scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Comprehensive genotyping of Brazilian Cassava (Manihot esculenta Crantz) Germplasm Bank: insights into diversification and domestication

2020 ◽  
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Eder Jorge de Oliveira ◽  
Lukas A. Mueller ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

AbstractCassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonas region. In this study, 3,354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 Single Nucleotide Polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1,536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, 1,300 to 4,700 SNP markers were selected for large quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity (Ho), effective population size estimate and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggest earliest population split from Amazonas to Atlantic forest and Caatinga eco-regions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These Findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.Key messageBrazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups, and spatial genetic differentiation.

scholarly journals High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255290
Author(s):  
Bright Gyamfi Adu ◽  
Richard Akromah ◽  
Stephen Amoah ◽  
Daniel Nyadanu ◽  
Alex Yeboah ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Resources ◽  
Manihot Esculenta ◽  
Polymorphic Information Content ◽  
Starch Content ◽  
Plant Genetic Resources ◽  
Snp Markers ◽  
Ex Situ ◽  
Manihot Esculenta Crantz ◽  
Expected Heterozygosity

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower’s genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

scholarly journals Morphological characterization and genetic diversity analysis of Tunisian durum wheat (Triticum turgidum var. durum) accessions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maroua Ouaja ◽  
Bochra A. Bahri ◽  
Lamia Aouini ◽  
Sahbi Ferjaoui ◽  
Maher Medini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Durum Wheat ◽  
Morphological Characterization ◽  
Wheat Breeding ◽  
Ex Situ ◽  
Breeding Programs ◽  
Genetic Groups ◽  
Southern Tunisia ◽  
Population Structure Analysis

Abstract Background Tunisia is considered a secondary center of diversification of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genetic features of these landraces would allow their rehabilitation and utilization in wheat breeding programs. Here, we investigated a diverse collection of 304 local accessions of durum wheat collected from five regions and three climate stages of central and southern Tunisia. Results Durum wheat accessions were morphologically characterized using 12 spike- and grain-related traits. A mean Shannon-Weaver index (H′) of 0.80 was obtained, indicating high level of polymorphism among accessions. Based on these traits, 11 local landraces including Mahmoudi, Azizi, Jneh Khotifa, Mekki, Biskri, Taganrog, Biada, Badri, Richi, Roussia and Souri were identified. Spike length (H′ = 0.98), spike shape (H′ = 0.86), grain size (H′ = 0.94), grain shape (H′ = 0.87) and grain color (H′ = 0.86) were the most polymorphic morphological traits. The genetic diversity of these accessions was assessed using 10 simple sequence repeat (SSR) markers, with a polymorphic information content (PIC) of 0.69. Levels of genetic diversity were generally high (I = 0.62; He = 0.35). In addition, population structure analysis revealed 11 genetic groups, which were significantly correlated with the morphological characterization. Analysis of molecular variance (AMOVA) showed high genetic variation within regions (81%) and within genetic groups (41%), reflecting a considerable amount of admixture between landraces. The moderate (19%) and high (59%) levels of genetic variation detected among regions and among genetic groups, respectively, highlighted the selection practices of farmers. Furthermore, Mahmoudi accessions showed significant variation in spike density between central Tunisia (compact spikes) and southern Tunisia (loose spikes with open glume), may indicate an adaptation to high temperature in the south. Conclusion Overall, this study demonstrates the genetic richness of local durum wheat germplasm for better in situ and ex situ conservation and for the subsequent use of these accessions in wheat breeding programs.

scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

scholarly journals Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

2021 ◽  
Vol 12 ◽  
Author(s):  
Lian-Ying Shen ◽  
Hang Luo ◽  
Xiao-Ling Wang ◽  
Xue-Meng Wang ◽  
Xiao-Jing Qiu ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
Effective Population ◽  
Last Glacial Period ◽  
Population Structure Analysis ◽  
History Of ◽  
Ziziphus Jujuba ◽  
Fruit Flavor ◽  
High Quality Genome ◽  
The Last Glacial

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.

scholarly journals Morphological characterization and genetic diversity analysis of Tunisian durum wheat (Triticum turgidum var. durum) accessions

2021 ◽  
Author(s):  
Maroua Ouaja ◽  
Bochra Amina Bahri ◽  
Lamia Aouini ◽  
Sahbi Ferjaoui ◽  
Maher Medini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Durum Wheat ◽  
Morphological Characterization ◽  
Wheat Breeding ◽  
Ex Situ ◽  
Breeding Programs ◽  
Genetic Groups ◽  
Southern Tunisia ◽  
Population Structure Analysis

Abstract Background: Tunisia is considered a secondary center of diversification of durum wheat and has a large number of abandoned old local landraces. An accurate investigation and characterization of the morphological and genetic features of these landraces would allow their rehabilitation and utilization in wheat breeding programs. Here, we investigated a diverse collection of 304 local accessions of durum wheat collected from five regions and three climate stages of central and southern Tunisia. Results: Durum wheat accessions were morphologically characterized using 12 spike- and grain-related traits. A mean Shannon-Weaver index (H') of 0.80 was obtained, indicating high level of polymorphism among accessions. Based on these traits, 11 local landraces including Mahmoudi, Azizi, Jneh Khotifa, Mekki, Biskri, Taganrog, Biada, Badri, Richi, Roussia and Souri were identified. Spike length (H' = 0.98), spike shape (H' = 0.86), grain size (H' = 0.94), grain shape (H' = 0.87) and grain color (H' = 0.86) were the most polymorphic morphological traits. The genetic diversity of these accessions was assessed using 10 simple sequence repeat (SSR) markers, with a polymorphic information content (PIC) of 0.69. Levels of genetic diversity were generally high (I = 0.62; He = 0.35). In addition, population structure analysis revealed 11 genetic groups, which were significantly correlated with the morphological characterization. Analysis of molecular variance (AMOVA) showed high genetic variation within regions (81%) and within genetic groups (41%), reflecting a considerable amount of admixture between landraces. The moderate (19%) and high (59%) levels of genetic variation detected among regions and among genetic groups, respectively, highlighted the selection practices of farmers. Furthermore, Mahmoudi accessions showed significant variation in spike density between central Tunisia (compact spikes) and southern Tunisia (loose spikes with open glume), may indicate an adaptation to high temperature in the south. Conclusion: Overall, this study demonstrates the genetic richness of local durum wheat germplasm for better in situ and ex situ conservation and for the subsequent use of these accessions in wheat breeding programs.

scholarly journals Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

2017 ◽  
Vol 8 ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Jhon Berdugo-Cely ◽  
Roberto Antonio Coronado ◽  
Yeny Patricia Zapata ◽  
Constanza Quintero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Theobroma Cacao ◽  
Germplasm Bank ◽  
Population Structure Analysis ◽  
Theobroma Cacao L

scholarly journals The conservation status of the Galápagos marine iguanas, Amblyrhynchus cristatus: a molecular perspective

2016 ◽  
Vol 37 (1) ◽  
pp. 91-109 ◽  
Author(s):  
Amy MacLeod ◽  
Sebastian Steinfartz
Keyword(s):  
Population Structure ◽  
Microsatellite Loci ◽  
Conservation Management ◽  
Conservation Status ◽  
Mitochondrial Control Region ◽  
Molecular Data ◽  
Effective Population ◽  
Amblyrhynchus Cristatus ◽  
Population Structure Analysis ◽  
Anthropogenic Threats

Traditionally, conservation management focuses efforts on taxonomic units. However, when the taxa used do not reflect biologically meaningful units, such methods should be reconsidered to avoid the loss of irreplaceable biodiversity. The Galápagos marine iguana (Amblyrhynchus cristatus) is listed as Vulnerable on the IUCN Red List of Threatened Species and is facing growing anthropogenic threats. Currently, management is based on a taxonomy which is questionable in the light of recent molecular data. As such, there is a danger that evolutionarily significant populations may be left vulnerable to extirpation. Herein, we apply molecular data to elucidate the population structure of this species across the Galápagos archipelago, and thus advise conservation management in the absence of a revised taxonomy. Applying a wealth of molecular data including 12 microsatellite loci and 1181 bp of the mitochondrial control region in over 1200 individuals, we delineate distinct populations and prioritize their management. Bayesian population structure analysis revealed 10 distinct population clusters, which we propose as management units (MUs). All MUs are significantly differentiated, with one unit on San Cristóbal Island being particularly distinct in terms of both microsatellite loci and mitochondrial data. Based on estimates of the genetic effective population size (Ne), we find the MUs comprised of populations occurring on Floreana, Española, Marchena, and San Cristóbal to be alarmingly small. In consideration of both Neand anthropogenic threats, we recommend that conservation practitioners focus efforts on Floreana and San Cristóbal islands, and argue that better census size estimates of populations are urgently needed.

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