scholarly journals Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (Dioscorea rotundata Poir.)

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1437
Author(s):  
Ranjana Bhattacharjee ◽  
Paterne Agre ◽  
Guillaume Bauchet ◽  
David De Koeyer ◽  
Antonio Lopez-Montes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Optimum Number ◽  
Admixture Analysis ◽  
Clustering Methods ◽  
Breeding Lines ◽  
White Yam

White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam.

scholarly journals Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

2016 ◽  
Vol 14 (3) ◽  
pp. 226-233 ◽  
Author(s):  
Xingping Yang ◽  
Runsheng Ren ◽  
Rumiana Ray ◽  
Jinhua Xu ◽  
Pingfang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Citrullus Lanatus ◽  
Genetic Relationships ◽  
Snp Markers ◽  
Phenotypic Characterization ◽  
Breeding Lines ◽  
I 11 ◽  
Genome Level

Watermelon [Citrullus lanatus(Thunb.) Matsum. & Nakai var.lanatus] is an economically important vegetable belonging to theCucurbitaceaefamily. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

scholarly journals The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1677
Author(s):  
Rodrigo Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Bottle Gourd ◽  
Conservation Strategies ◽  
Lagenaria Siceraria ◽  
Genomic Resources ◽  
Ssr Loci ◽  
Pharmaceutical Industries

Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

scholarly journals Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kanamon Riangwong ◽  
Samart Wanchana ◽  
Wanchana Aesomnuk ◽  
Chatree Saensuk ◽  
Phakchana Nubankoh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Molecular Breeding ◽  
Reference Genome ◽  
Genetic Relationships ◽  
Cocos Nucifera ◽  
Genotyping By Sequencing ◽  
Phylogenetic Tree Analysis ◽  
Simple Sequence

Abstract Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.

scholarly journals Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11593
Author(s):  
Vipin Tomar ◽  
Guriqbal Singh Dhillon ◽  
Daljit Singh ◽  
Ravi Prakash Singh ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Genome Wide Association Studies ◽  
Breeding Lines ◽  
Structure Information

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

scholarly journals Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

2020 ◽  
Vol 24 (5) ◽  
pp. 474-480
Author(s):  
I. I. Suprun ◽  
S. A. Plugatar ◽  
I. V. Stepanov ◽  
T. S. Naumenko
Keyword(s):  
Genetic Diversity ◽  
Bayesian Methods ◽  
Dna Markers ◽  
Wild Species ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
Clustering Methods ◽  
Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

scholarly journals Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

2020 ◽  
Author(s):  
Brenda G. Díaz ◽  
Maria I. Zucchi ◽  
Alessandro. Alves-Pereira ◽  
Caléo P. de Almeida ◽  
Aline C. L. Moraes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Structure ◽  
Genetic Relationships ◽  
Geographical Area ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Productive Capacity ◽  
Snp Analysis ◽  
Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

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