scholarly journals Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9609
Author(s):  
Ying Liu ◽  
Fei Yi ◽  
Guijuan Yang ◽  
Yuting Wang ◽  
Ciren Pubu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Genetic ◽  
Genotyping By Sequencing ◽  
Mean Value ◽  
Gene Exchange ◽  
Subgroup Ii ◽  
Yarlung Zangbo River ◽  
High Level ◽  
Sophora Moorcroftiana

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.

Genetic variation in lowland sorghum (Sorghum bicolor (L.) Moench) landraces assessed by simple sequence repeats

2014 ◽  
Vol 13 (2) ◽  
pp. 131-141 ◽  
Author(s):  
Beyene Amelework ◽  
Hussien Shimelis ◽  
Pangirayi Tongoona ◽  
Mark Laing ◽  
Fentahun Mengistu
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Target Area ◽  
Eastern Ethiopia ◽  
Important Indicator ◽  
High Level ◽  
Analytical Approaches

The regions of north-eastern Ethiopia are known for their high levels of sorghum genetic diversity, and for being drought prone. For centuries, sorghum has been developed and maintained by farmers for its adaptation to the marginal and heterogeneous environment of these regions. The objective of this study was to examine the genetic diversity and population structure of 200 sorghum landraces collected from seven lowland districts, using 30 microsatellite markers sampled from all linkage groups of the sorghum genome. Both distance-based and model-based analytical approaches were used to analyse the data. The data analysis revealed that there was a large variation among all the markers under study. The values of polymorphic information content ranged from 0.26 to 0.88, with a mean value of 0.61, reflecting the high discriminating ability of the markers studied. The mean value of total gene diversity was 0.69, which partitioned 86% among the landraces and 14% within the landraces. Gene diversity among the landraces was largely due to the variation among the genotypes within the geographic origins. Landraces sampled from different collection sites appeared to cluster together, indicating the existence of a high level of gene flow among the sites of collection. This indicates that a relatively small, random collection of landraces would capture the bulk of genetic diversity in the target area. A moderately high level of genetic differentiation and a relatively low level of gene flow were observed between sorghum races and maturity groups. Given that the target area is marginal, drought prone and heterogeneous, the study of genetic diversity among sorghum landraces could serve as an important indicator of valuable alleles for drought tolerance in future sorghum improvement programmes.

scholarly journals Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 135 ◽  
Author(s):  
Jingxue Zhang ◽  
Miaoli Wang ◽  
Zhipeng Guo ◽  
Yongzhuo Guan ◽  
Jianyu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Cynodon Dactylon ◽  
Latitudinal Gradients ◽  
Wind Pollination ◽  
Ploidy Levels ◽  
Sexual And Asexual Reproduction ◽  
Genetic Pattern

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.

scholarly journals Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

2018 ◽  
Vol 7 (4.38) ◽  
pp. 122
Author(s):  
Kairat Dossybayev ◽  
Aizhan Mussayeva ◽  
Bakytzhan Bekmanov ◽  
Beibit Kulataev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mean Value ◽  
Fixation Index ◽  
Merino Sheep ◽  
Str Markers ◽  
Sheep Breeds ◽  
Str Loci ◽  
High Level ◽  
Two Populations

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.   

Use of expressed sequence tag microsatellite markers for population genetic research of Helicoverpa armigera (Lepidoptera: Noctuidae) from India

2015 ◽  
Vol 148 (2) ◽  
pp. 187-199
Author(s):  
Thiruvengadam Venkatesan ◽  
Vaddi Sridhar ◽  
Yan R. Tomason ◽  
Sushil Kumar Jalali ◽  
Gajanan T. Behere ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Expressed Sequence Tag ◽  
Genetic Research ◽  
Western India ◽  
Diversity Analysis ◽  
Lepidoptera Noctuidae ◽  
Expressed Sequence

AbstractCotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), is a serious pest of several crops throughout the world, representing millions of United States of America dollars worth of damage. This pest can adapt to various cropping systems in a wide geographical range and has high migratory potential. It features high fecundity and can develop resistance to almost all insecticides used for its management. Several investigations to develop microsatellite markers for H. armigera have not been successful because of the paucity of microsatellites in the lepidopteran genome. As well, collections of H. armigera from cotton fields of southern and western India were not yet studied for molecular genetic diversity. The current study aimed to screen publicly available expressed sequence tag resources for simple sequence repeats and assess their potential as DNA markers for assessment of gene flow between collections of southern and western India. We identified 30 polymorphic microsatellites for potential use in diversity analysis of H. armigera collections. Genetic diversity analysis revealed that the collections were widely diverse with population differentiation index (Fst) of 0.17. Furthermore, gene flow analysis revealed a mean frequency of private alleles of 11% within the collections. The microsatellite resources we developed could be widely used for molecular diversity or population genetic research involving this important pest of cotton and food crops.

Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

2002 ◽  
Vol 53 (6) ◽  
pp. 629 ◽  
Author(s):  
J. M. Musial ◽  
K. E. Basford ◽  
J. A. G. Irwin
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Random Amplified Polymorphic Dna ◽  
Population Diversity ◽  
Breeding Programs ◽  
Population Genetic Diversity ◽  
Medicago Sativa L ◽  
Components Analysis ◽  
High Level ◽  
Selection Of

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

scholarly journals Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [Cynodon dactylon (L.) Pers.] along longitude gradients

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11953
Author(s):  
Jing-Xue Zhang ◽  
Miaoli Wang ◽  
Jibiao Fan ◽  
Zhi-Peng Guo ◽  
Yongzhuo Guan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Distance ◽  
Ploidy Level ◽  
Population Genetic ◽  
Annual Precipitation ◽  
Mean Annual Precipitation ◽  
Ploidy Levels ◽  
Population Genetic Diversity

Background Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure. Methods Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E). Results There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.

scholarly journals Assessment of Genetic Diversity and Marker-Trait Associations Using Selected Early Maize Inbreds Derived From Local Landraces of Eastern Himalayan Regions

2021 ◽  
Author(s):  
E. Lamalakshmi Devi ◽  
Umakanta Ngangkham ◽  
Akoijam Ratankumar Singh ◽  
Bhuvaneswari S ◽  
Konsam Sarika ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Mean Value ◽  
Cross Combination ◽  
High Genetic Diversity ◽  
Average Value ◽  
Maize Inbreds ◽  
High Level ◽  
Trait Associations

Abstract North- Eastern parts of India fall under Eastern Himalayan region and it is a diversity hotspot of many crops including maize. Evaluation of genetic diversity is required to tape the potentiality of genetic resources in any crop improvement programmes. In the present study, genetic diversity at fifty two microsatellite markers were conducted in 30 early maize inbreds developed from local landraces of NE India. Genetic diversity analysis revealed a total of 189 alleles with a mean of 3.63 alleles/ locus. The allele size ranged from 50 bp (phi 036) to 295 bp (p 101049) which revealed a high level of genetic diversity among the loci. The PIC among the 30 genotypes ranged from 0.17 (umc 1622) to 0.76 (umc 1153) with an average value of 0.49. The value of Expected Heterozygosity (HExp) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (HObs) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis grouped the 30 inbreds into distinct three sub-clusters. Similarly, population structure and principal coordinate analysis) analysis also classified the 30 inbred lines into three-subpopulations. AMOVA revealed that 6% of total variance is due to differences among populations, while 94% of total molecular variance is accounted by within populations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present finding, these results show that the thirty maize inbreds have high genetic diversity which would be useful for choosing promising parents and for making cross combination based on genetic distance and clustering for genetic improvement programmes of maize.

scholarly journals The Sensitiveness of Expected Heterozygosity and Allelic Richness Estimates for Analyzing Population Genetic Diversity

2021 ◽  
Author(s):  
María Eugenia Barrandeguy ◽  
María Victoria García
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variability ◽  
Population Size ◽  
Genetic Drift ◽  
Population Genetic ◽  
Allelic Richness ◽  
Theoretical Background ◽  
Computational Simulations ◽  
Expected Heterozygosity

Genetic diversity comprises the total of genetic variability contained in a population and it represents the fundamental component of changes since it determines the microevolutionary potential of populations. There are several measures for quantifying the genetic diversity, most notably measures based on heterozygosity and measures based on allelic richness, i.e. the expected number of alleles in populations of same size. These measures differ in their theoretical background and, in consequence, they differ in their ecological and evolutionary interpretations. Therefore, in the present chapter these measures of genetic diversity were jointly analyzed, highlighting the changes expected as consequence of gene flow and genetic drift. To develop this analysis, computational simulations of extreme scenarios combining changes in the levels of gene flow and population size were performed.

scholarly journals Landscape genomics of an obligate mutualism: discordant population structures between a leafcutter-ant and its fungal cultivars

2018 ◽  
Author(s):  
Chad C. Smith ◽  
Jesse N. Weber ◽  
Alexander S. Mikheyev ◽  
Flavio Roces ◽  
Martin Bollazzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Range Limit ◽  
Range Margin ◽  
Landscape Genomics ◽  
Temperature And Precipitation ◽  
Obligate Mutualism

AbstractTo explore landscape genomics at the range limit of an obligate mutualism, we used genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of hostsymbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. At local scales, genome-wide differentiation between ants associated with either of the two fungal types is greater than the differentiation associated with the abiotic factors temperature and precipitation, suggesting that specific ant-fungus genome-genome combinations may have been favored by selection. For the ant hosts, we found a broad cline of genetic structure across the range, and a reduction of genetic diversity along the axis of range expansion towards the range margin. In contrast, genetic structure was patchy in the cultivated fungi, with no consistent reduction of fungal genetic diversity at the range margins. This discordance in population-genetic structure between ant hosts and fungal symbionts is surprising because the ant farmers co-disperse with their vertically-transmitted fungal symbionts, but apparently the fungi disperse occasionally also through between-nest horizontal transfer or other unknown dispersal mechanisms. The discordance in populationgenetic structure indicates that genetic drift and gene flow differ in magnitude between each partner in this leafcutter mutualism. Together, these findings imply that variation in the strength of drift and gene flow experienced by each mutualistic partner affects adaptation to environmental stress at the range margin, and genome-genome interactions between host and symbiont influences adaptive genetic differentiation of the host during range evolution in this obligate mutualism.

scholarly journals Genetic diversity in maize dent landraces assessed by morphological and molecular markers

Genetika ◽  
2013 ◽  
Vol 45 (3) ◽  
pp. 811-824 ◽  
Author(s):  
Danijela Ristic ◽  
Vojka Babic ◽  
Violeta Andjelkovic ◽  
Jelena Vancetovic ◽  
Snezana Mladenovic-Drinic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Genetic Distance ◽  
Morphological Traits ◽  
Mean Value ◽  
Ecological Data ◽  
Phenotypic Analysis ◽  
High Level ◽  
Maize Research Institute

Maize Research Institute ?Zemun Polje? genebank maintains a collection of landraces grouped into 18 agro-ecological collected from ex-Yugoslavia territories. The application and comparison of different marker systems are important for the characterization and use of maize landraces in breeding program, as potential sources of desirable traits. In this study, 15 morphological traits, 7 RAPD primers and 10 SSR primer pairs were applied to i) to determine genetic distance between 21 maize dent landraces and ii) compare results obtained on morphological and molecular markers. Phenotypic analysis showed high level of heterogeneity between landraces. Higher level of genetic diversity was obtained with SSR than with RAPD. Genetic distance mean value for RAPD data was 0.35 i.e. for SSR 0.48. Based on the morphological traits and molecular markers, unweighted pairgroup method (UPGMA) analysis was applied for cluster analysis, using statistical NTSYSpc program package. Cluster analysis of morphological and molecular markers distances did not show the same population grouping. Better agreement with agro-ecological data was obtained with RAPD markers. Correlations between dissimilarity matrices for different types of markers were low. Data obtained in this work could be useful for further study of a larger number of landraces, and conservation of genetic resources and their genetic diversity.

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