Analysis of Diversity And Identification of SSR, SCoT, And ITAP Informative Amplicons For Grain Fe And Zn Content In Wheat Genotypes

2021 ◽  
Author(s):  
Hedieh Badakhshan ◽  
Rozhin Nosratifar
Keyword(s):  
Genetic Diversity ◽  
Start Codon ◽  
High Genetic Diversity ◽  
Wheat Genotypes ◽  
Zn Content ◽  
Content Identification ◽  
High Heritability ◽  
Genotype Interaction ◽  
Simple Sequence ◽  
Selection Of

Abstract Biofortification provides a promising method of solving microelement malnutrition in developing countries. For this purpose, a study was conducted to understand the grain Fe and Zn content variation in seventy prevalent Iranian wheat genotypes across three consecutive years, to assess genetic diversity, and to identify informative amplicons for high grain Fe and Zn content using three simple sequence repeat (SSR), start codon targeted (SCoT) polymorphism, and intron targeted amplified polymorphism (ITAP) markers. Grain Fe and Zn content was highly variable each year with high heritability. Despite the highly significant effect of year-genotype interaction, some stable genotypes were ranked highly all the three years for grain Fe and Zn content. The grain Fe and Zn contents were positively correlated in the second and third years. High genetic diversity was detected among the wheat genotypes using three different marker systems. A number of informative SSR, SCoT, and ITAP amplicons for high grain Fe and Zn were identified overall or in individual years. A few informative amplicons were common and stable for grain Fe and Zn content in the different years. The SSR alleles located on 3A, 4A, 4B, and 6B chromosomes were positively correlated with high Fe and Zn content, indicating that co-location of genes affected Fe and Zn content. Identification of informative alleles and amplicons for high grain Fe and Zn content could contribute to the development of sequence-based markers and improve the selection of genotypes with high micronutrient content.

scholarly journals Genetic Dissimilarity in Conyza sumatrensis Revealed by Simple Sequence Repeat (SSR) Markers

2020 ◽  
Vol 38 ◽  
Author(s):  
T. SCHNEIDER ◽  
M.A. RIZZARDI ◽  
S.P. BRAMMER ◽  
S.M. SCHEFFER-BASSO ◽  
A.L. NUNES
Keyword(s):  
Genetic Diversity ◽  
Management Strategies ◽  
Rapid Evolution ◽  
Jaccard Coefficient ◽  
Mechanisms Of Resistance ◽  
High Genetic Diversity ◽  
Resistance To Herbicides ◽  
Geographic Regions ◽  
Genetic Dissimilarity ◽  
Simple Sequence

ABSTRACT: In view of the rapid evolution of Conyza sumatrensis populations resistant to glyphosate, it is necessary to understand the genetic diversity aimed to improve strategies for managing this weed. We investigated the genetic dissimilarity among 15 biotypes of C. sumatrensis from different geographic regions using microsatellite loci. The biotypes, were cultivated in a greenhouse to obtain vegetal material for DNA extraction. Nineteen microsatellite markers (SSR), were developed for C. sumatrensis biotypes. The genetic dissimilarity was estimated by the Jaccard coefficient (JC) and the biotypes grouped by the UPGMA method. The results demonstrated a high dissimilarity (JC = 7.14 to 82.62) of the analyzed material, with the biotypes forming five groups, being one group formed just by the susceptible biotype and in the others grouped by biotypes from distinct locations in the same group The high genetic diversity of C. sumatrensis indicates that the biotypes may show different responses to different management strategies, and that the mechanisms of resistance to herbicides and characteristics of evolution of populations due to adaptability may be some of the factors involved in the genetic variability of the species.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

scholarly journals Analysis of genetic diversity and population structure in Asparagus species using SSR markers

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Manish Kapoor ◽  
Pooja Mawal ◽  
Vikas Sharma ◽  
Raghbir Chand Gupta
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Mean Value ◽  
Discrete Groups ◽  
Base Pairs ◽  
High Genetic Diversity ◽  
Pharmaceutical Industries ◽  
Improvement Programs ◽  
Northwest India ◽  
Simple Sequence

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

scholarly journals Heritability of Productivity Elements of Chickpeas and its Importance for Practical Breeding

2021 ◽  
Author(s):  
Svetlana Kuzmina ◽  
Nina Kazydub ◽  
Vladimir Panchenko
Keyword(s):  
Genetic Diversity ◽  
Quantitative Traits ◽  
Genetic Factors ◽  
Plant Genetic Resources ◽  
Practical Interest ◽  
Forest Steppe ◽  
High Genetic Diversity ◽  
Federal Research ◽  
Growing Conditions ◽  
Selection Of

This study examined the genetics of the variability in quantitative traits and showed the possibility of selecting hybrids with a new, more favorable combination of traits, which is of practical interest for breeding. The main goal of our research was to determine the coefficients of heritability by the mass of seeds and the number of beans per plant in hybrid combinations of chickpeas, which allowed establishing the potential of parental varieties in the transfer of valuable genes responsible for plant productivity to offspring and expanding the spectrum of plant genetic diversity. The experiments were conducted in the fields of the educational and experimental farm of the Omsk State Agrarian University in the southern forest-steppe of the Omsk region in 2016-2018. The research included 6 chickpea samples with a complex of valuable traits from the Federal Research Center of the All-Russian Institute of Plant Genetic Resources named after N.I. Vavilov (VIR, St. Petersburg) and 8 hybrid combinations obtained on their basis. It was found that the mass of seeds per plant was characterized by low heritability (H2 = 22.8%) and the number of beans per plant was high (H2 = 54.0%). The variability of the mass of seeds per plant was largely paratypical and was influenced by environmental conditions; the variability in the number of beans per plant was due to genetic factors and indicated a high genetic diversity in the studied splitting chickpea populations. Selection based on the number of beans per plant was highly effective even in early generations of the hybrids. Selection by the mass of seeds from the plant was ineffective; it should be carried out in later hybrid generations under favorable growing conditions. The selection of valuable genotypes was most successful in hybrid chickpea populations by seed weight per plant: C-35 x ILC-2394, C-80 x ILC-2394, C-27 x ILC-2394, and by the number of beans per plant: C-27 x ILC-2394, C-27 x ILC-2402 Keywords: chickpeas, heritability, selection, genetics, productivity

scholarly journals Diversity and efficiency of bradyrhizobium strains isolated from soil samples collected from around sesbania virgata roots using cowpea as trap species

2010 ◽  
Vol 34 (4) ◽  
pp. 1113-1123 ◽  
Author(s):  
Ligiane Aparecida Florentino ◽  
Pedro Martins de Sousa ◽  
Jacqueline Savana Silva ◽  
Karina Barroso Silva ◽  
Fatima Maria de Souza Moreira
Keyword(s):  
Genetic Diversity ◽  
High Genetic Diversity ◽  
N Accumulation ◽  
Dna Elements ◽  
Sesbania Virgata ◽  
Salinity Levels ◽  
Band Profile ◽  
Repetitive Dna Elements ◽  
Unique Band ◽  
Selection Of

The genetic diversity of ten Bradyrhizobium strains was evaluated for tolerance to high temperatures, to different salinity levels and for the efficiency of symbiosis with cowpea plants (Vigna unguiculata (L.) Walp.). Eight of these strains were isolated from nodules that appeared on cowpea after inoculation with suspensions of soil sampled from around the root system of Sesbania virgata (wand riverhemp) in ecosystems of South Minas Gerais. The other two strains used in our analyses as references, were from the Amazon and are currently recommended as cowpea inoculants. Genetic diversity was analyzed by amplifying repetitive DNA elements with the BOX primer, revealing high genetic diversity with each strain presenting a unique band profile. Leonard jar assays showed that the strains UFLA 03-30 and UFLA 03-38 had the highest N2-fixing potentials in symbiosis with cowpea. These strains had more shoot and nodule dry matter, more shoot N accumulation, and a higher relative efficiency than the strains recommended as inoculants. All strains grew in media of pH levels ranging from 4.0 to 9.0. The strains with the highest N2-fixing efficiencies in symbiosis with cowpea were also tolerant to the greatest number of antibiotics. However, these strains also had the lowest tolerance to high salt concentrations. All strains, with the exceptions of UFLA 03-84 and UFLA 03-37, tolerated temperatures of up to 40 ºC. The genetic and phenotypic characteristics of the eight strains isolated from soils of the same region were highly variable, as well as their symbiotic efficiencies, despite their common origin. This variability highlights the importance of including these tests in the selection of cowpea inoculant strains.

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

Microbiology ◽  
2000 ◽  
Vol 81 (1) ◽  
pp. 243-255 ◽  
Author(s):  
M. Bousalem ◽  
E. J. P. Douzery ◽  
D. Fargette
Keyword(s):  
Genetic Diversity ◽  
Mosaic Virus ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
High Genetic Diversity ◽  
Single Clade ◽  
Cultivated Species ◽  
Selection Of

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis–Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3′-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis–D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

Assessment of genomic diversity among wheat genotypes as determined by simple sequence repeats

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 646-651 ◽  
Author(s):  
M Ahmad
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Simple Sequence Repeats ◽  
Common Ancestor ◽  
Genetic Relationships ◽  
Genomic Diversity ◽  
Pedigree Information ◽  
Wheat Genotypes ◽  
Wide Range ◽  
Simple Sequence

Simple sequence repeats (SSRs) have been used to examine the genomic diversity of wheat (Triticum aestivum L.) germplasm. Thirteen wheat genotypes of diverse origin were analyzed with 43 selected SSRs to provide uniform and maximum genome coverage. A total of 156 allelic variants were detected at 43 SSR loci, ranging from two to eight per locus with an average of 3.6. The polymorphic information content (PIC) values of the loci ranged from 0.10 (Xgwm264) to 0.89 (Xgwm471 and Xgwm577). Genetic similarities calculated from SSR data ranged from 30.1 ('Era' and 'Klasic') to 90.1 ('Neepawa' and 'Thatcher') between genotypes. UPGMA analysis based on genetic distance estimates produced three loose groupings that were generally consistent with available pedigree information. Cultivars 'Neepawa' and 'Thatcher' are closely related. Their genetic relationship was confirmed by the facts that they share a common ancestor and are clustered together. There were two different 'Era' genotypes, one used in the 'Otane' pedigree and one used in this study. None of the other genotypes had a close common ancestor indicating any close genetic relationships. Principal coordinate analysis also confirmed this pattern of genetic diversity. A wide range of genomic diversity was observed among all the genotypes, proving them to be prime candidates for selective breeding for specific traits and broadening the genetic base.Key words: simple sequence repeats, genetic diversity, Triticum aestivum, genetic similarity estimates, cluster analysis.

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