Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 698-709 ◽  
Author(s):  
L. Jungmann ◽  
B. B.Z. Vigna ◽  
K. R. Boldrini ◽  
A. C.B. Sousa ◽  
C. B. do Valle ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Morphological Traits ◽  
Agricultural Research ◽  
Warm Season ◽  
Germplasm Collection ◽  
Eastern Africa ◽  
Pasture Grass ◽  
Ploidy Levels ◽  
Brachiaria Humidicola ◽  
Population Structure Analysis

Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.

scholarly journals Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1451
Author(s):  
Kodjo M. Gbedevi ◽  
Ousmane Boukar ◽  
Haruki Ishikawa ◽  
Ayodeji Abe ◽  
Patrick O. Ongom ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Improvement ◽  
Agricultural Research ◽  
Polymorphic Information Content ◽  
Germplasm Collection ◽  
Mean Value ◽  
Economic Life ◽  
Dart Markers ◽  
Crop Genetic Diversity

Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

scholarly journals A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions

2021 ◽  
Vol 12 ◽  
Author(s):  
Aamir Saleem ◽  
Hilde Muylle ◽  
Jonas Aper ◽  
Tom Ruttink ◽  
Jiao Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oil Content ◽  
Selective Sweep ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Selective Sweeps ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Signatures Of Selection

Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.

scholarly journals A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of Panama

2020 ◽  
Author(s):  
Kristin Saltonstall ◽  
Graham D. Bonnett ◽  
Karen S. Aitken
Keyword(s):  
Genetic Diversity ◽  
Perennial Grass ◽  
Germplasm Collection ◽  
High Survival ◽  
Saccharum Spontaneum ◽  
Local Conditions ◽  
Ploidy Levels ◽  
Germplasm Collections ◽  
High Ploidy ◽  
Sugarcane Germplasm

AbstractPolyploidy may contribute to invasive ability as it can lead to high survival and fitness during establishment and enhance the processes of adaptation to novel environments by increasing genetic diversity in invading propagules. Many grasses are polyploid and many are aggressive invaders, making them persistent problems in disturbed environments worldwide. Today, vast areas of central Panama are dominated by Saccharum spontaneum, a perennial grass that originates from Asia. While widely regarded as invasive, it is not known when or how it arrived in Panama. We explore hypotheses regarding the timing and origins of this invasion through literature review and comparisons of genetic diversity in Panama with accessions from available sugarcane germplasm collections, highlighting historical accessions that were likely brought to Panama in 1939 as part of a USDA sugarcane germplasm collection. Samples were haplotyped at two chloroplast loci and genotyped using eight microsatellite markers. All sequenced individuals from Panama belong to a single chloroplast lineage which is common worldwide and was common in the Historic germplasm collection. Although genotypic diversity was extremely high in all samples due to high ploidy, samples from Panama had reduced diversity and clustered with several accessions in the Historic collection which had the same haplotype and high ploidy levels. Our results suggest that accidental escape from the historical sugarcane germplasm collection is the likely origin of the S. spontaneum invasion in Panama. Intraspecific hybridization among several historical accessions and pre-adaptation to local conditions may have facilitated its rapid spread and persistence. We discuss the implications of our findings for biosecurity of germplasm collections.

scholarly journals Genetic Characterization of Rainfed Durum Wheat Genotypes Based On Functional Markers Associated With Grain Quality Proteins

2021 ◽  
Author(s):  
Zahra Moradi Kheibary ◽  
Reza Azizinezhad ◽  
Ali Mehras Mehrabi ◽  
Mahmood Khosrowshahli ◽  
Alireza Etminan
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Agricultural Research ◽  
Conservation Strategies ◽  
Functional Markers ◽  
Wheat Genotypes ◽  
Allele Number ◽  
Population Structure Analysis ◽  
Gliadin Alleles

Abstract Analysis of genetic diversity provides helpful information necessary to develop the breeding and conservation strategies of crops. In this study, the genetic diversity and population structure of 90 durum wheat genotypes maintained at Sararud Dryland Agricultural Research Institute, Kermanshah, Iran, were evaluated by using 23 gene-specific markers (functional markers, FMs) encoding high and low molecular weight glutenin and gliadin alleles. Results showed that 12 out of the 23 FMs used were polymorphic and amplified 52 polymorphic loci. Primer Ax2 ⃰ had the highest discriminatory power. The population structure analysis classified the durum wheat collection into four populations. On average, population 4, consisting of 8 genotypes, had the highest allele number as well as genetic variation. Analysis of molecular variance indicated that 82% of the total variation was distributed among populations. The diversity among populations and gene flow were 0.14 and 3.03, respectively. The Jaccard distance coefficient revealed that genetic dissimilarities ranged from 0.031 between G62 and G65 to 0.725 between G36 and G51. Neighbor-joining method clustered individuals into six main groups. Results showed a remarkable level of genetic diversity among studied durum wheat genotypes which can be of interest for future breeding programs.

scholarly journals Genetic diversity and population structure of cowpea [Vigna unguiculata (L.) Walp.] accessions from Togo using SSR Markers

2021 ◽  
Author(s):  
Yao Dodzi Dagnon ◽  
Koffi Kibalou Palanga ◽  
Damigou Bammite ◽  
Ghislain Comlan AKABASSI ◽  
Koffi Tozo
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Vigna Unguiculata ◽  
Polymorphic Information Content ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Conservation Program ◽  
Population Structure Analysis

Cowpea [ Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional potential. I is very appreciate by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. Twenty-eight out of the thirty-two (32) primer pairs screened for polymorphism were polymorphic, and a total of 164 alleles were detected for the 28 loci with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.18 to 0.895, with an average value of 0.67. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 85% of genetic variation existed among individuals within regions. The fixation index (Fst) value, which was 0.018, was low, indicating relatively low population differentiation. The Togolese cowpea germplasm collection was grouped into four groups independently of theirs origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.

scholarly journals Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 244 ◽  
Author(s):  
Harvey D. Blackburn ◽  
Carrie S. Wilson ◽  
Bethany Krehbiel
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Agricultural Research ◽  
Germplasm Collection ◽  
The United States ◽  
United States Department ◽  
Livestock Sector ◽  
Wide Range ◽  
The Status ◽  
Span 60

A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic conservation and security for the U.S. livestock sector. Samples in the collection span 60 years, suggesting a wide range of genetic diversity and genetic change is represented for rare and major breeds. Classifying breeds into four groups based upon registration or census estimates of population size of < 1000, < 5000, < 20,000, and > 20,000 indicated that 50% of the collection is comprised of rare breeds in the < 1000 category. As anticipated, collections for breeds in the < 20,000 and > 20,000 are more complete (86% and 98%, respectively) based upon an index combining the number of germplasm samples and the number of animals. For the rarest breeds (< 1000), collection completeness was 45%. Samples from over 6000 animals in the collection have been used for adding diversity to breeds, genomic evaluation, reconstituting populations, or various research projects. Several aspects of collecting germplasm samples from rare breeds are discussed. In addition, approaches that could be used to enhance the status of rare breeds via the repository use are presented. However, given the array of obstacles confronting rare breeds, the gene bank may be the most secure prospect for the long-term conservation of rare breed genetics.

scholarly journals Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1643
Author(s):  
Didas Kimaro ◽  
Rob Melis ◽  
Julia Sibiya ◽  
Hussein Shimelis ◽  
Admire Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Population Structure Analysis ◽  
The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

PROFILING OF GUAVA GENOTYPES GROWN IN VIDARBHA CONDITIONS ON THE BASIS OF MORPHOLOGICAL TRAITS

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
R.A. PATIL ◽  
S.G. BHARAD ◽  
S.N. SAWANT
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Morphological Traits ◽  
Considerable Extent ◽  
Fruit Traits ◽  
Breeding Programmes ◽  
Tree Leaf ◽  
Qualitative Characteristics ◽  
Intrapopulation Diversity

Assessment of genetic diversity in the available germplasm is the prerequisite for development of improved genotypes through planned breeding programmes. In the view of this Forty-eight genotypes of seedling origin guava along with 1 check (L-49/Sardar) collected and conserved at germplasm block, Main Garden, Department of Horticulture, Dr. P. D. A. University, Akola were evaluated for genetic variability and diversity based on the qualitative characteristics. The genotypes were evaluated for sixteen morphological traitsviz. tree, leaf, floral and fruit traits. Results Show considerable extent of variability amongst the 49 genotypes in each traits. A sizeable amount of intrapopulation diversity recorded can be used to identify diverse parents which can be utilized in hybridization programmes.

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