Morphological and Chemical Diversity and Antioxidant Capacity of the Service Tree (Sorbus domestica L.) Fruits from Two Eco-Geographical Regions

Service tree, Sorbus domestica L., is a rare and neglected wild fruit tree species of southern and central Europe. Being distributed in different eco-geographical regions, with fragmented and low-density populations, S. domestica represents an interesting model case for investigating patterns of within- and between-population diversity at geographical and environmental scales. This study aimed to analyze the proximate composition, antioxidant activity, and morphometric fruit characteristics. We examined the diversity and population divergences of 49 S. domestica individuals originating from seven populations across continental and Mediterranean eco-geographical regions. In addition, tests of isolation by distance and environment were performed to detect the magnitude of divergence explained by geographic and environmental variables. Significant differences between the studied populations were found in almost all of the studied morphometric and chemical fruit characteristics. The studied service tree populations were characterized by high phenotypic variation despite the low number of trees per population. Model-based population structure analysis using morphometric and chemical fruit characteristics revealed three groups of service tree populations. We concluded that non-effective pollen and seed dispersal along with genetic drift and specific environmental factors resulted in a distinct phenotype with a specific chemical composition in the isolated island population. In addition, a pattern of isolation by the environment was revealed. We infer that morphological and chemical differences between the studied populations in the true service tree from different eco-geographical regions were mediated by adaptation to the specific environmental conditions.

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Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Forests ◽

10.3390/f10080681 ◽

2019 ◽

Vol 10 (8) ◽

pp. 681 ◽

Cited By ~ 1

Author(s):

Huiquan Zheng ◽

Dehuo Hu ◽

Ruping Wei ◽

Shu Yan ◽

Runhui Wang

Keyword(s):

Population Structure ◽

Genetic Structure ◽

High Throughput ◽

High Throughput Sequencing ◽

Breeding Population ◽

Population Diversity ◽

Chinese Fir ◽

High Density ◽

Population Structure Analysis ◽

Snp Panel

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

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Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models

Journal of Heredity ◽

10.1093/jhered/esz065 ◽

2019 ◽

Vol 110 (7) ◽

pp. 857-865 ◽

Cited By ~ 3

Author(s):

Mengmeng Lu ◽

Konstantin V Krutovsky ◽

Carol A Loopstra

Keyword(s):

Climate Change ◽

South Carolina ◽

Genetic Variation ◽

Loblolly Pine ◽

Greenhouse Gas Emission ◽

Isolation By Distance ◽

Adaptive Genetic Variation ◽

Climate Conditions ◽

Geographical Regions ◽

Bioclimatic Variables

Abstract Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.

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Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers

PLoS ONE ◽

10.1371/journal.pone.0253600 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253600

Author(s):

Charles U. Uba ◽

Happiness O. Oselebe ◽

Abush A. Tesfaye ◽

Wosene G. Abtew

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

West Africa ◽

East Africa ◽

Unknown Origin ◽

Snp Markers ◽

Bambara Groundnut ◽

Conservation Strategy ◽

Population Structure Analysis ◽

Geographical Regions

Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.

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The burrowing bettongs of Barrow Island: demographic and genetic insights into a threatened macropod

Australian Journal of Zoology ◽

10.1071/zo17049 ◽

2017 ◽

Vol 65 (4) ◽

pp. 257 ◽

Cited By ~ 1

Author(s):

Felicity Donaldson ◽

Roberta Bencini ◽

Keith Morris ◽

Roy Teale ◽

Celeste H. Wale ◽

...

Keyword(s):

Isolation By Distance ◽

Distance Effect ◽

Nuclear Microsatellites ◽

Island Population ◽

Effective Population ◽

Genetic Characteristics ◽

European Settlement ◽

Dry Conditions ◽

Geographic Separation ◽

Dispersal Distances

Islands provide the last refuge for many Australian species that have succumbed to range contractions since European settlement. These species have heightened vulnerability when developments are planned for the islands. The burrowing bettong (Bettongia lesueur), a threatened macropod, was once widespread across Australia but now occurs naturally only on Barrow Island and two other Western Australian offshore islands. Here, we document the demographic, social and genetic characteristics of the Barrow Island population, using nuclear microsatellites, mtDNA and demographic parameters from 286 individuals trapped around 29 warrens. The Barrow Island population utilises complex warren systems scattered across the landscape and exhibits continuous breeding, even during extensive dry conditions. Males (759 g) were significantly heavier than females (735 g), with the latter reaching sexual maturity at ~600 g. Warrens varied markedly in size and number of individuals, with 20% of females and 25% of males moving between nearby warrens. There were two deep mtDNA haplotype clades that coalesce around 298 000 years ago, indicating that this island population has maintained an effective population size that has permitted the retention of one marked feature of its preisolation genetic diversity. Dispersal and gene flow between warrens was severely constrained. Both mtDNA and 11 nuclear microsatellites showed a strong isolation by distance effect, with genetic differences between warrens increasing linearly with geographic separation. While this was marked in both sexes, it was stronger in females and consistent with shorter dispersal distances for females than for males. The trapping and genetic data are concordant, with between-warren sociality correlated with genetic similarity. Long-term conservation, management and translocation programs will benefit from cognisance of the strong fidelity to natal areas, as evidenced by both recapture data and genetic analyses.

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Multivariate Analysis of Seed Chemical Diversity among Jatropha curcas in Botswana

Agronomy ◽

10.3390/agronomy11081570 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1570

Author(s):

Shota Tadano ◽

Gwafila Chiyapo ◽

Yudai Ishimoto ◽

Takafumi Konaka ◽

Charles Mazereku ◽

...

Keyword(s):

Jatropha Curcas ◽

Seed Weight ◽

Phorbol Esters ◽

Chemical Properties ◽

Principal Component ◽

Chemical Diversity ◽

Chemical Compositions ◽

Severe Drought ◽

Bioenergy Feedstock ◽

Specific Chemical

Jatropha (Jatropha curcas L.) has been identified as a potential bioenergy feedstock in arid regions, but knowledge of the diversity of its chemical characteristics is limited. In this study, 61 Jatropha accessions growing in Botswana, where both severe drought and winter frosts frequently occur, were analyzed for their seed chemical properties. Histogram analyses and meta-analysis comparisons with seeds from other countries/continents showed that the median/mean dry seed weight, toxic compound phorbol esters, and C18:0 fatty acid levels in the Botswanan accessions were lower than those from other countries/continents. A clustered heat map analysis indicated five clades for the Botswanan accessions, and their physicochemical traits were also categorized into five groups. Many positive and negative correlations were observed among the chemical traits, including negative correlations between the C18:3 (linolenic acid) content and yield-related traits (lipid content and dry seed weight). Principal component analysis highlighted the existence of accessions with highly deviated seed chemical compositions, such as those enriched in C18:0/C18:1 and C16:0/C16:1/C18:3 fatty acids. Overall, the present study suggests considerable diversity in the seed chemical compositions of Botswanan Jatropha accessions. Various accessions could be useful as feedstock for specific industrial products, as well as for breeding materials for the fortification of specific chemical ingredients.

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Assessing Genetic Diversity of Canada Thistle (Cirsium arvense) in North America with Microsatellites

Weed Science ◽

10.1614/ws-d-09-00070.1 ◽

2010 ◽

Vol 58 (4) ◽

pp. 387-394 ◽

Cited By ~ 9

Author(s):

Tracey A. Bodo Slotta ◽

Michael E. Foley ◽

Shaioman Chao ◽

Ruth A. Hufbauer ◽

David P. Horvath

Keyword(s):

Genetic Diversity ◽

Invasive Species ◽

North America ◽

North American ◽

Isolation By Distance ◽

Genetic Distances ◽

Population Diversity ◽

Canada Thistle ◽

Long Distance ◽

Distance Analysis

Invasive species such as Canada thistle pose a significant threat to ecosystems. The risk of introducing invasive species has increased with human activities, and the effects of such events have economic and aesthetic impacts. Native to Europe, Canada thistle is now established throughout temperate North America. Although there is documentation of early occurrences to North America, little is known on how it has become established in diverse habitats or how it continues to spread. We examined genetic diversity within and among nearly 1,700 Canada thistle individuals from 85 North American locations with the use of seven microsatellite markers in order to address these questions. PAUP and STRUCTURE programs were used to assess genetic diversity and relationships within and between populations. Populations exhibited greater within-population diversity (> 60%) than expected for a reported clonally reproducing species. Total diversity of sampled locations in North America (0.183) was less than previously reported for European locations (0.715), but the greater mean difference between North American populations (0.264 relative to 0.246 from England) suggests strong founder effects or restriction of gene flow influencing individual populations. Furthermore, analyses identified numerous instances where individuals from geographically distant regions clustered together, indicating long-distance translocation of propogules. However, isolation by distance analysis showed significant correlation between location and population genetic distances (r = 0.1917, P = 0.006). Within populations, nearly 92% of individuals sampled harbored unique multilocus genotypes, strongly suggesting that sexual reproduction is common. Within populations, analysis of genetic structure indicated significant admixture of genotypes throughout the invasive range in North America. The recurrent distribution of seed throughout North America has led to a highly diverse gene pool and increased the adaptive success Canada thistle to a wide variety of habitats. Future technologies developed for control of Canada thistle should consider this diversity.

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Authentication, genetic fingerprinting and assessing relatedness of rice (Oryza Sativa) genotypes by SSR molecular markers

Caryologia ◽

10.36253/caryologia-550 ◽

2021 ◽

Vol 74 (1) ◽

pp. 13-22

Author(s):

Neda Sepahian ◽

Zahra Noourmohammadi ◽

Masoud Sheidai ◽

Hamid-Reza Zamanizadeh

Keyword(s):

Oryza Sativa ◽

Molecular Markers ◽

Genetic Relatedness ◽

Isolation By Distance ◽

Genetic Difference ◽

Rice Cultivars ◽

Geographical Regions ◽

Ssr Loci ◽

Rice Samples ◽

Rice Genotypes

Rice (Oryza sativa L.), is a staple food and cash crop in many countries and studies on geneticstructure and differentiation patterns of rice land races along with the cultivated rice, provide important data for future rice breeding. Therefore, the aims of present investigation were 1-To study the genetic diversity present withinIranian rice genotypes, 2-To study genetic relatedness of these rice genotypes, and 3-To providebarcoding of the rice genotypes based on SSR molecular markers and produce data for rice varieties authentication. In total, 201 rice samples originated from 10 geographical regions of Iran were studied in this project. All rice samples underwent fragment analysis in every 64 SSR loci and different clustering and ordination methods performed. In general four major clusters were formed. Both landraces as well as rice cultivars were distributed in different clusters due to their genetic difference. STRUCTURE analysis of the studied genotypes followed by Evanno test produced the optimal number of genetic groups K = 2. The mean Nm = 13.6, for the studied genotypes indicates that a high degree of gene flow/ancestral common alleles are present in the rice genotypes studied. Mantel test indicated a significant positive association between genetic distance and geographic distance of the rice genotype studied and presence of an overall isolation by distance (IBD) model of differentiation across the geographical regions of Iran. Overall, the significant genetic difference observed between rice landraces and rice cultivars ofthe country may be used in future hybridization and breeding of rice in the country. The landracerice genotypes may contain useful genes to be transferred to the popular rice cultivars. Moreover, SSR loci that can differentiate rice genotypes are identified and can be used in rice cultivars authentication.

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High-throughput genotype-based population structure analysis of selected buffalo breeds

Translational Animal Science ◽

10.1093/tas/txab033 ◽

2021 ◽

Vol 5 (2) ◽

Author(s):

Prakash B Thakor ◽

Ankit T Hinsu ◽

Dhruv R Bhatia ◽

Tejas M Shah ◽

Nilesh Nayee ◽

...

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Structure Analysis ◽

Principal Component ◽

Snp Markers ◽

Sequence Information ◽

Population Structure Analysis ◽

Geographical Regions ◽

Indian River ◽

Single Cluster

Abstract India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.

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Origins and geographic diversification of African rice (Oryza glaberrima)

10.1101/398693 ◽

2018 ◽

Author(s):

Margaretha A. Veltman ◽

Jonathan M. Flowers ◽

Tinde R. van Andel ◽

M. Eric Schranz

Keyword(s):

Isolation By Distance ◽

Atlantic Coast ◽

Plant Domestication ◽

Oryza Glaberrima ◽

Geographic Diversification ◽

African Rice ◽

Asian Rice ◽

Genome Wide ◽

Population Structure Analysis ◽

Genetic Clusters

AbstractRice is a staple food for the majority of our world’s growing population. Whereas Asian rice (Oryza sativaL.) has been extensively studied, the exact origins of African rice (Oryza glaberrimaSteud.) are still contested. Previous studies have supported either a centric or a non-centric origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice – either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest - suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.

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Population structure and geographically structured reproductive strategies of the haplodiplontic seaweed Dictyota dichotoma

10.1101/595587 ◽

2019 ◽

Cited By ~ 1

Author(s):

Frédérique Steen ◽

Verlaque Marc ◽

Sofie D’hondt ◽

Christophe Vieira ◽

Olivier De Clerck

Keyword(s):

South Africa ◽

Genetic Structure ◽

Sexual Reproduction ◽

Canary Islands ◽

Isolation By Distance ◽

Glacial Refugia ◽

Population Diversity ◽

Mediterranean Populations ◽

Dictyota Dichotoma ◽

Southern Norway

AbstractBoth mating system variation and the propensity of many seaweeds to reproduce both sexually and asexually, leave a strong imprint in the genetic structure of species. In this respect, we study the population genetic structure of Dictyota dichotoma, a common haplodiplont brown subtidal seaweed. This benthic species is widespread in the NE-Atlantic, from the Canary Islands and Mediterranean Sea to southern Norway, but lately populations have been reported from Argentina and South Africa. Phenology and reproduction of D. dichotoma was monitored year-round in four populations to investigate how the species has adapted to the steep thermal gradient in southern and northern ranges of its distribution. Thirteen microsatellites are developed in order to assess patterns of population diversity and structure across the biogeographic range, as shaped by past and present processes. Last, we assess the genetic structure of South African and South American populations and their relationship to the northern hemisphere populations.Throughout its range, D. dichotoma shows a varying reproductive effort, with sexual reproduction being more abundant in the northern range. In contrast, the Mediterranean populations show a clear sporophyte dominance, suggesting that sexual reproduction is not the prime mode of reproduction, and indicating that the species potentially resorts to other modes of propagation as for instance fragmentation or apospory.Genetic diversity is highest in the southern population decreasing gradually northward, indicative for a recolonization pattern after the demise of the last glacial maximum where these areas served as glacial refugia. European mainland populations show an isolation by distance pattern, while the population in the Canary Islands has its own genetic identity, being significantly diverged from the mainland population. Populations in South Africa and Argentina are seemingly introduced from mainland Europe, but no conclusion can be made on the exact timing of these introductions.

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