scholarly journals Phenotypic, Genetic, and Epigenetic Variation among Diverse Sweet Cherry Gene Pools

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 680
Author(s):  
Evangelia V. Avramidou ◽  
Theodoros Moysiadis ◽  
Ioannis Ganopoulos ◽  
Michail Michailidis ◽  
Christos Kissoudis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sweet Cherry ◽  
Allelic Variation ◽  
Sugar Content ◽  
Fruit Size ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Gene Pools ◽  
Epigenetic Diversity ◽  
Fruit Size And Shape

Sweet cherry germplasm contains a high variety of phenotypes which are associated with fruit size and shape as well as sugar content, etc. High phenotypic variation can be a result of genetic or epigenetic diversity that may interact through time. Recent studies have provided evidence that besides allelic variation, epiallelic variation can establish new heritable phenotypes. Herein we conducted a genetic and an epigenetic study (using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) markers, respectively), accompanied by phenotypic traits correlation analysis in sweet cherry gene pools. The mean genetic diversity was greater than the epigenetic diversity (hgen = 0.193; hepi = 0.185), while no significant relationship was found between genetic and epigenetic distance according to a Mantel test. Furthermore, according to correlation analyses our results provided evidence that epigenetic diversity in predefined populations of sweet cherry had a stronger impact on phenotypic traits than their rich genetic diversity.

scholarly journals Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

2010 ◽  
Vol 90 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Z I Talukder ◽  
E Anderson ◽  
P N Miklas ◽  
M W Blair ◽  
J Osorno ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Allelic Variation ◽  
Gene Pools ◽  
Gene Sequences ◽  
Mineral Contents ◽  
Discriminatory Ability ◽  
Fe Content ◽  
Mapping Populations ◽  
Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

scholarly journals Analysis of pomological traits in new promising sweet cherry genotypes

Genetika ◽  
2013 ◽  
Vol 45 (3) ◽  
pp. 873-880 ◽  
Author(s):  
Milica Fotiric-Aksic ◽  
Tihomir Nikolic
Keyword(s):  
Sweet Cherry ◽  
Sugar Content ◽  
Fruit Size ◽  
Fruit Weight ◽  
Solid Content ◽  
Soluble Solid Content ◽  
Fresh Market ◽  
Total Sugar Content ◽  
Ripening Time ◽  
Chemical Content

Sweet cherry breeding programs are interested in developing new cultivars that are very early or very late in ripening, high yielding, with excellent fruit size and quality. The aim of this study was to evaluate new, promising, sweet cherry genotypes (G-1 and G-2) for ripening time, fruit morphology and fruit chemical content, and compare it with the standard sweet cherry cultivars (Bigarreau Jaboulay, B. H. Burlat, Seneca, Hedelfiger Riesenkirsche, Germersdorfer Grosse Kirsche, Emperor Francis and Bing). Experiment was done during four consecutive years (2006-2009) in Grocka, near Belgrade. The earliest fruit ripening was recorded in G-2 (22nd April) while the latest in `Bing` (2nd June). Fruit weight varied from 5.83 g (G-2) up to 8.93 g (G-1). Soluble solid content and total sugar content were the lowest in genotype G-2 (10.48%; 8.45%, respectively) but the highest in Emperor Francis (18.28%; 15.98%, respectively). No matter the fact that some standard cultivars showed better results for some traits, genotypes G-1 and G-2 are considered very promising. So, genotype G-1 could be intended for table consumption since it ripens 2-3 days after cv. B. H. Burlat, but have much higher fruit weight. Also, genotype G-2, the earliest in this trial, showed satisfactory fruit weight for this ripening time, which makes it very interesting for fresh market production.

The effect of Candidatus Phytoplasma pruni infection on sweet cherry fruit

2021 ◽  
Author(s):  
Alice Ann Wright ◽  
Madalyn K Shires ◽  
Christopher Beaver ◽  
Garrett Bishop ◽  
S. Tianna Dupont ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Early Stage ◽  
Sugar Content ◽  
Fruit Size ◽  
Disease Symptoms ◽  
Small Fruit ◽  
Eastern Washington ◽  
Sweet Cherry Cultivars ◽  
Metabolite Content

In sweet cherry (Prunus avium L.), infection by Candidatus Phytoplasma pruni results in small fruit with poor color and taste, rendering the fruit unmarketable. Yet, the disease pathology is poorly understood, particularly at the cultivar level. Therefore, in this study we examined the physiological effects of Ca. P. pruni infection across a range of cultivars and locations within eastern Washington. We found that infection could be separated into early and established stages based on pathogen titer, that correlated with disease severity, including fruit size, color, and sugar and metabolite content. Furthermore, we also observed that the effects of early-stage infections were largely indistinguishable from healthy, uninfected plants. Cultivar and location-specific disease outcomes were observed with regards to size, color, sugar content, and citric acid content. This study presents the first in-depth assessment of X-disease symptoms and biochemical content of fruit from commercially grown sweet cherry cultivars known to be infected with Ca. P. pruni.

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

Agronomy ◽  
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.

scholarly journals Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China by 3 Types of Genetic Markers

2021 ◽  
Author(s):  
Yu Zhang ◽  
Yewen Wang ◽  
Peijiang Li ◽  
Yuexing Wang ◽  
Shimao Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Markers ◽  
Ssr Markers ◽  
Diversity Index ◽  
Indica Rice ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Phenotypic Analysis

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

scholarly journals Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China By 3 Types of Genetic Markers

2022 ◽  
Author(s):  
Yu Zhang ◽  
Qiaoqiao He ◽  
Xixi Zhou ◽  
Yewen Wang ◽  
Peijiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Markers ◽  
Ssr Markers ◽  
Diversity Index ◽  
Indica Rice ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Phenotypic Analysis

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

scholarly journals Intra-population genetic diversity of cultivated carrot (Daucus carota L.) assessed by analysis of microsatellite markers.

1970 ◽  
Vol 60 (4) ◽  
Author(s):  
Anna Maksylewicz ◽  
Rafal Baranski
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Daucus Carota ◽  
Allelic Variation ◽  
Population Variation ◽  
F1 Hybrids ◽  
Gene Pools ◽  
Homozygous State ◽  
Daucus Carota L ◽  
Genomic Ssr

Intra-population variation of 18 cultivated carrot (Daucus carota L. ssp. sativus) populations of diverse origins was evaluated using codominant microsatellite (SSR) markers. Using 27 genomic and EST-derived SSR markers, 253 alleles were identified with a mean 9.4 alleles per marker. Most of the alleles (60.5%) were rare i.e., with the frequency ≤ 0.05 while only 3.95% of alleles occurred with frequency > 0.6. EST-derived SSR markers were less polymorphic than genomic SSR markers. Differences in allele occurrence allowed 16 out of 18 populations to be assigned to either the Western or Asian carrot gene pools with high probability. Populations could be also discriminated due to the presence of private alleles (25.3% of all alleles). Most populations had excess of alleles in the homozygous state indicating their inbreeding, although heterozygous loci were common in F1 hybrids. Genetic diversity was due to allelic variation among plants within populations (62% of total variation) and between populations (38%). Accessions originating from continental Asia and Europe had more allelic variants and higher diversity than those from Japan and USA. Also, allelic richness and variability in landraces was higher than in F1 hybrids and open-pollinated cultivars.

scholarly journals Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1054
Author(s):  
Charles Nelimor ◽  
Baffour Badu-Apraku ◽  
Ana Luísa Garcia-Oliveira ◽  
Antonia Tetteh ◽  
Agre Paterne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Pool ◽  
Allelic Variation ◽  
Sub Saharan Africa ◽  
Genetic Enhancement ◽  
Gene Pools ◽  
International Institute ◽  
Improvement Program ◽  
Wide Range

Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

scholarly journals GENETIC DIVERSITY AND DIFFERENTIATION OF Pseudotsuga menziesii (Mirb.) Franco POPULATIONS IN MÉXICO

2011 ◽  
Vol 34 (4) ◽  
pp. 233 ◽  
Author(s):  
Jorge Cruz-Nicolás ◽  
J. Jesús Vargas-Hernández ◽  
Porfirio Ramírez-Vallejo ◽  
Javier López-Upton
Keyword(s):  
Genetic Diversity ◽  
Pseudotsuga Menziesii ◽  
In Situ Conservation ◽  
Mantel Test ◽  
Douglas Fir ◽  
Population Divergence ◽  
Central Mexico ◽  
Gene Pools ◽  
Polymorphic Loci ◽  
Northwestern Mexico

Mexican populations of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] constitute valuable gene pools for conservation and breeding programs of this species. Genetic diversity and population divergence were estimated using 18 isozyme loci and samples from 11 natural Douglas-fir populations in México. Genetic diversity was high at the species level (83.3 % polymorphic loci and 2.9 alleles per locus), but low at the population level (28.3 % polymorphic loci and 1.52 alleles per locus), particularly for populations from central México. A high level of population differentiation was found (Fst = 0.298), indicating that each population shares only a small fraction of the genetic diversity within the species and that genetic drift might have an important role in shaping the structure of genetic diversity in these populations. Genetic distances among populations in the Sierra Madre Oriental were positively correlated with geographic distances (r = 0.849), but the association was not significant according to the Mantel test. Populations from northeastern México separated from all others, whereas population Mohinora from northwestern México, joined those from central México. These results emphasize the priority for in situ conservation of Douglas-fir populations in central México.

scholarly journals Genotypic and Phenotypic Variation among Pepper Accessions Resistant to Phytophthora capsici

HortScience ◽  
2011 ◽  
Vol 46 (9) ◽  
pp. 1235-1240 ◽  
Author(s):  
Cecilia McGregor ◽  
Vickie Waters ◽  
Savithri Nambeesan ◽  
Dan MacLean ◽  
Byron L. Candole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phytophthora Capsici ◽  
Fruit Size ◽  
Phytophthora Blight ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Phytophthora Root Rot ◽  
Ssr Loci ◽  
Fruit Size And Shape ◽  
Pericarp Thickness

Developing high levels of resistance to Phytophthora blight (Phytophthora capsici Leonian) of pepper (Capsicum annuum L.) is a goal of many pepper breeding programs. Genetic diversity and plant characteristics were evaluated on 21 pepper accessions previously identified as having high levels of Phytophthora root rot resistance. Accessions were evaluated for plant height, fruit size and shape, pericarp thickness, and pungency. Accessions varied widely from very unadapted material to those with more obvious breeding potential. Genetic diversity among the accessions was estimated using 22 simple sequence repeat (SSR) loci. Phytophthora capsici resistant accessions were identified that were not closely related to previously described sources of resistance. This information will allow breeders and researchers to further identify and incorporate novel sources of resistance to P. capsici into breeding programs. Accessions PI 201237 and PI 640532 appear to have the most potential for introgressing P. capcisi resistance into bell pepper.

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