

Simple SummaryClassifying a target population at the genetic level can provide important information for the preservation and commercial use of a breed. In this study, the minimum number of markers was used in combination, to distinguish target populations based on high-density single nucleotide polymorphism (SNP) array data. Subsequently, a genome-wide association study for filtering target-population-specific SNPs between the case and control groups and principal component analysis with machine learning algorithms could be used to explore various combinations with the minimum number of markers. In addition, the optimal combination of SNP markers was able to produce stable results for the target population in verification studies, in which samples were analyzed.A marker combination capable of classifying a specific chicken population could improve commercial value by increasing consumer confidence with respect to the origin of the population. This would facilitate the protection of native genetic resources in the market of each country. In this study, a total of 283 samples from 20 lines, which consisted of Korean native chickens, commercial native chickens, and commercial broilers with a layer population, were analyzed to determine the optimal marker combination comprising the minimum number of markers, using a 600 k high-density single nucleotide polymorphism (SNP) array. Machine learning algorithms, a genome-wide association study (GWAS), linkage disequilibrium (LD) analysis, and principal component analysis (PCA) were used to distinguish a target (case) group for comparison with control chicken groups. In the processing of marker selection, a total of 47,303 SNPs were used for classifying chicken populations; 96 LD-pruned SNPs (50 SNPs per LD block) served as the best marker combination for target chicken classification. Moreover, 36, 44, and 8 SNPs were selected as the minimum numbers of markers by the AdaBoost (AB), Random Forest (RF), and Decision Tree (DT) machine learning classification models, which had accuracy rates of 99.6%, 98.0%, and 97.9%, respectively. The selected marker combinations increased the genetic distance and fixation index (Fst) values between the case and control groups, and they reduced the number of genetic components required, confirming that efficient classification of the groups was possible by using a small number of marker sets. In a verification study including additional chicken breeds and samples (12 lines and 182 samples), the accuracy did not significantly change, and the target chicken group could be clearly distinguished from the other populations. The GWAS, PCA, and machine learning algorithms used in this study can be applied efficiently, to determine the optimal marker combination with the minimum number of markers that can distinguish the target population among a large number of SNP markers.

Genetic Diversity of Indigenous Chicken (Gallus Gallus domesticus) from Ecozones of Egypt and Kingdom of Saudi Arabia

Genetic diversity of two chicken ecotypes from Ismailia-Egypt (ISM) and Taif-Saudi Arabia (TA) was evaluated using 39 microsatellites. DNA was extracted from blood of 25 chickens/ecotype. The number of alleles was 157 and 138, the number of alleles/locus averaged 4.2±2.2 and 3.6±1.6, and the highest number of private alleles was 9 and 5 for ISM and TA, respectively. Percentage of shared alleles between the two ecotypes was 45%. This panel of markers is reasonably informative as the mean polymorphic information content for ISM and TA was 0.47±0.21, and 0.41±0.2. Similar average of observed heterozygosity was attained for both ecotypes. Conversely, averages of expected heterozygosity differed between two ecotypes, 0.52±0.23 vs. 0.45±0.21 for ISM and TA. 8 and 12 loci have significantly deviated from HWE of ISM and TA. Estimate of genetic distance was 0.2 and FST index was 0.29. Results showed only 6% of genetic diversity is shared between these two ecotypes.

Genetic Study of X-Linked Recessive Ichthyosis in Eastern Ukraine

X-linked recessive ichthyosis (OMIM 308100) is a form of ichthyosis caused by abnormal keratinization and can result in disability, social maladaptation, and decreased quality of life for patients and their families. In most cases the disease is caused by a complete or partial deletion of the steroid sulfatase (STS) gene. This study estimated the prevalence of X-linked recessive ichthyosis, the inbreeding coefficient (or fixation index) FST, and the selection coefficient in individuals of eastern Ukraine (namely, Kharkiv oblast). The genealogical method was used to assess the genetic structure of families with a history of this disease. Fluorescent in situ hybridization (FISH) was carried out to detect the deletion of the STS gene in patients and their relatives. The prevalence of the disease in eastern Ukraine was 1.5 × 10–4 males, it ranged from 4.9 × 10–5 to 4.9 × 10–4 males in the districts, and from 2.2 × 10–4 males in the town of Krasnograd to 3.7 × 10–3 males in a village of Balakliia district. The burden of X-linked recessive ichthyosis was found to be positively correlated with the inbreeding coefficient FST in all the studied districts (r = 0.976). Over the past 10 years, the inbreeding coefficient FST increased 1.8 times and the prevalence of X-linked recessive ichthyosis increased 1.4–4.3 times in most districts of the region. The clinical genealogical analysis of nine large families revealed no females with X-linked recessive ichthyosis among relatives of probands, while 21.4% (n = 14) of the first-degree male relatives and 12.0% (n = 25) of the second-degree male relatives had ichthyosis. In most patients and their mothers from eastern Ukraine, FISH detected an interstitial deletion of the STS gene, ish del(X)(p22.31p22.31)(STS-), but no KAL1 gene deletions. In men with X-linked recessive ichthyosis, the average number of children per person was 2.5 times lower than in healthy relatives, and their offspring was characterized by the prevalence of females over males in a 3 : 1 ratio. In obligate heterozygous females, the average number of children per person was 2.2, and the sex ratio in the offspring approached 1 : 1.

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles.

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94–97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970–2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (Fst) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.