scholarly journals Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ademola Aina ◽  
Ana Luísa Garcia-Oliveira ◽  
Christopher Ilori ◽  
Peter L. Chang ◽  
Muyideen Yusuf ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Phenotypic Diversity ◽  
Snp Markers ◽  
International Institute ◽  
Clustering Methods ◽  
Breeding Programs ◽  
Relationship Analysis ◽  
African Yam Bean ◽  
Geographical Regions

Abstract Background African Yam Bean (AYB) is an understudied and underutilized tuberous legume of tropical West and Central African origin. In these geographical regions, both seeds and tubers of AYB are important components of people’s diets and a potential target as a nutritional security crop. The understanding of the genetic diversity among AYB accessions is thus an important component for both conservation and potential breeding programs. Results In this study, 93 AYB accessions were obtained from the International Institute of Tropical Agriculture (IITA) genebank and genotyped using 3722 SNP markers based on Restriction site-Associated DNA sequencing (RAD-Seq). Genetic data was analysed using multiple clustering methods for better understanding the distribution of genetic diversity across the population. Substantial genetic variability was observed in the present set of AYB accessions and different methodologies demonstrated that these accessions are divided into three to four main groups. The accessions were also analysed for important agronomic traits and successfully associated with their genetic clusters where great majority of accessions shared a similar phenotype. Conclusions To our knowledge, this is the first study on predicting genotypic-phenotypic diversity relationship analysis in AYB. From a breeding perspective, we were able to identify specific diverse groups with precise phenotype such as seed or both seed and tuber yield purpose accessions. These results provide novel and important insights to support the utilization of this germplasm in AYB breeding programs.

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 Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

2019 ◽  
Vol 17 (5) ◽  
pp. 412-420
Author(s):  
G. Afolayan ◽  
S. P. Deshpande ◽  
S. E. Aladele ◽  
A. O. Kolawole ◽  
I. Angarawai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Crop Research ◽  
International Crop Research Institute ◽  
Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

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

PLoS ONE ◽  
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.

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.

scholarly journals Magnitude of the genetic base of commercial popcorn and in recommendation in Brazil

2010 ◽  
Vol 10 (4) ◽  
pp. 289-297 ◽  
Author(s):  
Thiago Otávio Mendes de Paula ◽  
Leandro Simões Azeredo Gonçalves ◽  
Antonio Teixeira do Amaral Júnior ◽  
Érica Cristina de Oliveira ◽  
Vanessa Quitete Ribeiro da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Group Formation ◽  
Distance Matrix ◽  
Molecular Data ◽  
Issr Markers ◽  
Private Institutions ◽  
Final Test ◽  
Breeding Programs ◽  
Public And Private

The purpose of this study was to quantify the genetic diversity among popcorn genotypes on the market and in the final test phase, suitable for three environments in Brazil, based on 11 agronomic traits and ISSR markers. In the environment Campos dos Goytacazes a more reliable group formation was observed than in the other environments. The molecular data indicated the presence of cultivars recommended in the same group, as in the case of UFVM2 Barão de Viçosa, IAC 125, Zélia and Jade. This result is an appeal to the few popcorn breeders in Brazil to pay particular attention to increase the genetic diversity among breeding programs conducted by public and private institutions in the country. There was virtually no correlation between the distance matrix obtained by the ISSR marker and the matrices obtained by the agronomic data.

scholarly journals Genetic dissimilarity among jabuticaba trees native to southwestern Paraná, Brazil

2011 ◽  
Vol 33 (2) ◽  
pp. 517-525 ◽  
Author(s):  
Moeses Andrigo Danner ◽  
Idemir Citadin ◽  
Simone Aparecida Zolet Sasso ◽  
Silvia Scariot ◽  
Giovani Benin
Keyword(s):  
Genetic Diversity ◽  
Mahalanobis Distance ◽  
Agronomic Traits ◽  
High Potential ◽  
Multivariate Techniques ◽  
Fruit Traits ◽  
Breeding Programs ◽  
Canonical Variables ◽  
Genetic Dissimilarity ◽  
Collection Sites

Knowledge on the genetic diversity within and between genotype groups is of great importance for breeding programs. The purpose of this study was to estimate the genetic dissimilarity among 36 native jabuticaba trees (Plinia cauliflora) from five sites in the southwestern region of Paraná, Brazil. Sixteen fruit traits were analyzed, based on multivariate techniques (canonical variables, Tocher and UPGMA), using Mahalanobis' distance as dissimilarity measure. By the techniques of clustering and graphic dispersion, together with the comparison of means, the genetic diversity among native jabuticaba trees was efficiently identified, indicating a high potential of these genotypes for breeding programs. The traits of greatest importance for dissimilarity were percentage of pulp and of skin, which are easily measured. The clustering structure is related to the collection sites and for breeding programs, genotypes from different sites should be crossed to generate progenies to be tested. Genotypes 'CV5' and 'VT3' should be conserved in genebanks, due to its important agronomic traits.

scholarly journals Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1116
Author(s):  
Vladimir Aleksandrov ◽  
Tania Kartseva ◽  
Ahmad M. Alqudah ◽  
Konstantina Kocheva ◽  
Krasimira Tasheva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Bread Wheat ◽  
Clustering Algorithm ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Geographic Region ◽  
Snp Markers ◽  
Genetic Diversity And Structure

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r2), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

One century of Nordic barley breeding: nitrogen use efficiency, agronomic traits and genetic diversity

2016 ◽  
Vol 155 (4) ◽  
pp. 582-598 ◽  
Author(s):  
A. RAJALA ◽  
P. PELTONEN-SAINIO ◽  
M. JALLI ◽  
L. JAUHIAINEN ◽  
A. HANNUKKALA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nitrogen Use Efficiency ◽  
Agronomic Traits ◽  
N Uptake ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Nitrogen Use ◽  
Single Nucleotide ◽  
Snp Data ◽  
Use Efficiency

SUMMARYThe current study aimed to evaluate breeding effect on nitrogen use efficiency (NUE), its components and some agronomic traits and disease resistance in barley by using extensive germplasm covering 72 landraces and 123 cultivars released since 1910. Trials were established in southern Finland with a modified strip-plot experimental design. Prior to sowing, blocks were placement fertilized with compound nitrogen : phosphorus : potassium (NPK) fertilizer (N-P-K: 20–3–8) at the rate of 35 and 70 kg N/ha and unfertilized plots were placed at the other end of the fertilization block. The germplasm collection was genotyped with 1536 single nucleotide polymorphism (SNP) markers and phenotyped during a 2-year field experiment in 2011/12. Independent of row type, a positive breeding effect was evident in NUE and for other plant N traits, except that grain N slightly decreased. Breeding has improved NUE by 0·08 kg/year (26% over the century). Nitrogen utilization and N uptake efficiencies were also improved by breeding as were straw length, lodging tolerance, grain yield and yield components, without any sign of levelling-off. Bred cultivars were more resistant to leaf-damaging diseases, especially to net blotch. The SNP data indicated no reduction in overall genetic diversity. However, genetic diversity differed along the barley chromosomes showing either reduced or increased diversity in certain regions when landraces were compared with modern varieties.

scholarly journals Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2562
Author(s):  
Lassana Bakayoko ◽  
Désiré N’Da Pokou ◽  
Abou Bakari Kouassi ◽  
Paterne A. Agre ◽  
Amani Michel Kouakou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cote D'ivoire ◽  
Côte D’Ivoire ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Research Centre ◽  
Dioscorea Alata ◽  
Cote D’Ivoire ◽  
Côte D'ivoire ◽  
Water Yam

Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d’Ivoire.

scholarly journals Estimates of genetic divergence in cowpea by multivariate analysis in different environments

2019 ◽  
Vol 35 (6) ◽  
Author(s):  
Larissa Pereira Ribeiro ◽  
Jeniffer Santana Pinto Coelho Evangelista ◽  
Michelle Brandão Damacena ◽  
Arthur Mayrink Elizeu ◽  
Igor Ferreira Coelho ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Genetic Variability ◽  
Agronomic Traits ◽  
Optimization Methods ◽  
Clustering Methods ◽  
Mato Grosso ◽  
Genetic Potential ◽  
Pod Length ◽  
Mato Grosso Do Sul

Cowpea is a legume of great importance in the Brazilian nutrition, mainly in the Northeast region. Despite the low yield of Brazilian cowpea, the species presents a genetic potential to be explored. Thus, this work aimed to characterize the genetic diversity of cowpea genotypes by agronomic traits and select genotypes for possible crosses by multivariate analysis. Four value for cultivation and use tests were carried out with cowpea genotypes in 2005 and 2006, in the municipalities of Aquidauana, Chapadão do Sul, and Dourados, in the state of Mato Grosso do Sul. The experimental design was a complete randomized block with 20 genotypes and four replications. The evaluated traits were value for cultivation, plant lodging, pod length, grain weight of five pods, number of grains per pod, pod weight, severity of powdery mildew, and grain yield. To estimate the genetic diversity among the genotypes, the optimization methods of Tocher and UPGMA were used. The generalized distance of Mahalanobis was used as a dissimilarity measure. The clustering methods revealed genetic variability among the cowpea genotypes evaluated. The methods used formed a different number of groups for each environment. Genotypes TE97-309G-24, MNC99-542F-5, BRS Paraguaçu, BRS Paraguaçu, BR 17-Gurguéia, and CNC x 409-11F-P2 can be used to obtain promising combinations and high genetic variability.

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