Latitudinal structured populations of the Mexican wild squash Cucurbita argyrosperma subsp. sororia revealed by microsatellite markers

Crop wild relatives represent an important agronomic resource for crop improvement and biodiversity conservation. The wild squash Cucurbita argyrosperma subsp. sororia. (Cucurbitaceae) has been considered the wild ancestor of cultivated forms of C. argyrosperma. In order to characterise the geographic patterns of genetic variation in this wild cucurbit and to identify priority areas for conservation, we analysed the genetic diversity and structure of natural populations along the Mexican Pacific coast. By using 14 polymorphic microsatellites, we genotyped 378 individuals sampled from 61 locations. Standard population genetics analyses and group testing were conducted on the genotypes with the aid of principal coordinate analysis and Bayesian analysis. Overall, we found an average of 12.3 alleles per locus and an expected heterozygosity of 0.756. We found greater genetic diversity in southern populations. The fixation index was 0.113, suggesting a mixed mating system. The Mantel test revealed a minor distance effect on genetic differentiation between individuals (r = 0.321). Finally, we found three main groups of populations arranged in a mostly latitudinal pattern, from Sinaloa (north-west) to Oaxaca–Guerrero (south-east). The greater genetic diversity and heterogeneity among southern populations (Guerrero–Oaxaca), suggests that this region is an important centre of diversity of this wild squash with important implications for conservation.

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

AoB Plants ◽

10.1093/aobpla/plaa038 ◽

2020 ◽

Vol 12 (4) ◽

Author(s):

Elizabeth A Sinclair ◽

Jane M Edgeloe ◽

Janet M Anthony ◽

John Statton ◽

Martin F Breed ◽

...

Keyword(s):

Genetic Diversity ◽

Mating System ◽

Western Australia ◽

Reproductive Effort ◽

Genetic Data ◽

Fruit Production ◽

Mixed Mating ◽

Mixed Mating System ◽

Shark Bay ◽

Range Edge

Abstract Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.

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Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽

10.3390/d11090154 ◽

2019 ◽

Vol 11 (9) ◽

pp. 154 ◽

Cited By ~ 2

Author(s):

Lucia Lioi ◽

Diana L. Zuluaga ◽

Stefano Pavan ◽

Gabriella Sonnante

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Genotyping By Sequencing ◽

Fixation Index ◽

Most Probable Number ◽

Probable Number ◽

Individual Snps ◽

Starting Point ◽

Genetic Diversity And Structure ◽

The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

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Genetic diversity and structure of Jatropha curcas L. in its centre of origin

Plant Genetic Resources ◽

10.1017/s1479262114000550 ◽

2014 ◽

Vol 13 (1) ◽

pp. 9-17 ◽

Cited By ~ 17

Author(s):

M. Salvador-Figueroa ◽

J. Magaña-Ramos ◽

J. A. Vázquez-Ovando ◽

M. L. Adriano-Anaya ◽

I. Ovando-Medina

Keyword(s):

Genetic Diversity ◽

Jatropha Curcas ◽

Isolation By Distance ◽

Random Mating ◽

Mantel Test ◽

Reproductive Pattern ◽

Chain Reactions ◽

Polymerase Chain Reactions ◽

Centre Of Origin ◽

Genetic Diversity And Structure

To investigate the genetic diversity and structure of Jatropha curcas L. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites of J. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite was Jcps20 (nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular variance revealed that the populations were structured and moderately differentiated (FST 0.087) and that this differentiation was not due to isolation by distance, as the Mantel test was not significant (P= 0.137), but rather due to allopatry. Bayesian analysis revealed that the accessions belonged to only four genetic groups and confirmed the differentiation between the regions. Because some loci were in Hardy–Weinberg disequilibrium, it is proposed that differentiation is due to the clonal reproduction of J. curcas practised by farmers in Chiapas, along with the anthropogenic dispersion at regional levels. The results of this study reveal that J. curcas in Chiapas has genetic diversity that is greater than that reported in other parts of the world, which represents a potential germplasm pool for the selection of genotypes.

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Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽

10.1371/journal.pone.0255418 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255418

Author(s):

Siou Ting Gan ◽

Chin Jit Teo ◽

Shobana Manirasa ◽

Wei Chee Wong ◽

Choo Kien Wong

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Oil Palm ◽

Core Collection ◽

Elaeis Guineensis ◽

Germplasm Conservation ◽

Ex Situ ◽

Fixation Index ◽

Core Set ◽

Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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Limited impact of fragmentation and disturbance on the mating system of tuart (Eucalyptus gomphocephala, Myrtaceae): implications for seed-source quality in ecological restoration

Australian Journal of Botany ◽

10.1071/bt13032 ◽

2013 ◽

Vol 61 (2) ◽

pp. 148 ◽

Cited By ~ 14

Author(s):

Donna Bradbury ◽

Siegfried L. Krauss

Keyword(s):

Genetic Diversity ◽

Mating System ◽

Ecological Restoration ◽

Habitat Disturbance ◽

Mixed Mating ◽

Mixed Mating System ◽

Fragmented Population ◽

Eucalyptus Gomphocephala ◽

Multiple Trees ◽

Seed Sourcing

Variation in patterns of mating within and among plant populations can be impacted by habitat disturbance and have significant implications for offspring fitness. An understanding of this variation will inform predictions of seed genetic quality, benefiting ecological restoration through better seed-sourcing guidelines. We assessed mating system variation in six populations of tuart (Eucalyptus gomphocephala DC.), an iconic tree of significance to ecological restoration in Western Australia. A mixed mating system was observed with predominant outcrossing (tm = 0.76 ± 0.05) and low biparental inbreeding (tm–ts = 0.03 ± 0.02). We detected some evidence of increased inbreeding in a naturally fragmented population (tm–ts = 0.10 ± 0.04) and in a disturbed urban remnant (tm = 0.52 ± 0.12), including a family with complete selfing. However, most variation in outcrossing rate occurred among individuals within populations (82%), rather than among populations (2.6%) or among groups of populations defined by fragmentation or disturbance (15.4%). Genetic diversity was not consistently lower in offspring from fragmented, smaller and/or disturbed populations. These data reinforce the importance of sourcing seeds from multiple trees for ecological restoration, and emphasise that tuart’s mating system and the genetic diversity of offspring is robust to some habitat disturbance and/or fragmentation.

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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Scientific Reports ◽

10.1038/s41598-021-93867-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Md Mahmudul Hasan Khan ◽

Mohd Y. Rafii ◽

Shairul Izan Ramlee ◽

Mashitah Jusoh ◽

Md Al Mamun ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Sustainability ◽

Crop Improvement ◽

Principal Component ◽

Issr Markers ◽

Bambara Groundnut ◽

Fixation Index ◽

Vigna Subterranea ◽

Information Index ◽

Issr Primers

AbstractAs a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.

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