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

2021 ◽  
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.

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

Genes ◽  
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.

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

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
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.

scholarly journals Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Efficient Manner ◽  
Lilium Species ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

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 Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1282
Author(s):  
Yu Wang ◽  
Zhongyi Jiao ◽  
Jiwei Zheng ◽  
Jie Zhou ◽  
Baosong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Management Strategies ◽  
Natural Populations ◽  
Snp Markers ◽  
Fixation Index ◽  
Landscape Genomics ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure ◽  
Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

scholarly journals Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

2022 ◽  
Author(s):  
Prasanth Tej Kumar Jagannadham ◽  
Thirugnanavel Anbalagan ◽  
Devendra Y Upadhyay ◽  
Snehal A. Kamde ◽  
Prafulla R. Jalamkar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Polymorphic Information Content ◽  
Citrus Fruit ◽  
Molecular Data ◽  
Expected Heterozygosity ◽  
Indel Markers ◽  
Population Structure Analysis

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

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.

scholarly journals Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Debjani Roy Choudhury ◽  
Ramesh Kumar ◽  
Vimala Devi S ◽  
Kuldeep Singh ◽  
N. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Tamil Nadu ◽  
East Coast ◽  
Snp Markers ◽  
The Core ◽  
Core Set ◽  
Population Structure Analysis ◽  
The Mean

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN SELECTED BEEF BREEDS

AGROFOR ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Kristína LEHOCKÁ ◽  
Radovan KASARDA ◽  
Barbora OLŠANSKÁ ◽  
Nina MORAVČÍKOVÁ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Beef Cattle ◽  
Genetic Drift ◽  
High Linkage Disequilibrium ◽  
Snp Markers ◽  
Data Set ◽  
Population Structure Analysis ◽  
Red Angus

The aim of the study was to estimate genetic drift and gene flow related to population structure and genetic diversity in selected beef cattle. For the evaluation of the genetic drift and gene flow among analysed populations, the Bayesian Population Structure Analysis and software Treemix were used. The genetic analysis included two cattle breeds bred in Slovakia (Charolais and Limousine). In addition to the Limousine and Charolais breeds, other beef cattle (Angus N = 90, Belgian Blue N = 4, Blonde d'Aquitaine N= 5, Hereford N = 98 and Red Angus N = 15) were analysed. The 50k Bead chip was used; the dataset consisted of 34,834 SNPs. To avoid detection bias, SNPs with high linkage disequilibrium (r2 = 0.05) were pruned from the database; the final data set consisted of 296 animals and 2,539 SNP markers. Our results reflected four modes of gene flow between Angus, Red Angus, Charolais, Limousine and Hereford. Analysed breeds were not confirmed to influence genetic make-up of Belgian Blue and Blonde d'Aquitaine populations. All migration edges reached weight values below 0.2. The only two migration edges higher in weight was observed, first between the ancestor of Limousine breed into Blond d'Aquitaine, and second among historical ancestor of Hereford breed into Red Angus. Our results reflect that the donor population has made a significant contribution to the recipient population.

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