Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis

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.

Download Full-text

High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

Scientific Reports ◽

10.1038/s41598-018-28718-x ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 6

Author(s):

Anupama Mukherjee ◽

Sabyasachi Mukherjee ◽

Rajan Dhakal ◽

Moonmoon Mech ◽

Imsusosang Longkumer ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

High Density ◽

Genomic Characterization

Download Full-text

Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

Eunju Seo ◽

Kipoong Kim ◽

Tae-Hwan Jun ◽

Jinsil Choi ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Useful Knowledge ◽

Population Structure Analysis ◽

Group 3 ◽

Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

Download Full-text

Genetic Diversity and Population Structure of Field Isolates of Ganoderma Boninense from Oil Palm Plantation in Solomon Islands

Proceedings ◽

10.3390/proceedings2019036056 ◽

2020 ◽

Vol 36 (1) ◽

pp. 56

Author(s):

Mudge ◽

Rama ◽

Pilotti ◽

Godwin

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Oil Palm ◽

Elaeis Guineensis ◽

Solomon Islands ◽

Economic Importance ◽

Ganoderma Boninense ◽

Perennial Crop ◽

Great Economic Importance

Oil palm (Elaeis guineensis Jacq.) is a long-term perennial crop of great economic importance to [...]

Download Full-text

Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Theoretical and Applied Genetics ◽

10.1007/s00122-009-1256-2 ◽

2010 ◽

Vol 120 (7) ◽

pp. 1289-1299 ◽

Cited By ~ 156

Author(s):

Delphine Van Inghelandt ◽

Albrecht E. Melchinger ◽

Claude Lebreton ◽

Benjamin Stich

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Snp Markers ◽

Breeding Program ◽

Maize Breeding ◽

Ssr And Snp Markers

Download Full-text

Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers

PLoS ONE ◽

10.1371/journal.pone.0253600 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253600

Author(s):

Charles U. Uba ◽

Happiness O. Oselebe ◽

Abush A. Tesfaye ◽

Wosene G. Abtew

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

West Africa ◽

East Africa ◽

Unknown Origin ◽

Snp Markers ◽

Bambara Groundnut ◽

Conservation Strategy ◽

Population Structure Analysis ◽

Geographical Regions

Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.

Download Full-text

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽

10.1371/journal.pone.0243238 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243238

Author(s):

Wilson Nkhata ◽

Hussein Shimelis ◽

Rob Melis ◽

Rowland Chirwa ◽

Tenyson Mzengeza ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Bean ◽

Southern Africa ◽

Crop Improvement ◽

Phenotypic Expression ◽

Snp Markers ◽

High Yield ◽

Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Download Full-text

Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection

Genes ◽

10.3390/genes12081233 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1233

Author(s):

Alemayehu Teressa Negawo ◽

Meki S. Muktar ◽

Yilikal Assefa ◽

Jean Hanson ◽

Alieu M. Sartie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Snp Markers ◽

Correction Coefficient ◽

Rhodes Grass ◽

Representative Subset ◽

Population Structure Analysis ◽

Chloris Gayana ◽

Molecular Information

Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future.

Download Full-text