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

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

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Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

Scientific Reports ◽

10.1038/s41598-021-87284-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jeewan Pandey ◽

Douglas C. Scheuring ◽

Jeffrey W. Koym ◽

Joseph Coombs ◽

Richard G. Novy ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Skin Color ◽

Potato Breeding ◽

Crop Improvement ◽

Snp Markers ◽

Breeding Program ◽

Potato Breeding Program ◽

The Usa

AbstractKnowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

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Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

PLoS ONE ◽

10.1371/journal.pone.0084136 ◽

2013 ◽

Vol 8 (12) ◽

pp. e84136 ◽

Cited By ~ 91

Author(s):

Nivedita Singh ◽

Debjani Roy Choudhury ◽

Amit Kumar Singh ◽

Sundeep Kumar ◽

Kalyani Srinivasan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Snp Markers ◽

Rice Varieties ◽

Ssr And Snp Markers

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Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

BMC Plant Biology ◽

10.1186/1471-2229-13-39 ◽

2013 ◽

Vol 13 (1) ◽

pp. 39 ◽

Cited By ~ 159

Author(s):

Francesco Emanuelli ◽

Silvia Lorenzi ◽

Lukasz Grzeskowiak ◽

Valentina Catalano ◽

Marco Stefanini ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Ssr And Snp Markers

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Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers

BMC Plant Biology ◽

10.1186/s12870-014-0360-x ◽

2015 ◽

Vol 15 (1) ◽

pp. 52 ◽

Cited By ~ 40

Author(s):

Carla V Filippi ◽

Natalia Aguirre ◽

Juan G Rivas ◽

Jeremias Zubrzycki ◽

Andrea Puebla ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Association Mapping ◽

Mapping Population ◽

Snp Markers ◽

Ssr And Snp Markers ◽

Association Mapping Population

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Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers

BMC Genomics ◽

10.1186/s12864-016-3041-3 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 35

Author(s):

Xiao Zhang ◽

Hua Zhang ◽

Lujiang Li ◽

Hai Lan ◽

Zhiyong Ren ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Southwest China ◽

Snp Markers ◽

Maize Breeding ◽

Genome Wide ◽

Breeding Germplasm

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

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

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.

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Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers

Molecular Biology Reports ◽

10.1007/s11033-020-05726-7 ◽

2020 ◽

Vol 47 (9) ◽

pp. 6705-6715

Author(s):

Marina Santos Carvalho ◽

Cintia Machado de Oliveira Moulin Carias ◽

Matheus Alves Silva ◽

Marcia Flores da Silva Ferreira ◽

Thiago Lívio Pessoa Oliveira de Souza ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Snp Markers ◽

Genetic Diversity And Structure ◽

Ssr And Snp Markers ◽

Landrace Accessions

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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.

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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.

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