scholarly journals Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2007
Author(s):  
A. S. M. Faridul Islam ◽  
Dean Sanders ◽  
Amit Kumar Mishra ◽  
Vijay Joshi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Genotyping By Sequencing ◽  
The United States ◽  
Snp Markers ◽  
Breeding Programs ◽  
The Us ◽  
The Mediterranean ◽  
Olive Breeding

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

scholarly journals Genetic diversity and population structure of Luffa acutangula accessions in a Thailand collection using SNP markers

2020 ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Paweena Chuenwarin
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Structure Analysis ◽  
Fruit Shape ◽  
Snp Markers ◽  
Distinguishing Characteristic ◽  
Breeding Programs ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula

AbstractThis study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. STRUCTURE analysis (ΔK at K=6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (−10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Population Structure Analysis Revealed Water or Ancient Hub-induced Genetic Diversity of Cultivated-type Tea Plants in Guizhou Plateau

2021 ◽  
Author(s):  
Zhifei Zhao ◽  
Qinfei Song ◽  
Dingchen Bai ◽  
Suzhen Niu ◽  
Yingqin He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Core Collection ◽  
Genotyping By Sequencing ◽  
Tea Plant ◽  
Transmission Model ◽  
Population Structure Analysis ◽  
Tea Plants ◽  
Guizhou Plateau

Abstract Background Tea plants originated from the southwest of China. Guizhou is one of the origin center of tea plants, which is rich in tea plant germplasm resources. However, the distribution characteristics and transmission model of tea plant were still unclear. Results We collected 253 cultivated-type tea plant accessions from Guizhou plateau and analyzed the genetic diversity, PCA, phylogenetic, population structure, LD, and development of core collection using the genotyping-by-sequencing (GBS) approach. A total of 112,072 high-quality SNPs were identified, which was further used to analyze the genetic diversity and population structure. In this study, we found that the genetic diversity in cultivated-type tea accessions of PR Basin were significantly higher than that in cultivated-type tea accessions of YR Basin. Moreover, four groups, including three pure groups (CG-1, CG-2 and CG-3) and one admixture group (CG-4), were identified based on population structure analysis, which was verified by PAC and phylogenetic analysis. Our results showed that the highest GD and Fst values were found in CG-2 vs CG-3, followed by CG-1 vs CG-2 and CG-1 vs CG-3. The lowest GD and Fst values were detected in CG-4 vs CG-1, CG-4 vs CG-2, and CG-4 vs CG-3. Conclusions This study provided the evidence to confirm the contribution of PR and YR Basins and ancient hub road section to the transmission of cultivated-type tea accessions in Guizhou plateau. The genetic diversity, population structure and core collection revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

scholarly journals Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 676 ◽  
Author(s):  
Farahani ◽  
Maleki ◽  
Mehrabi ◽  
Kanouni ◽  
Scheben ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Large Scale ◽  
Principal Component ◽  
Snp Markers ◽  
Genome Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Population Structure Analysis

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

2021 ◽  
Author(s):  
Maya Peringottillam ◽  
Smitha Kunhiraman Vasumathy ◽  
Hari Krishna Kumar ◽  
Manickavelu Alagu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Purity ◽  
Next Generation Sequencing Technology ◽  
Distance Analysis ◽  
Rice Landraces ◽  
Genetic Diversity And Structure ◽  
Rice Landrace

Abstract Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

scholarly journals Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

2019 ◽  
Author(s):  
Somayeh Farahani ◽  
Mojdeh Maleki ◽  
Rahim Mehrabi ◽  
Homayoun Kanouni ◽  
Reza Talebi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Large Scale ◽  
Principal Component ◽  
Snp Markers ◽  
Genome Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Population Structure Analysis

Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2≥0.8, while 2961 pairs of markers showed complete LD (r2=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection

2009 ◽  
Vol 120 (1) ◽  
pp. 13-23 ◽  
Author(s):  
Ming L. Wang ◽  
Chengsong Zhu ◽  
Noelle A. Barkley ◽  
Zhenbang Chen ◽  
John E. Erpelding ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Sweet Sorghum ◽  
Population Structure Analysis ◽  
The Us

scholarly journals Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 563 ◽  
Author(s):  
Monica Marilena Miazzi ◽  
Nunzio D’Agostino ◽  
Valentina di Rienzo ◽  
Pasquale Venerito ◽  
Vito Nicola Savino ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Gene Pools ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Snp Data ◽  
Data Points ◽  
Genetic Clusters

The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Baffour Badu-Apraku ◽  
Ana Luísa Garcia-Oliveira ◽  
César Daniel Petroli ◽  
Sarah Hearne ◽  
Samuel Adeyemi Adewale ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Snp Markers ◽  
Rapid Expansion ◽  
Sub Saharan Africa ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Early Maturing ◽  
Sub Saharan

Abstract Background Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. Results About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. Conclusions Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.

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