scholarly journals The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1677
Author(s):  
Rodrigo Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Bottle Gourd ◽  
Conservation Strategies ◽  
Lagenaria Siceraria ◽  
Genomic Resources ◽  
Ssr Loci ◽  
Pharmaceutical Industries

Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

Molecular confirmation of varietal status in bottle gourd (Lagenaria siceraria) using genotyping-by-sequencing

Genome ◽  
2020 ◽  
Vol 63 (11) ◽  
pp. 535-545
Author(s):  
Jacky Amenan Konan ◽  
Romain Guyot ◽  
Kouamé Kevin Koffi ◽  
Irié Vroh-Bi ◽  
Arsène Irié Bi Zoro
Keyword(s):  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cluster Analyses ◽  
Different Types ◽  
The Status ◽  
Edible Seeds

Bottle gourd (Lagenaria siceraria) is an important food, medicinal, and utilitarian crop with a large pan-tropical distribution. Two morphologically different types in the siceraria subspecies are sufficiently different to be considered as varieties, but they are assigned into different taxonomic ranks. Genotyping-by-sequencing (GBS) of 95 different accessions from the Nangui Abrogoua University collection was used to confirm the varietal status in bottle gourd. This analysis produced 22 575 single-nucleotide polymorphisms (SNPs). Cluster analyses conducted with 2250 (9.96%) SNPs distinctly separated hard-shelled from soft-shelled types. Analysis of 23 SNPs located in 11 genes coding for traits that differentiate the two types of gourds revealed that genes in the soft-shelled types had about 21% fewer SNPs than genes within hard-shelled gourds, but the latter had more non-synonymous SNPs. Cluster analyses conducted with the 23 SNPs fitted well with the structure defined by the 2250 SNPs, suggesting the implication of these SNPs in the varietal differentiation of bottle gourd. These nucleotide changes along with the genetic relationships between the accessions provide molecular proof supporting the status of two varieties. To prevent the confusion inherent in the use of synonyms and homonyms in bottle gourd, we suggest the terms hard-shelled and soft-shelled to designate, respectively, the varieties used as utensils and those grown for their edible seeds.

scholarly journals Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1437
Author(s):  
Ranjana Bhattacharjee ◽  
Paterne Agre ◽  
Guillaume Bauchet ◽  
David De Koeyer ◽  
Antonio Lopez-Montes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Optimum Number ◽  
Admixture Analysis ◽  
Clustering Methods ◽  
Breeding Lines ◽  
White Yam

White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam.

scholarly journals Mining of Simple Sequence Repeats Loci, Genetic Relationship And Population Structure of Bottle Gourd (Lagenaria Siceraria (Molina) Standl.) Accessions With Different Geographical Origin Using Single Nucleotide Polymorphism (SNPs) Markers

2021 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
South Africa ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Simple Sequence Repeats ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Lagenaria siceraria (Molina) Standl. (2n = 2x = 22) is an important horticultural and medicinal crop grown worldwide serving for food and pharmaceutical industries. The crop exhibit extensive phenotypic and genetic variation useful for cultivar obtention targeting economic traits, however limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd prevenient from Chile, Asia, and South Africa by using single nucleotide polymorphism (SNPs) markers and mining of simple sequence repeats (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs molecular markers classified as moderate to highly informative with mean polymorphic information content of 0.29. The mean gene diversity of 0.16, indicated low genetic differentiation of the accessions. Analysis of molecular variance revealed lower differentiation between (36%) than within (48%) bottle gourd accessions suggesting that random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising of South Africa accessions and an admixed group with genotypes of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

scholarly journals Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography

2020 ◽  
Vol 42 (10) ◽  
pp. 1169-1178
Author(s):  
Agraw Amane ◽  
Gurja Belay ◽  
Yao Nasser ◽  
Martina Kyalo ◽  
Tadelle Dessie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genetic Research ◽  
Principal Component ◽  
Conservation Strategies ◽  
Genetic Cluster ◽  
Sheep Population ◽  
Indigenous Sheep ◽  
Genome Wide

Abstract Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. Methods A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. Results Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. Conclusion The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations

scholarly journals Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kanamon Riangwong ◽  
Samart Wanchana ◽  
Wanchana Aesomnuk ◽  
Chatree Saensuk ◽  
Phakchana Nubankoh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Molecular Breeding ◽  
Reference Genome ◽  
Genetic Relationships ◽  
Cocos Nucifera ◽  
Genotyping By Sequencing ◽  
Phylogenetic Tree Analysis ◽  
Simple Sequence

Abstract Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.

Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

2012 ◽  
Vol 42 (1) ◽  
pp. 23-37 ◽  
Author(s):  
Anna W. Schoettle ◽  
Betsy A. Goodrich ◽  
Valerie Hipkins ◽  
Christopher Richards ◽  
Julie Kray
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Bark Beetles ◽  
Climatic Factors ◽  
Rocky Mountain ◽  
Conservation Strategies ◽  
Restricted Gene Flow ◽  
Populations At Risk ◽  
Bristlecone Pine ◽  
Pinus Aristata

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites across four mountain ranges in the core distribution of P. aristata were sampled and genetic diversity was assessed with 21 isozyme loci. Low species and population level genetic diversity (He = 0.070 and 0.062, respectively) occurred with moderate among-population differentiation (FST = 0.131). Genetic diversity correlated with longitude, latitude, and elevation and a strong mountain island effect may contribute to substructuring and isolation. Using multiple complementary analyses, sampled trees were assigned to three genetic lineages that varied in diversity and admixture and were associated with different climatic factors. The distribution of genetic diversity and substructuring of P. aristata may be an outcome of a combination of restricted gene flow due to geographic and phenological isolation, random processes of genetic drift, life history traits, natural selection, and postglacial migrations. The combination of low genetic diversity, moderate population isolation, and a protracted regeneration dynamic puts populations at risk for extirpation by novel stresses.

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

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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