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GENEPOP (Version 1.22): Population Genetics Software for Exact Tests and Ecumenicism
... Any individual oyster or microsatellite locus with > 25% missing data was excluded from further analyses. The remaining data were converted to a Genepop file format (Raymond and Rousset, 1995;Rousset, 2008). Oysters were grouped by sampling event (broodstock, S eyed , juveniles), treatment (S 13, S 15 ), and field deployment location (YR, RR), with each unique combination of these three factors constituting a sample. ...
... P-values were corrected for the falsediscovery rate (FDR; [Benjamini and Hochberg, 1995]). The Genepop software (Raymond and Rousset, 1995;Rousset, 2008) was used to identify significant differences in genic (allelic) frequencies among samples on a locus-by-locus basis using the exact G test, and significance was assessed with 100 batches of 1000 Markov Chain Monte Carlo (MCMC) iterations each following a burn-in of 1000 iterations. G-tests implemented in Genepop were used to identify significant differences among samples based on allele frequencies, and significant locus-bylocus comparisons (<0.05) were summed for each pairwise comparison. ...
... [18], the following parameters of genetic variability were calculated: effective number of alleles per locus (Ne), number of unique alleles, observed (Ho) and expected (He) heterozygosity, fixation index (F), and coefficient of genetic differentiation of populations (F ST ). The Hardy-Weinberg equilibrium (HWE) test was performed using GENEPOP v. 4.2 [19]. The frequency of null alleles was estimated using the method Brookfield [20], implemented in the MICRO-CHECKER 2.2.3 software [21]. ...
The structure of genetic variability of the prickly juniper Juniperus deltoides R.P. Adams (family Cupressaceae), an important component of Mediterranean arid and semiarid ecosystems, was studied. We genotyped samples from five populations of J. deltoids located at the northeastern limit of the range in Eurasia (Western Crimea, Transcaucasia) and one Balkan population (Bulgaria) using five nuclear microsatellite loci developed for Juniperus cedrus Webb & Berthel. Average values of intrapopulation genetic diversity were found (He varies from 0.428 to 0.602) with the lowest values in the Crimean populations. Phylogenetic analyses revealed that the populations were assigned into three genetic groups: Western Crimea, Caucasus (Kras-nodar krai), and Balkans (Bulgaria). Application of AMOVA to these groups showed statistically significant differentiation (9.9% of total variability, P < 0.001). The first two groups correspond to the previously identified Asian group of J. deltoides, and the third group corresponds to the Balkan group. The differentiation of the Crimean populations from geographically close Caucasian populations is shown for the first time.
... Over the years, breeders and geneticists have performed extensive research on the population structure and genetic diversity of wheat, corn, and other crops [4][5][6][7][8]. However, with advances in molecular biology technology, research on population structure has shifted from phenotypic to molecular biology-based [9][10][11][12][13][14]. Different software programs, including STRU CTU RE [15,16], ADMIXTURE [17], MEGA [18,19] POWERMARKER [20], GenAlEx [21], PLINK [22], and GENEPOP [23], have been developed to assist researchers in the analysis of the genetic composition, differentiation, classification, and diversity of populations. ...
Background
Henan is the province with the greatest wheat production in China. Although more than 100 cultivars are used for production, many cultivars are still insufficient in quality, disease resistance, adaptability and yield potential. To overcome these limitations, it is necessary to constantly breed new cultivars to maintain the continuous and stable growth of wheat yield and quality. To improve breeding efficiency, it is important to evaluate the genetic diversity and population genetic structure of its cultivars. However, there are no such reports from Henan Province. Therefore, in this study, single nucleotide polymorphism (SNP) markers were used to study the population genetic structure and genetic diversity of 243 wheat cultivars included in a comparative test of wheat varieties in Henan Province, aiming to provide a reference for the utilization of backbone parents and the selection of hybrid combinations in the genetic improvement of wheat cultivars.
Results
In this study, 243 wheat cultivars from Henan Province of China were genotyped by the Affymetrix Axiom Wheat660K SNP chip, and 21 characteristics were investigated. The cultivars were divided into ten subgroups; each subgroup had distinct characteristics and unique utilization value. Furthermore, based on principal component analysis, Zhoumai cultivars were the main hybrid parents, followed by Aikang 58, high-quality cultivars, and Shandong cultivars. Genetic diversity analysis showed that 61.3% of SNPs had a high degree of genetic differentiation, whereas 33.4% showed a moderate degree. The nucleotide diversity of subgenome B was relatively high, with an average π value of 3.91E-5; the nucleotide diversity of subgenome D was the lowest, with an average π value of 2.44E-5.
Conclusion
The parents used in wheat cross-breeding in Henan Province are similar, with a relatively homogeneous genetic background and low genetic diversity. These results will not only contribute to the objective evaluation and utilization of the tested cultivars but also provide insights into the current conditions and existing challenges of wheat cultivar breeding in Henan Province, thereby facilitating the scientific formulation of breeding objectives and strategies to improve breeding efficiency.
... The FSTAT v. 2.9.3.2 software was also used to calculate Weir and Cockerham's (1984) within year-class inbreeding coefficient (F IS ) and pairwise F ST values. Each year-class was checked for the presence of null alleles and scoring errors due to stuttering or large allele dropouts using the Brookfield 1 estimator (Brookfield 1996) (Guo and Thompson 1992;Raymond and Rousset 1995) using 1,000 de-memorization steps, 100 batches, and 1,000 iterations per batch. All tests included Bonferroni corrections (Rice 1989). ...
Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (Nb) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.
... The GenAlex v6.5 and Arlequin v3.5.2 programs were used to calculate the following parameters of genetic variability: average number of alleles per locus (N a ), number of unique alleles, percentage of polymorphic loci (%P), Shannon index (I), observed (H O ) and expected (H E ) heterozygosity, fixation index (F), and coefficient of genetic differentiation among populations (F ST ). The Hardy-Weinberg equilibrium (HWE) test was performed using GENEPOP v4.2 [20]. The frequency of null alleles was estimated using the Brookfield method [21] implemented in the MICRO-CHECKER 2.2.3 software [22]. ...
The structure of genetic variation of the common juniper (Juniperus communis L.), a widespread wind-pollinated holarctic shrub of Cupressaceae was surveyed. We used seven microsatellite markers, including three new ones, to genotype samples from 23 Eurasian populations and one from North America (Alaska). The geographical patterns are interpreted jointly with our previously available chloroplast DNA data. High genetic diversity was revealed with the highest values in the same northern populations (Sweden, Estonia, Mezen, Polar Urals, Yamal, and Kolyma, as well as in the Alps) as previously identified by cpDNA analysis. Nuclear markers exhibited a lower level of interpopulation differentiation (F ST = 9.8%) than chloroplast markers (F ST = 76%). Bayesian cluster analysis showed that the optimal number of genetic groups (K) was two. All 24 populations of J. communis were divided into an eastern group (the Northeast and Far East of Rus-sia, Alaska, and the Himalayas) and a western group (Europe, the Urals, and Siberia). In the Alpine and Mt. Shoria populations, genotypes from different genetic groups are combined.
... software (Perrier and Jacquemoud-Collet, 2019). Phenotype differentiation based on genetic information was performed using the test proposed by Raymond and Rousset (1995). After defining groups of phenotypes based on their historical origin, a hierarchical analysis of the variance was carried out using the analysis of molecular variance. ...
This study aimed to assess the genetic diversity and population structure of 12 guinea fowl phenotypes from three climatic zones (Guinean, Sudano-Guinean and Sudanian) of Benin. A total of 96 adult guinea fowl, aged at least 6 months, were selected for blood sampling. Fragment analysis was carried out using 17 polymorphic microsatellite markers. The informative marker combinations revealed a total of 83 alleles across all loci, with an average of 5 alleles per locus and a mean polymorphic information content (PIC) of 0.793. This study showed an observed heterozygosity of 0.492. The inbreeding coefficient values ranged from −0.086 in white phenotype to 0.226 in cinnamon, showing a deficit of heterozygotes, suggesting a moderate inbreeding level. A relatively low population differentiation was observed, with a mean fixation index (Fst) value of 0.033. The short genetic distances between phenotypes, unlike the strong genetic identities, revealed high genetic proximity between the 12 phenotypes of indigenous guinea fowl in Benin. These data indicate the existence of a single indigenous guinea fowl population with high intra-population genetic diversity with respect to climatic zones or phenotypes. This study will help in the selection of parental breeding stock for genetic improvement programs, as well as in the conservation for biodiversity maintenance and sustainable use of the indigenous guinea fowl in the study zones in Benin.
... The linkage disequilibrium (LD) between all pairs of loci using GENEPOP 4.7.5. The deviation of genotypic frequencies from the Hardy-Weinberg equilibrium (HWE) was tested in GENEPOP 4.7.5 (Raymond and Rousset 1995). AMOVA was performed using Arlequin 3.5. ...
The present study aimed to investigate the population genetics of Paramisgurnus dabryanus across six river basins in China. Two mitochondrial genes (Cytochrome b and control region) and 12 microsatellite markers were employed to analyze the population genetics of 370 and 994 individuals, respectively, collected from 37 geographic locations. The analyses of both mitochondrial and microsatellite DNA revealed high levels of genetic diversity in P. dabryanus populations across the six river basins. Interestingly, the northern populations (Songliao River, Haihe River, and Yellow River) showed lower levels of genetic diversity compared to the southern populations (Huaihe River, Yangtze River, and Pearl River). Furthermore, the genetic analysis based on mitochondrial genes revealed no clear boundary between populations from different river basins, indicating no bottlenecks of gene flow among populations. Microsatellite analysis, on the other hand, revealed significant genetic differentiation between northern and southern populations, suggesting the need of two management units for P. dabryanus. Demographic analysis indicated that the Yangtze River populations have probably experienced population bottlenecks in the past, but also experienced a population expansion during the Last Glacial Maximum (LGM) when the warm climate was suitable for Yangtze River dispersal and survival after a recent genetic bottleneck. The integration of mitochondrial and microsatellite DNA data suggested that the Yangtze River populations are the most suitable population as a donor for the other river basins of P. dabryanus. Our findings have important implications for the conservation and effective management strategies of P. dabryanus.
... С помощью программ GenAlex v6.5 и Arlequin v3.5.2 вычисляли следующие параметры генетической изменчивости: среднее число аллелей на локус (N a ), число уникальных аллелей, процент полиморфных локусов (%P), индекс Шеннона (I), наблюдаемая (H O ) и ожидаемая (H E ) гетерозиготность, индекс фиксации (F), коэффициент генетической дифференциации среди популяций (F ST ). Тест на равновесие Харди-Вайнберга (HWE) был выполнен с помощью GENEPOP v4.2 [20]. Частоту нулевых аллелей оценивали с помощью метода Брукфилда [21], реализованного в программном обеспечении MICRO-CHECKER 2.2.3 [22]. ...
25.04.2022 г. После доработки 16.09.2022 г. Принята к публикации 27.09.2022 г. Изучена структура генетической изменчивости можжевельника обыкновенного (Juniperus communis L.), широко распространенного голарктического ветроопыляемого кустарника семейства Cupressaceae. Для генотипирования выборок из 23 популяций этого вида со всего ареала в Евразии и одной попу-ляции из Северной Америки (Аляска) использовали семь ядерных микросателлитных локусов, три из которых были применены для данного вида впервые. Географические закономерности распреде-ления генетической изменчивости интерпретируются в сравнении с нашими предыдущими данны-ми по изменчивости хпДНК. Получены такие же высокие значения генетического разнообразия, с максимальными показателями в северных популяциях (Швеция, Эстония, Мезень, Полярный Урал, Ямал, Колыма, а также Альпы), но более низкий уровень межпопуляционной дифференциа-ции (F ST = 9.8% для ядерных маркеров, F ST = 76% для хлоропластных). С помощью байесовского кластерного анализа было установлено, что оптимальное число генетических групп (K) равно двум. Все 24 популяции J. communis делятся на восточную группу (северо-восток и Дальний Восток Рос-сии, Аляска и Гималаи) и западную группу (Европа, Урал и Сибирь). Для популяций из Альп и Гор-ной Шории характерно сочетание генотипов из разных генетических групп. Ключевые слова: J. communis, ядерные микросателлиты, SSR-маркеры, генетическое разнообразие. Холодостойкие кустарниковые виды растений играли важную роль в фитоценозах в прошлые геологические эпохи Земли, да и теперь имеют огромное значение в сложении растительного по-крова северных и горных территорий, укреплении, обогащении почв и создании условий для будущих стадий сукцессий при возможных изменениях кли-мата. При этом исследований их филогеографии и генетической изменчивости проведено гораздо меньше, чем для лесообразующих видов деревьев. Известно, что на распределение генетической изменчивости внутри видов растений значитель-но влияли плейстоценовые колебания климата [1, 2]. В период похолодания некоторые адапти-рованные к холоду виды деревьев и кустарников Северного полушария не ограничивались южны-ми ледниковыми рефугиумами, а сохраняли до-вольно обширные популяции вблизи ледниковых щитов [3]. Эти популяции расширяли свои ареа-лы во время теплых стадий и обладали значитель-ным потоком генов [4]. Одним из таких видов, которые могли выжи-вать во время холодных эпизодов плейстоцена в высоких широтах в Северной Европе во многих пе-ригляциальных микрорефугиумах, является мож-жевельник обыкновенный Juniperus communis L. Этот холодостойкий бореально-арктический хвой-ный кустарниковый вид из семейства Cupressaceae занимает обширный ареал благодаря широкой экологической толерантности, морфологической пластичности и эффективному способу распро-странения семян. Основная часть его ареала на-ходится на территории России, которая обладает значительными, еще недостаточно изученными биологическими ресурсами этого ценного вида (рис. 1). Целебные свойства этого вечнозеленого кустарника были известны в древности. В насто-ящее время в его растительном сырье обнаружено большое количество терпенов, полифенолов и их производных, доказана его антиоксидантная, про-тивомикробная, противовоспалительная, противо-раковая, нейропротекторная и гепатопротектор-ная активность и отмечен огромный потенциал УДК 581.15:575.8:582.477.6 ГЕНЕТИКА РАСТЕНИЙ
Here we presented 10 polymorphic microsatellite loci obtained from scarlet ibis through an enriched genomic library. The analysis of 45 individuals from three Brazilian natural populations showed allelic diversity ranged from three to 17 alleles, observed heterozygosity ranged from 0.03 to 0.92, and expected heterozygosity ranged from 0.06 to 0.92. These highly variable microsatellite loci can provide means for assessing overall genetic variation in its remnant natural populations, which may help the development of effective conservation programs.
The green alder (Alnus alnobetula s.l.) is a cold-resistant boreal-arctic shrub species with a complex intraspecific taxonomy and a wide distribution range covering northern Eurasia and North America. In this study, we assess the level and distribution of diversity in five subspecies (A. alnobetula subsp. fruticosa, kamtschatica, mandschurica, maximowiczii, and sinuata) throughout 34 populations within the native species range by using 7 characters of leaf morphology and 11 nuclear microsatellites (nSSR). The differentiation in both sets of characters that we found has proven to be inconsistent with our previously obtained chloroplast DNA (cpDNA) data. Only three groups were identified using nSSR vs. five cpDNA haplogroups. Both morphological and nSSR analyses support the recognition of A. alnobetula subsp. fruticosa from the western part of the Eurasian distribution range (northwestern Russia, the Urals, and Siberia) and A. alnobetula subsp. maximowiczii from the eastern part (most of Sakhalin Island, the Kuril Islands, and most of Kamchatka). Among other East Asian subspecies such as A. alnobetula subsp. kamtschatica and subsp. mandschurica, as well as in A. subsp. sinuata from North America, considerable genetic and morphological admixture has been recorded. The discordance between the patterns inferred from cpDNA and nSSR data reflects limited gene dispersal via seeds and extensive gene flow via pollen between major glacial refugia.
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